Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
This variantScenario
BenignPathogenic
Uncertain.The recorded classification is uncertain significance.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
About MUTYH
MUTYH encodes a DNA repair enzyme (a glycosylase) that fixes oxidative DNA damage by removing adenine bases that have been mistakenly paired with guanine or with oxidized guanine lesions. Inherited mutations in both copies of the gene cause MUTYH-associated polyposis (MAP), a recessive condition that strongly predisposes people to multiple colorectal polyps and colorectal cancer. The gene acts as a tumor suppressor whose loss of function allows DNA damage to accumulate, and somatic changes in it have also been reported in colon cancer, though whether they drive cancer on their own is not fully established.
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01The reasoning
How it was classified
The recorded framework is ClinGen MUTYH VCEP v1.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Met (moderate): E. coli complementation assay showed a 3.2-fold increased mutation rate, a partial defect comparable to founder-pathogenic p.G396D (1.7-fold).
PM2Supporting
PM2 · supporting
Met (supporting): gnomAD allele frequency 0.004% (0 homozygotes), about 25-fold below the 0.1% threshold for recessive disorders.
PP3Supporting
PP3 · supporting
Met (supporting): REVEL 0.724 falls in the supporting band (0.644-0.772) for a predicted deleterious missense effect.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
Because the MUTYH gene-specific (VCEP) framework provided no applicable rules, generic ACMG/AMP 2015 criteria were applied. PS3 (moderate), PM2 (supporting), and PP3 (supporting) were met, and no benign criteria were met. One moderate plus two supporting criteria falls three supporting criteria short of the closest likely-pathogenic rule (one moderate plus four supporting) and meets no benign threshold, so the final classification is VUS.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
64 / 1,614,038 alleles
gnomAD v4.1: 64 / 1,614,038 alleles. Recorded AF 3.96521e-05. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 3.88989e-05; MAF= 0.00389%, 11/282784 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000138389; MAF= 0.01384%, 1/7226 alleles, homozygotes = 0); grpmax FAF= 2.293e-05.
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MUTYH, a DNA glycosylase, is frequently mutated in colorectal cancer.
ACMG/AMP criteria under ClinGen MUTYH VCEP v1.0, with the data and sources behind each one.
28 criteria with recorded statuses: 3 met · 13 not met · 6 not assessed · 6 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Governing framework: InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel (MUTYH) VCEP v1.0 was detected (cspec doc 1742141534, preferred transcript NM_001128425.2) but its ruleset payload is empty in this case bundle (vcep_materials.json summaries empty, criteria.json []), so generic ACMG/AMP 2015 (PMID 25741868) criterion definitions were used as the fallback for this group.
Variant identity: NM_001128425.2:c.1465G>A p.(Ala489Thr) (NP_001121897.1; exon 14). The same genomic variant (1:g.45796865C>T) is reported in the literature under three additional numbering systems, cross-verified via anchor variants (p.Gly396Asp c.1187G>A, p.Gly503Glu c.1508G>A): c.1381G>A p.Ala461Thr (NM_001048174.2, ClinVar VCV000142138), c.1423G>A p.A489T (NM_001048171.1, Komine 2015), and c.1423G>A p.A475T (535-aa convention, Kairupan 2005 and Jo 2005).
PS1 not met (high confidence): the amino acid change p.Ala489Thr is the variant under assessment and is not established as pathogenic - ClinVar VUS across 15 submitters with no expert panel input; four reporting papers assign uncertain status; and no alternative nucleotide change producing p.Ala489Thr exists (sole path c.1465G>A).
PM1 not met (medium confidence, human review recommended): hotspot component negative (CancerHotspots no_result; Komine 2015 'without a clear hot spot'); domain component not affirmatively established - Kairupan 2005 states the residue is not in a known functional domain, Jo 2005 places it 2 codons from the nudix domain, and no authoritative domain-boundary or VCEP domain list is available in the bundle.
PM5 not assessed: no alternate missense at residue 489 was found in any available source (4 papers, Komine 47-variant panel, ClinVar record), but the systematic same-residue comparator harvest was skipped (pm5_candidates.json found=false) and no gene-level ClinVar/LOVD inventory exists in the bundle, so a pathogenic comparator cannot be affirmatively excluded.
PP2 not assessed: missense is a common mechanism of MUTYH disease (founder missense variants; >200 missense variants in LOVD), but the required 'low rate of benign missense variation' component is unverifiable because gnomAD gene-level missense constraint metrics are absent from the evidence bundle.
BP1 not met (high confidence): MUTYH disease is missense-predominant rather than primarily truncating, so the BP1 premise fails.
Functional data (Komine 2015: p.Ala489Thr partially defective in MutY-complementation assay; SIFT A 0.01; PolyPhen-2 D 0.973) bear on PS3/BS3 and are deliberately not applied to any criterion in this group.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel MUTYH specification v1.0 (cspec doc 1742141534) was found and confirms autosomal recessive inheritance (familial adenomatous polyposis 2, MONDO:0012041, preferred transcript NM_001128425.2), but its ruleset payload was empty in this case (framework_complete=false, criteria=[], rule_payload={}); PS2/PM6/PP1/BS4 were therefore adjudicated under generic ACMG/AMP 2015 (PMID:25741868).
PS2 and PM6 are not applicable: MUTYH-associated polyposis is autosomal recessive, so a single de novo allele cannot establish pathogenicity, and no parental/trio testing data exists anywhere in the case bundle (no de novo observation in PMID:20618354, PMID:25820570, or any of the 15 ClinVar submissions).
PP1 is not assessed: the variant is reported only as a monoallelic finding in one AFAP patient (PMID:20618354, Table 2 patient 35) and in one AFAP individual (PMID:25820570) with untested relatives; ClinVar submitter segregation assertions (SCV000261194, SCV000185906) lack primary pedigree data and were not used as evidence.
BS4 is not assessed: no affected family members have been genotyped, so no non-segregation evidence exists in either direction.
No other criterion in this group (PS2/PM6/PP1/BS4) receives any strength; the group contributes no segregation or de novo evidence to the overall classification.
Governing framework: InSiGHT Hereditary Colorectal Cancer/Polyposis EP MUTYH v1.0 (cspec doc 1742141534) identified, but rule payload/criteria list empty in this case; generic ACMG/AMP 2015 (PMID 25741868) PS3/BS3 definitions applied.
PS3 met (moderate): PMID 25820570 directly tested the variant (p.A489T = c.1465G>A, verified identical to the paper's c.1423G>A on NM_001048171.1) in a validated E. coli CC104mutY complementation assay; ~3.2-fold increased mutation rate falls in the 'partially defective' bin (1.7-4.8-fold) calibrated against known pathogenic (p.Y179C, p.G396D) and polymorphic (p.V22M, p.Q338H, p.S515F) variants; the variant is more impaired than founder pathogenic p.G396D; strength set to moderate because the effect is partial and from a single study.
BS3 not met: no functional evidence shows an absence of damaging effect; the available functional evidence indicates partial loss of BER function, the opposite of BS3.
In-silico predictions (SIFT A 0.01, PolyPhen-2 D 0.973 in PMID 25820570 Table 1; REVEL 0.724) were not used for PS3/BS3; they belong to the in-silico group.
ClinVar submissions (15 labs, all Uncertain significance) and their PS3 signals were used only as leads; the PS3 call rests on direct verification of the primary assay paper, not on any submitter classification.
Framework: the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specification for MUTYH v1.0 (cspec doc 1742141534) is registered for this case (framework_mode=unstructured_ruleset) but its rule payload is empty (criteria=[], rule_payload={}, framework_complete=false, official_clingen=false), so no variant-level VCEP rules for PS4/PP4/PP5/BP5/BP6 were retrievable. Generic ACMG/AMP 2015 (PMID 25741868) therefore governs this group. MUTYH-associated polyposis (MAP; MONDO:0012041, familial adenomatous polyposis 2) is autosomal recessive.
Variant identity: NM_001128425.2:c.1465G>A = NP_001121897.1:p.(Ala489Thr) (exon 14); the ClinVar exact-match record VCV000142138 is reported under the alternate transcript NM_001048174.2:c.1381G>A (p.Ala461Thr), matched by transcript HGVS.
PS4: not assessed - no case-control enrichment study exists for this exact variant; the only exact-variant observation in the reviewed literature is a single monoallelic case-series observation (PMID:20618354, Table 2 patient 35) with no control comparison.
PP4: not met - the single monoallelic AFAP observation (PMID:20618354) is insufficient to establish a highly specific MAP phenotype, and no proband phenotype data is available; laboratory PP4 assertions were not inherited.
PP5: not met - ClinVar has 0 expert-panel submissions for this variant (all 15 submissions are clinical laboratories, aggregate VUS); no expert-panel Pathogenic/Likely pathogenic classification exists.
BP5: not assessed - no alternate-molecular-basis or co-occurrence data is available for this variant.
BP6: not met - ClinVar has 0 expert-panel submissions for this variant; no expert-panel Benign/Likely benign classification exists.
Inheritance context: MUTYH-associated polyposis (familial adenomatous polyposis 2, MONDO:0012041) is an autosomal recessive condition per the governing CSPEC raw_rule_origin; PM3 (in trans with a pathogenic variant) is the relevant pathogenic allelic test, and the dominant-disease clause of BP2 is inapplicable.
PM3 not met: the variant has never been documented in trans with a pathogenic variant. The only published observation (PMID 20618354) is monoallelic in one AFAP patient; the only co-occurrence report (GeneDx SCV000568578) has explicitly unknown phase and no validated PMID; gnomAD shows no homozygotes. Phase determination (parental/offspring testing) is the outstanding gap; needs human review if phasing data become available.
BP2 not met: no cis configuration with a pathogenic variant is documented, and the gene is recessive, so neither BP2 clause is satisfied. A monoallelic observation in an AR condition does not generate BP2 evidence.
Framework note: the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MUTYH v1.0 (CSPEC doc 1742141534) was identified but delivered no machine-readable criteria rules (empty rule_payload, criteria=[], framework_complete=false); generic ACMG/AMP 2015 (PMID 25741868) rule definitions were therefore applied.
Citation-grounding note: ClinVar submissions cite PMIDs 15761860 and 16234049 for this variant, but neither full text mentions it (gene-level citations); PMID 35668106 (CRC cases) full text was not available for verification. Only PMID 20618354 and PMID 25820570 verifiably mention the variant (as p.Ala489Thr / p.A489T).
PP3 met at supporting strength: REVEL 0.724 (local lookup, source key 'revel') falls in the ClinGen SVI supporting band (0.644-0.772) of the REVEL calibration (Pejaver et al. 2022, PMID 36413997); PP3 applied exactly once per ACMG/AMP 2015 (PMID 25741868) caveat.
BP4 not met: no multiple lines of computational evidence suggesting no impact; the single calibrated predictor (REVEL 0.724) supports a deleterious effect, and the remaining tools (SpliceAI threshold unverified for BP4, BayesDel uncalibrated, aGVGD absent) cannot form a benign-leaning line.
Framework: generic ACMG/AMP 2015 fallback used because the InSiGHT MUTYH CSPEC v1.0 (source key 'cspec') contains no PP3/BP4 rules (empty criteria payload, no gene-specific PP3/BP4 lookup spreadsheet).
BP7 not applicable: variant is missense (p.Ala489Thr), not synonymous; BP7 is outside this group's output schema and was not adjudicated.
Governing framework: the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MUTYH v1.0 (cspec doc 1742141534) was found (framework_mode 'vcep', precedence_rank 1, preferredTranscript NM_001128425.2, autosomal recessive inheritance, MONDO:0012041) but was retrieved as an unstructured ruleset with an empty rule_payload (framework_complete=false). No MUTYH-specific population-frequency rules (BA1/BS1/BS2/PM2 calibrations) were therefore available; per instruction, criteria were adjudicated with generic ACMG/AMP 2015 definitions (PMID 25741868) and this lab's non-VCEP operating thresholds (PM2<0.1%, BS1>0.3%, BA1>1%), with the VCEP rule unavailability recorded as a gap.
Variant identity: NM_001128425.2(MUTYH):c.1465G>A = p.(Ala489Thr); ClinVar lists the same genomic change under the canonical transcript as NM_001048174.2:c.1381G>A (p.Ala461Thr) (variation 142138, also 2453369). gnomAD queries used the GRCh37/GRCh38 coordinates (1-45796865-C-T / chr1-45331193-C-T).
Population frequency: the variant is rare in all datasets - gnomAD v2.1 total AF 0.00389% (11/282,784 alleles) and gnomAD v4.1 total AF 0.00397% (64/1,614,038 alleles), 0 homozygotes in both. Highest ancestry-specific frequency 0.01468% (v4.1, African/African American; 11/74,908 alleles). grpmax FAF 2.293e-05 (v2.1) and 8.155e-05 (v4.1) confirm the low frequency is not driven by an ancestry artifact.
BA1 not met: AF ~0.004% is far below the 5% ACMG stand-alone threshold and the 1% lab operating threshold (largest margin factor ~68x even at max subpopulation).
BS1 not met: AF ~0.004% is ~75x below the 0.3% lab operating threshold and well below expected carrier frequencies for MAP (autosomal recessive); the variant is a rare allele, not a common population allele.
BS2 not met: 0 homozygous observations in gnomAD v2.1/v4.1 and no healthy-adult/control observation in ClinVar or in any retrieved publication full text (the variant is not mentioned in any paper in the bundle).
PM2 met (supporting): total AF 0.00397% and max subpopulation AF 0.01468% both remain below the 0.1% recessive-disorder threshold, with 0 homozygotes - consistent with an extremely low-frequency (possibly private) allele. Supporting strength only; PM2 alone is insufficient for a benign/benign-leaning conclusion.
Net population-group effect: one supporting pathogenic-leaning criterion (PM2); no benign population criterion (BA1/BS1/BS2) is met. These results are robust to the unretrieved VCEP thresholds because the observed frequencies are orders of magnitude from every relevant cutoff.
No criteria match.
Met · 3
PS3ModerateMet (moderate): E. coli complementation assay showed a 3.2-fold increased mutation rate, a partial defect comparable to founder-pathogenic p.G396D (1.7-fold).
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Reasoning
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP specification for MUTYH v1.0 (cspec doc 1742141534) was identified and consulted, but its rule payload and criteria list are empty in this case bundle (vcep_db/MUTYH/criteria.json = []), so no gene-specific PS3 calibration is available; generic ACMG/AMP 2015 (PMID 25741868) PS3 is applied. Direct functional evidence: PMID 25820570 (Komine et al. 2015) tested this variant (p.A489T; c.1423G>A on NM_001048171.1, verified identical to NM_001128425.2:c.1465G>A / g.45796865C>T by CDS alignment) in a validated E. coli CC104mutY complementation assay measuring rifampicin-resistance mutation rate (G:C->T:A transversion accumulation, the canonical readout of MUTYH base excision repair). The variant produced a 32.0/10^8 mutation rate (SD 3.3), approximately 3.2-fold over wild type, placing it in the 'partially defective' category (cut-offs 1.7- and 4.8-fold). Assay calibration/controls: cut-offs were set using five variants of clear clinical status - pathogenic founders p.Y179C (4.8-fold) and p.G396D (1.7-fold) and polymorphic p.V22M (1.2-fold), p.Q338H (0.7-fold), p.S515F (1.0-fold) - with empty-vector and wild-type controls; results were concordant with prior independent glycosylase assays for the majority of overlapping variants, supporting reliability. Importantly, A489T (3.2-fold) is more impaired than the disease-defining founder pathogenic variant p.G396D (1.7-fold), which sits in the same partially defective category. Additional readouts in the same study: protein stability by western blot (band intensity 1.07x, essentially normal) and nuclear localization (unaffected). Strength calibration: the assay is validated with calibrated controls and the effect is variant-specific and biologically direct, but the result is a partial (intermediate) defect from a single study in a bacterial complementation system, and the authors caution that intermediate defects cannot be precisely mapped to MAP pathogenesis; PS3 is therefore applied at moderate strength (not strong), consistent with ACMG/AMP 2015 PS3 ('Well-established in vitro or in vivo functional studies supportive of a damaging effect') and standard SVI-style downgrade reasoning for partial/intermediate single-study results. SIFT (A, 0.01) and PolyPhen-2 (D, 0.973) in the same table are in-silico predictions and were NOT used for PS3.
Rule
PS3 (ACMG/AMP 2015, PMID 25741868): well-established in vitro/in vivo functional studies supportive of a damaging effect on the gene or gene product; applied at moderate strength (validated complementation assay with calibrated controls and direct variant-specific result, but partial/intermediate effect from a single study)
Evidence considered
PMID:25820570 (Komine et al. 2015) - E. coli CC104mutY complementation assay, rifampicin-resistance mutation rate; variant tested as p.A489T c.1423G>A (NM_001048171.1) = c.1465G>A (NM_001128425.2), same genomic nucleotide g.45796865C>T (verified by CDS alignment); 32.0 rifR/10^8 (SD 3.3) ~ 3.2-fold vs wild type -> 'partially defective' (1.7-4.8-fold bin), more impaired than founder pathogenic p.G396D (1.7-fold); cut-offs calibrated against known pathogenic (p.Y179C, p.G396D) and known polymorphic (p.V22M, p.Q338H, p.S515F) variants; protein stability 1.07x; nuclear localization unaffected
PMID:25741868 (ACMG/AMP 2015) - PS3 definition: 'Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product'; used as the applicable generic criterion since the VCEP rule payload was empty
cspec (InSiGHT MUTYH VCEP v1.0, doc 1742141534) - consulted as governing framework; no PS3 rule text available in bundle
Still missing
VCEP (InSiGHT MUTYH v1.0, cspec 1742141534) rule payload empty in this case; PS3 strength calibrated with generic ACMG/AMP 2015 + SVI reasoning - a VCEP rule, if available, could recalibrate strength
Single functional study for this specific variant; no independent corroborating assay (in vitro glycosylase, human cell BER, or cDNA complementation) of p.A489T has been published
Result is a partial (intermediate) defect; authors of PMID 25820570 note the contribution of intermediate defects to MAP pathogenesis is not precisely calibrated
PM2SupportingMet (supporting): gnomAD allele frequency 0.004% (0 homozygotes), about 25-fold below the 0.1% threshold for recessive disorders.
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Reasoning
PM2 (absent in controls, or at extremely low frequency if recessive; PMID 25741868) is met at supporting strength. For this autosomal-recessive disorder, the lab's non-VCEP operating threshold is PM2 AF <0.1%. Observed frequencies are ~25-fold below that: gnomAD v4.1 total AF 0.00397% (64/1,614,038 alleles) and gnomAD v2.1 total AF 0.00389% (11/282,784 alleles), with 0 homozygotes in both datasets. The highest ancestry-specific frequency (AFR 0.01468% in v4.1, 11/74,908 alleles; 'Remaining individuals' 0.01384% in v2.1, 1/7,226 alleles) remains below 0.1%, and the grpmax filtering allele frequencies (v2.1 2.293e-05; v4.1 8.155e-05) are even lower, indicating the frequency is not inflated by ancestry-stratified artifacts. PM2 met (supporting).
Rule
Generic ACMG/AMP 2015 PM2 (PMID 25741868): absent in controls, or extremely low frequency if recessive (supporting). Lab non-VCEP operating threshold AF <0.1% for autosomal-recessive disorders. Total AF 0.004% and max subpopulation AF 0.0147% both <0.1% - met (supporting). MUTYH InSiGHT VCEP present but rule payload unparsed.
Evidence considered
gnomAD v4.1 (gnomad_v4): total AF 3.96521e-05 (0.00397%), 64/1,614,038 alleles, 0 homozygotes; max subpopulation AFR AF 0.000146847 (0.01468%, 11/74,908 alleles); grpmax FAF 8.155e-05
gnomAD v2.1 (gnomad_v2): total AF 3.88989e-05 (0.00389%), 11/282,784 alleles, 0 homozygotes; max subpopulation AF 0.000138389 (0.01384%, 1/7,226 alleles); grpmax FAF 2.293e-05
PM2 definition ('Absent in controls (or at extremely low frequency if recessive)'): Richards et al. 2015 (PMID 25741868), Table 3
Lab non-VCEP operating threshold PM2 <0.1% for autosomal-recessive disorders (generic ACMG fallback; no VCEP-specific threshold retrievable)
Still missing
MUTYH InSiGHT VCEP-specific PM2 threshold not retrievable (rule_payload empty; framework_complete=false) - decision is robust under the generic <0.1% recessive threshold because even the max subpopulation AF (0.01468%) is ~7-fold below it, but confirm against cspec doc 1742141534
gnomAD Canada (HostSeq) record not retrieved and could not be used as an additional low-frequency corroboration
PP3SupportingMet (supporting): REVEL 0.724 falls in the supporting band (0.644-0.772) for a predicted deleterious missense effect.
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Reasoning
Missense variant MUTYH c.1465G>A (p.Ala489Thr). No applicable gene-specific PP3/BP4 rule: the InSiGHT MUTYH CSPEC v1.0 framework (cspec) was found but carries an empty criteria payload (criteria=[], rule_payload={}, framework_complete=false, official_clingen=false) and no PP3/BP4 lookup spreadsheet or index guidance entries; generic ACMG/AMP 2015 (PMID 25741868) with ClinGen SVI calibration (PMID 36413997) is therefore used. REVEL score 0.724 (local REVEL v1.3 lookup, source key 'revel') falls in the SVI supporting band for PP3 (0.644-0.772; supporting >= 0.644, moderate >= 0.773, strong >= 0.932 per Pejaver et al. 2022, PMID 36413997). PP3 applied once only, per the ACMG caveat that in silico algorithms are not independent criteria. SpliceAI max delta 0.00 (source key 'spliceai') predicts no splice impact and does not add to PP3; BayesDel 0.234861 (source key 'bayesdel') and aGVGD were not usable (no verified published calibration thresholds with a named publication/table, so treated as not_available per group calibration rules). No double counting across the splice and missense axes.
Rule
Generic ACMG/AMP 2015 PP3 (Richards et al., PMID 25741868), applied once per its caveat, with strength mapped by ClinGen SVI REVEL calibration (Pejaver et al., PMID 36413997): REVEL >= 0.644 supporting, >= 0.773 moderate, >= 0.932 strong. REVEL 0.724 -> PP3 supporting.
Evidence considered
REVEL score 0.724 for MUTYH c.1465G>A p.(Ala489Thr) (local REVEL v1.3 lookup, source_registry key 'revel'); ClinGen SVI REVEL calibration (Pejaver et al., Am J Hum Genet 2022; PMID 36413997) maps PP3 as supporting >= 0.644, moderate >= 0.773, strong >= 0.932; 0.724 lies in the supporting band (0.644-0.772), so PP3 supporting.
SpliceAI max delta score 0.00 (source_registry key 'spliceai'): no splice impact predicted; not counted toward PP3 to avoid double counting the same prediction across splice and missense axes.
BayesDel score 0.234861 (source_registry key 'bayesdel'): treated as not_available for PP3/BP4 because no verified published calibration threshold with a named publication/table is available to this pipeline (per group rule, any BayesDel score is insufficiently calibrated for PP3/BP4 unless a citable publication and table are named).
aGVGD: no score present anywhere in the case evidence bundle; not available.
PP3 rule definition and 'use only once' caveat per ACMG/AMP 2015 (Richards et al., Genet Med 2015; PMID 25741868), Table 5.
Still missing
Only one calibrated in-silico line (REVEL) supports PP3; BayesDel and aGVGD could not be used because no verified published calibration threshold with a named publication/table is available to this pipeline.
No gene-specific InSiGHT MUTYH PP3/BP3 rule or PP3/BP4 lookup spreadsheet was available in vcep_materials (criteria payload empty); generic SVI calibration applied instead.
PS1Not met: p.Ala489Thr is not established as pathogenic - ClinVar VCV000142138 is Uncertain significance across all 15 submitters.
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Reasoning
PS1 requires the same amino acid change to have been previously established as pathogenic regardless of nucleotide change. Here the amino acid change under assessment, p.Ala489Thr (NP_001121897.1; equivalently p.Ala461Thr on NM_001048174.2 per ClinVar VCV000142138, and p.A475T in the 535-aa numbering used by Kairupan 2005 and Jo 2005), is the variant itself and is NOT established as pathogenic: ClinVar VCV000142138 is Uncertain significance across all 15 submitters (2 stars, no expert panel submissions, no conflicts); the reporting papers assign uncertain status (Kairupan 2005: 'more problematic to assign causative status'; Jo 2005: 'functional significance of this missense mutation is unknown'; Morak 2010: monoallelic, unclassified finding; Komine 2015: partially defective in a MutY-complementation assay but not categorized as defective). Additionally, no alternative nucleotide change producing p.Ala489Thr exists: codon 489 (GCG) can only reach a Thr codon (ACG) via c.1465G>A, the sole single-nucleotide path, so the 'different nucleotide change' scenario cannot arise. PS1 therefore not met. Note: the partially defective functional result (Komine 2015) is functional evidence relevant to PS3/BS3 and is adjudicated by the functional group, not PS1.
Rule
PS1: Same amino acid change as a previously established pathogenic variant regardless of nucleotide change (ACMG/AMP 2015, PMID 25741868)
Evidence considered
ClinVar VCV000142138: Uncertain significance, 15 submitters (14 + 1), criteria provided multiple submitters no conflicts, 0 expert panel submissions; ClinVar title NM_001048174.2(MUTYH):c.1381G>A (p.Ala461Thr) confirms same variant
PMID:25820570 (Komine 2015) Table 1: p.A489T c.1423G>A (NM_001048171.1 numbering; same variant, verified via anchor variants p.G396D c.1145G>A and p.G503E c.1466G>A): functional complementation partially defective (32.0-fold), AFAP (1); variant not classified pathogenic by the authors
PMID:20618354 (Morak 2010): patient 35 monoallelic c.1465G>A; p.Ala489Thr, second allele not identified (WT exons 2+3) - unclassified monoallelic finding
PMID:15761860 (Kairupan 2005): A475T (G1423A) first report; 'more problematic to assign causative status'
PMID:16234049 (Jo 2005): patient 281 G382D/A475T compound heterozygote; 'functional significance of this missense mutation is unknown'
Rule: ACMG/AMP 2015 PS1 definition (PMID 25741868): 'Same amino acid change as a previously established pathogenic variant regardless of nucleotide change'
PM1Not met: residue 489 lies outside any confirmed mutational hotspot or defined critical functional domain.
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Reasoning
PM1 requires location in a mutational hot spot and/or a critical, well-established functional domain without benign variation. Hotspot component: the CancerHotspots query (MUTYH A489, evidence.json 'hotspots' section) returned no statistically significant hotspot, and Komine 2015 states functionally defective MUTYH variants are 'distributed widely in the two functional domains ... without a clear hot spot', arguing against a hotspot model for this gene/residue. Domain component: residue 489 lies in the C-terminal region of MUTYH, but no available source affirmatively places it inside a critical functional domain with defined boundaries: Kairupan 2005 states A475T (same residue in the 535-aa numbering) 'does not occur in a known functional domain of MYH but it is conserved between Mouse and Man'; Jo 2005 places it '2 codons from a highly conserved domain ... the so-called nudix domain' (i.e., adjacent to, not within, the nudix box); a single LabCorp ClinVar assertion (SCV000919797) describes A489T as located in the C-terminal domain of MUTYH, but submitter assertions are not independent established evidence. Komine 2015 describes the C-terminal domain as a MutT-like/nudix-type domain that functions in 8-oxoG recognition, but gives no residue boundaries enabling placement of A489. The InSiGHT MUTYH VCEP v1.0 (cspec doc 1742141534) was detected but its ruleset payload is empty in this case bundle, so any VCEP-defined PM1 domain list could not be consulted. Neither PM1 component is affirmatively established on available evidence; PM1 not met, with human review recommended to close the domain-mapping gap (UniProt/Pfam boundaries or the InSiGHT VCEP domain definitions).
Rule
PM1: Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation (ACMG/AMP 2015, PMID 25741868)
Evidence considered
CancerHotspots query 'MUTYH A489' (evidence.json hotspots section): search_status no_result - variant does not lie in a statistically significant hotspot
PMID:25820570 (Komine 2015): 'Mapping of the secondary structure of MUTYH showed that the functionally defective variants were distributed widely in the two functional domains (i.e., the N-terminal catalytic domain and the C-terminal MutT-like domain) without a clear hot spot'; C-terminal domain described as MutT-like/nudix-type without residue boundaries
PMID:15761860 (Kairupan 2005): A475T (same residue, 535-aa numbering) 'does not occur in a known functional domain of MYH but it is conserved between Mouse and Man'
PMID:16234049 (Jo 2005): A475T 'lies 2 codons from a highly conserved domain in DNA repair genes ... the so-called nudix domain'
oncokb: OncoKB did not identify variant-specific reviewed functional evidence for this variant; no curated hotspot annotation
Rule: ACMG/AMP 2015 PM1 definition (PMID 25741868): 'Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation'
Still missing
Authoritative functional-domain mapping for MUTYH residue 489 (e.g., UniProt/Pfam domain boundaries or InSiGHT MUTYH VCEP v1.0 PM1 domain list) not available in the evidence bundle; the CSPEC ruleset payload is empty (vcep_materials.json, criteria.json)
CancerHotspots result is present in evidence.json but is not a source_registry key, so it is cited in rationale only
PM3Not met: trans configuration with a pathogenic allele is unconfirmed - the only co-occurrence report states phase was unknown.
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Reasoning
PM3 (generic ACMG/AMP 2015, PMID 25741868) requires, for recessive disorders, that the variant be detected in trans with a pathogenic variant, with phase determined by testing of parents/offspring. MUTYH-associated polyposis (MAP; familial adenomatous polyposis 2, MONDO:0012041) is autosomal recessive, so PM3 is the relevant allelic test. No source in this case establishes trans configuration: (1) Morak et al. 2010 (PMID 20618354) reports c.1465G>A p.Ala489Thr as a MONOALLELIC variant in a single AFAP patient (patient 35, second allele wild-type in exons 2+3) - i.e., not biallelic, no in-trans observation; (2) Komine et al. 2015 (PMID 25820570) lists p.A489T as observed in one AFAP patient with no biallelic or phase information; (3) the only co-occurrence evidence (GeneDx ClinVar SCV000568578) states the variant was observed 'with a pathogenic MUTYH variant in individuals with multiple polyps and/or colon cancer; however, it was unknown if the variants were on the same o[rigin/chromosome]' - phase explicitly unknown, and this submission carries no validated PMID and is not usable as a criterion lead; (4) gnomAD shows 0 homozygotes (v2.1: 11/282,784 alleles; v4.1: 64/1,614,038 alleles), providing no homozygous observation that would support trans configuration. Because phase is not established, PM3 cannot be applied. Flagged for human review: if parental/phasing studies establish that the co-occurring pathogenic MUTYH variant (per SCV000568578) is on the opposite chromosome, PM3 would become applicable (moderate, with potential upgrade per PMID 25741868 if multiple independent in-trans observations are documented).
Rule
PM3: For recessive disorders, detected in trans with a pathogenic variant (generic ACMG/AMP 2015, PMID 25741868). Note: requires testing of parents (or offspring) to determine phase. Default strength moderate; upgrade to strong possible with multiple in-trans observations.
Evidence considered
PMID:20618354 - Morak et al. 2010: c.1465G>A p.Ala489Thr documented as monoallelic (second allele WT in exons 2+3) in one AFAP patient; no biallelic/in-trans observation.
PMID:25820570 - Komine et al. 2015: p.A489T observed in 1 AFAP patient (Table 1); functional assay partially defective; no phase/biallelic data reported.
PMID:15761860 and PMID:16234049 - full-text searched; variant not mentioned (cited by ClinVar submissions at gene level only); no allelic evidence.
clinvar (SCV000568578, GeneDx): co-occurrence with a pathogenic MUTYH variant reported in individuals with multiple polyps and/or colon cancer, but phase unknown ('unknown if the variants were on the same o...'); submission has no validated PMIDs.
gnomad_v2 / gnomad_v4: AF ~0.004%, 0 homozygotes - no support for biallelic/trans configuration.
PMID:25741868 - generic ACMG/AMP 2015 PM3 definition applied ('This requires testing of parents (or offspring) to determine phase').
Still missing
Phase (cis vs trans) of the reported co-occurrence with a pathogenic MUTYH variant (GeneDx SCV000568578) was never determined; parental or offspring testing is required to establish trans configuration.
No validated publication (PMID with variant mention) documents an in-trans or biallelic observation of c.1465G>A/p.Ala489Thr; the only published observation (PMID 20618354) is monoallelic.
No homozygous observation in gnomAD v2.1/v4.1 to support biallelic inheritance.
ClinGen InSiGHT MUTYH VCEP specification (CSPEC doc 1742141534, v1.0) was identified but its machine-readable rule payload is empty (criteria=[], framework_complete=false); no VCEP-specific PM3 rule could be applied - generic ACMG/AMP 2015 was used.
PP4Not met: the only observation is a single heterozygous carrier, which does not establish the biallelic phenotype of this recessive disorder.
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Reasoning
PP4 (phenotype or family history highly specific for a disease with a single genetic etiology) is not met. The only exact-variant phenotypic observation is a single monoallelic carrier (43-year-old male, AFAP group III, >10<100 adenomas, polypectomy; family history of CRC/gastric cancer) reported in PMID:20618354 (Table 2, patient 35), classified by the authors as an unclassified variant (UV). MUTYH-associated polyposis is autosomal recessive and this observation is heterozygous, so it does not establish a biallelic MAP phenotype; a single heterozygous observation in an APC-negative case series is insufficient to demonstrate a highly specific phenotype. No proband phenotype or family history is provided in the case bundle. PP4 assertions made by ordinary clinical laboratory submissions (Color, All of Us, Quest) were not inherited per adjudication rules, and the papers those submissions cite (PMID:15761860, 16234049, 25820570, 35668106) do not verifiably report this exact variant.
Rule
Generic ACMG/AMP 2015 (PMID 25741868): PP4 - phenotype or family history is highly specific for a disease with a single genetic etiology.
Evidence considered
PMID:20618354, Table 2, patient 35: monoallelic c.1465G>A (p.Ala489Thr) in an AFAP III patient (>10<100 adenomas, polypectomy; aunt CRC at 50, uncle and grandfather gastric cancer); authors classified the variant as unclassified (UV/-).
Still missing
No biallelic observations of this variant with a MAP phenotype have been reported.
No proband phenotype/family history is provided in the case bundle.
No retrievable InSiGHT MUTYH CSPEC PP4 specification (empty rule payload) to confirm VCEP-specific PP4 criteria.
PP5Not met: no ClinVar expert panel has classified this variant - all 15 submissions are from clinical laboratories.
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Reasoning
PP5 requires an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The ClinVar submission audit for VCV000142138 shows expert_panel_submissions = 0; all 15 submissions are ordinary clinical laboratory submissions with aggregate classification Uncertain significance (API review stars = 2, 'criteria provided, multiple submitters, no conflicts'). No InSiGHT/ClinGen expert panel has classified this variant. Aggregate ClinVar labels and ordinary laboratory assertions never trigger PP5.
Rule
PP5 applies only for an exact-variant ClinVar expert-panel classification of Pathogenic/Likely pathogenic (supporting strength); ordinary laboratory submissions and aggregate ClinVar labels never trigger PP5.
BA1Not met: gnomAD allele frequency 0.004% is far below the >1% stand-alone benign threshold.
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Reasoning
BA1 (stand-alone benign) requires an allele frequency above the population threshold. Under the generic ACMG/AMP 2015 definition (PMID 25741868: AF >5% in ESP/1000 Genomes/ExAC) and this lab's non-VCEP operating threshold (>1%), the variant is far below: gnomAD v2.1 total AF = 3.88989e-05 (0.00389%, 11/282,784 alleles) and gnomAD v4.1 total AF = 3.96521e-05 (0.00397%, 64/1,614,038 alleles). Even the highest observed ancestry-specific frequency (African/African American, AF = 0.01468%, 11/74,908 alleles in gnomAD v4.1) is ~68-fold below the 1% operating threshold and ~340-fold below the 5% ACMG threshold. No ancestry population approaches a benign stand-alone frequency. BA1 not met.
Rule
Generic ACMG/AMP 2015 BA1 (PMID 25741868): AF >5% in reference populations = stand-alone benign; lab non-VCEP operating threshold >1%. MUTYH InSiGHT VCEP present but rule payload unparsed (framework_complete=false), so no VCEP-specific BA1 threshold applied.
Evidence considered
gnomAD v4.1 (gnomad_v4): total AF 3.96521e-05 (0.00397%), 64/1,614,038 alleles, 0 homozygotes; max subpopulation AFR 0.01468% (11/74,908 alleles); grpmax FAF 8.155e-05
gnomAD v2.1 (gnomad_v2): total AF 3.88989e-05 (0.00389%), 11/282,784 alleles, 0 homozygotes; max subpopulation 'Remaining individuals' 0.01384% (1/7,226 alleles); grpmax FAF 2.293e-05
BA1 definition and 5% stand-alone threshold: Richards et al. 2015, Genet Med 17:405-424 (PMID 25741868), Table 4
MUTYH InSiGHT VCEP v1.0 (cspec doc 1742141534) was retrieved as an unstructured ruleset with empty rule_payload (framework_complete=false); no VCEP-specific BA1 threshold could be applied - confirm no MUTYH-specific BA1 calibration exists
gnomAD Canada (HostSeq) variant record listed in source_registry was not retrieved into the evidence bundle
BS1Not met: gnomAD allele frequency 0.004% is far below the >0.3% threshold and below MUTYH founder carrier frequencies.
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Reasoning
BS1 requires the allele frequency to be greater than expected for the disorder. MUTYH-associated polyposis (MAP) is autosomal recessive (MONDO:0012041, familial adenomatous polyposis 2; framework preferredModeOfInheritance = Autosomal recessive). Observed frequencies are orders of magnitude below both the lab's non-VCEP BS1 operating threshold (>0.3%) and any plausible MAP carrier-frequency expectation: gnomAD v4.1 total AF 0.00397% (64/1,614,038 alleles) and gnomAD v2.1 total AF 0.00389% (11/282,784 alleles); highest ancestry subpopulation AF 0.01468% (v4.1 AFR) and 0.01384% (v2.1 'Remaining'). Frequencies ~0.004-0.015% are far below the >0.3% operating threshold and below the ~1-2% carrier frequencies reported for the common founder MUTYH alleles (e.g., p.Tyr179Cys/p.Gly396Asp), indicating this is a rare variant, not a population-common one. BS1 not met.
Rule
Generic ACMG/AMP 2015 BS1 (PMID 25741868): AF greater than expected for disorder (strong benign); lab non-VCEP operating threshold >0.3% for this autosomal-recessive disorder. MUTYH InSiGHT VCEP present but rule payload unparsed, so no VCEP-specific BS1 threshold applied.
Evidence considered
gnomAD v4.1 (gnomad_v4): total AF 3.96521e-05 (0.00397%), 64/1,614,038 alleles; max subpopulation AFR AF 0.000146847 (0.01468%, 11/74,908 alleles); 0 homozygotes
gnomAD v2.1 (gnomad_v2): total AF 3.88989e-05 (0.00389%), 11/282,784 alleles; max subpopulation AF 0.000138389 (0.01384%, 1/7,226 alleles); 0 homozygotes
BS1 definition ('Allele frequency is greater than expected for disorder', see Table 6): Richards et al. 2015 (PMID 25741868), Table 4
BS2Not met: no healthy homozygous individuals observed - 0 homozygotes in gnomAD v2.1 and v4.1.
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Reasoning
BS2 requires observation of the variant in a healthy adult individual - for an autosomal-recessive disorder, in the homozygous state - with full penetrance expected at an early age (PMID 25741868). The variant has 0 homozygotes in both gnomAD v2.1 (11/282,784 alleles) and gnomAD v4.1 (64/1,614,038 alleles). No healthy-adult/homozygous observation is documented in ClinVar (all 15 submissions are VUS; no population-based or expert-panel benign assertion), and the variant is absent from the full text of all retrieved publications (searched c.1465G>A, p.Ala489Thr, c.1381G>A, p.Ala461Thr), so no control-cohort observation exists in the literature bundle. BS2 not met.
Rule
Generic ACMG/AMP 2015 BS2 (PMID 25741868): for autosomal-recessive disorders, requires homozygous observation in a healthy adult; strong benign. No homozygotes observed in gnomAD v2.1/v4.1, so not met. MUTYH InSiGHT VCEP present but rule payload unparsed.
ClinVar (clinvar): variation 142138 - 15 submissions, all Uncertain significance; no expert panel submission and no population/homozygous healthy-individual assertion
BS2 definition ('Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age'): Richards et al. 2015 (PMID 25741868), Table 4
Still missing
No homozygous carriers observed in gnomAD v2.1 or v4.1 (the prerequisite observation for BS2 in an autosomal-recessive disorder); a future homozygous observation in a healthy adult cohort would re-open BS2
gnomAD Canada (HostSeq) record not retrieved; it could not be used to check for additional homozygote observations
No case-control study in the retrieved literature reports this variant in unaffected control subjects (variant absent from all full-text publications)
BS3Not met: the only functional data show a damaging effect (3.2-fold increased mutation rate), directly contradicting a no-effect conclusion.
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Reasoning
BS3 requires well-established in vitro or in vivo functional studies showing NO damaging effect on protein function or splicing (ACMG/AMP 2015, PMID 25741868). No such benign functional evidence exists for this variant: OncoKB (registry key 'oncokb') reports no variant-specific functional evidence of any direction; no glycosylase-rescue, cDNA-complementation, or normofunction assay has been published for p.A489T. On the contrary, the only direct functional data available (PMID 25820570, E. coli CC104mutY complementation assay) demonstrate a damaging effect - approximately 3.2-fold increased mutation rate (partially defective category, same bin as founder pathogenic p.G396D). The available functional evidence therefore affirmatively contradicts BS3, and the criterion is not met. No VCEP-specific BS3 rule was available (InSiGHT MUTYH v1.0 rule payload empty).
Rule
BS3 (ACMG/AMP 2015, PMID 25741868): well-established in vitro/in vivo functional studies show no damaging effect on protein function or splicing - not satisfied; the only available functional evidence shows a damaging (partial loss) effect
Evidence considered
PMID:25820570 (Komine et al. 2015) - functional data for p.A489T show a damaging (partially defective) effect, the opposite of what BS3 requires
PMID:25741868 (ACMG/AMP 2015) - BS3 definition: 'Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing'
oncokb (OncoKB MUTYH A489T) - negative check: no variant-specific functional evidence identified (Unknown Oncogenic Effect, not reviewed); no benign functional data
Still missing
No benign/normofunction functional assay data for this variant (e.g., full glycosylase activity rescue or complementation equivalent to wild type) have been published; the available functional evidence instead indicates partial loss of function
BP1Not met: MUTYH-associated polyposis is caused predominantly by missense variants, so the truncating-disease premise does not apply.
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Reasoning
BP1 applies a supporting benign weight to missense variants only in genes for which primarily truncating variants are known to cause disease. This premise is false for MUTYH: MUTYH-associated polyposis is caused predominantly by biallelic missense loss-of-function variants - the two most common MAP variants (p.Tyr179Cys, p.Gly396Asp, reported in up to 70% of Caucasian MAP patients; screened as Y165C/G382D in earlier numbering by Kairupan 2005 and Jo 2005) are missense, and Komine 2015 states 'The majority of MUTYH alterations are missense variants' with more than 200 unique missense variants registered in LOVD. The gene summary (gene_context.json) confirms a loss-of-function DNA-glycosylase mechanism consistent with missense-driven disease. Therefore the truncating-predominant premise of BP1 fails and BP1 is not met; the missense-predominant mechanism instead supports the missense-common-mechanism component considered under PP2 (see PP2, currently not_assessed pending constraint data).
Rule
BP1: Missense variant in a gene for which primarily truncating variants are known to cause disease (ACMG/AMP 2015, PMID 25741868)
Evidence considered
PMID:25820570 (Komine 2015): 'The majority of MUTYH alterations are missense variants'; founder variants p.Y179C/p.G396D are missense
PMID:16234049 (Jo 2005): common MYH mutations screened are missense (Y165C, G382D)
PMID:15761860 (Kairupan 2005): common MYH mutations (Y165C, G382D) are missense
gene_context.json: MUTYH is a base excision repair glycosylase whose biallelic loss-of-function causes MAP
Rule: ACMG/AMP 2015 BP1 definition (PMID 25741868): 'Missense variant in a gene for which primarily truncating variants are known to cause disease'
BP2Not met: no cis configuration with a pathogenic variant is reported - the only co-occurrence report states phase was unknown.
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Reasoning
BP2 (generic ACMG/AMP 2015, PMID 25741868) is met when a variant is (a) observed in trans with a pathogenic variant for a fully penetrant DOMINANT gene/disorder, or (b) observed in cis with a pathogenic variant in any inheritance pattern. Clause (a) is not applicable: MUTYH-associated polyposis is autosomal recessive (CSPEC raw_rule_origin: MONDO:0012041, 'Autosomal recessive inheritance'; MAP is a recessive condition), not a fully penetrant dominant disorder, so an in-trans observation would bear on PM3, not BP2. Clause (b) is unmet: no source reports the variant in cis with a pathogenic variant - the only co-occurrence report (GeneDx SCV000568578) explicitly states phase was unknown, and the single published observation (PMID 20618354, patient 35) is monoallelic with the second allele wild-type. A monoallelic (carrier-like) observation in a recessive condition does not constitute BP2 evidence. BP2 therefore does not contribute benign-supporting evidence here.
Rule
BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant in any inheritance pattern (generic ACMG/AMP 2015, PMID 25741868). MUTYH MAP is autosomal recessive - dominant-disease clause not applicable.
Evidence considered
PMID:20618354 - p.Ala489Thr observed monoallelic (not in cis with a pathogenic variant; second allele WT).
PMID:25820570 - p.A489T in 1 AFAP patient; no cis observation.
PMID:15761860 and PMID:16234049 - full-text searched; variant not mentioned.
clinvar (SCV000568578) - co-occurrence with a pathogenic MUTYH variant with unknown phase; cannot support a cis configuration.
PMID:25741868 - BP2 definition: 'Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern'; MUTYH/MAP is autosomal recessive, so the dominant clause does not apply.
Still missing
No cis-configuration evidence exists to evaluate; phase testing of the SCV000568578 co-occurrence would be needed to assess any cis/trans scenario.
BP4Not met: the calibrated in-silico evidence (REVEL 0.724) predicts a deleterious effect, directly contradicting BP4.
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Reasoning
BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product. For this missense variant the only calibrated in-silico line, REVEL 0.724, predicts a deleterious effect (PP3 supporting, PMID 36413997) and therefore directly contradicts BP4; PP3 and BP4 are mutually exclusive for the same variant. The benign-leaning signals that exist are not usable: SpliceAI max delta 0.00 (no splice impact) has no verified published threshold with a named publication for BP4 strength mapping in this pipeline (informational only), BayesDel 0.234861 is uncalibrated (not_available), and aGVGD is absent. 'Multiple lines of computational evidence suggest no impact' is not satisfied. BP4 not met.
Rule
Generic ACMG/AMP 2015 BP4 (Richards et al., PMID 25741868): multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). Not satisfied for this variant.
Evidence considered
SpliceAI max delta score 0.00 (source_registry key 'spliceai'): predicts no splice impact, but no verified published threshold with a named publication/table is available for BP4 strength mapping in this pipeline; treated as informational and not sufficient alone for BP4.
REVEL score 0.724 (source_registry key 'revel'): supports PP3 at supporting strength per ClinGen SVI calibration (PMID 36413997), contradicting BP4; PP3 and BP4 cannot both be applied to the same variant.
BayesDel score 0.234861 (source_registry key 'bayesdel'): uncalibrated, treated as not_available for BP4 (no verified published threshold with a named publication/table).
aGVGD: no score present anywhere in the case evidence bundle; not available.
BP4 rule definition and 'use only once' caveat per ACMG/AMP 2015 (Richards et al., Genet Med 2015; PMID 25741868), Table 4; the 'multiple lines of computational evidence suggest no impact' requirement is not met.
Still missing
No calibrated benign-leaning in-silico evidence was available: BayesDel uncalibrated (no named published threshold), aGVGD absent, and SpliceAI has no verified published BP4 threshold with a named publication in this pipeline.
SpliceAI max delta 0.00 could not be used as a BP4 line because the strength mapping threshold for BP4 could not be attributed to a verifiable publication.
BP6Not met: no ClinVar expert panel has classified this variant as Benign or Likely benign.
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Reasoning
BP6 requires an exact-variant ClinVar expert-panel classification of Benign or Likely benign. The ClinVar submission audit for VCV000142138 shows expert_panel_submissions = 0; the aggregate classification is Uncertain significance across 15 clinical laboratory submissions. No expert-panel Benign/Likely benign assertion exists for this variant, so BP6 is not met.
Rule
BP6 applies only for an exact-variant ClinVar expert-panel classification of Benign/Likely benign (supporting strength); ordinary laboratory submissions and aggregate ClinVar labels never trigger BP6.
PS4Not assessed: no case-control or cohort-enrichment study of this exact variant exists - only a single monoallelic case report without controls.
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Reasoning
PS4 (prevalence of the variant significantly increased in affected individuals versus controls) cannot be assessed: no case-control or cohort-enrichment study reporting this exact variant exists in the evidence corpus. Full-text review of all PS4-flagged case-observation papers found the exact variant c.1465G>A (p.Ala489Thr) only in PMID:20618354, as a single MONOALLELIC observation (Table 2, patient 35) in a case series with no control comparison. The other flagged papers (PMID:15761860, PMID:16234049) do not mention the variant at all, and PMID:16234049 screened only the two founder mutations Y165C/G382D, so it could not have detected it. ClinVar aggregate status is Uncertain significance (15 laboratory submissions) and provides no enrichment data. No enrichment statistics, odds ratios, or case/control allele counts for this variant are available.
Rule
Generic ACMG/AMP 2015 (PMID 25741868): PS4 - prevalence of the variant in affected individuals is significantly increased compared with controls (case-control enrichment). No applicable VCEP-specific PS4 rule: the InSiGHT MUTYH CSPEC (doc 1742141534) was retrieved with an empty rule payload (framework_complete=false).
Evidence considered
Full-text review of all PS4-flagged case-observation papers: PMID:15761860 (Kairupan 2005), PMID:16234049 (Jo 2005), PMID:20618354 (Morak 2010). Exact variant appears only in PMID:20618354 (Table 2, patient 35, monoallelic unclassified variant); no case-control enrichment data for this variant anywhere in the corpus.
ClinVar VCV000142138: aggregate Uncertain significance across 15 submissions; no enrichment or prevalence data.
Still missing
No case-control or cohort-enrichment study reports this exact variant; only a single monoallelic case-series observation (PMID:20618354) is available.
PMID:35668106 (tumor mutational signature study) is cited by some ClinVar laboratory submissions for colorectal cancer observations, but no full text or abstract with exact-variant content is present in the bundle, so any enrichment contribution is unverifiable.
No VCEP-specific PS4 rule was retrievable (InSiGHT MUTYH CSPEC payload empty), so generic ACMG/AMP 2015 (PMID 25741868) PS4 semantics apply.
PM5Not assessed: no pathogenic alternate missense at codon 489 was identified, and no complete variant inventory was available to exclude one.
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Reasoning
PM5 requires a different missense change at the same residue that has been determined pathogenic. Manual review of all available sources identified NO alternate missense variant at residue 489: (i) the four papers reporting variants at this residue (Kairupan 2005 p.A475T; Jo 2005 p.A475T; Morak 2010 c.1465G>A p.Ala489Thr; Komine 2015 p.A489T) all describe the same p.Ala489Thr change only; (ii) the Komine 2015 panel of 47 MUTYH variants (drawn from LOVD) contains only p.A489T at this residue; (iii) the ClinVar record VCV000142138 contains no same-residue comparator. However, the dedicated PM5 comparator-collection step was not performed for this case: pm5_candidates.json has found=false ('Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting'), and the bundle contains no gene-level ClinVar/LOVD variant inventory for MUTYH, so a pathogenic alternate missense at codon 489 (e.g., p.Ala489Val/Ser/Asp) cannot be affirmatively excluded. Evidence therefore insufficient for a confident determination: PM5 returned not_assessed with the gap identified. The pipeline artifact itself instructs: 'do not apply PM5 from this artifact alone.'
Rule
PM5: Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before (ACMG/AMP 2015, PMID 25741868)
ClinVar VCV000142138 (clinvar): only the index variant (VUS); no same-residue comparator present in the record
PMID:25820570 (Komine 2015) Table 1: among 47 LOVD-derived MUTYH variants functionally tested, only p.A489T occurs at residue 489; no alternate missense at this residue
PMID:15761860, PMID:16234049, PMID:20618354: each reports the p.Ala475Thr/p.Ala489Thr change itself; no other variant at this residue
Rule: ACMG/AMP 2015 PM5 definition (PMID 25741868): 'Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before'
Still missing
Systematic same-residue comparator inventory not completed: output/pm5_candidates.json found=false (automatic candidate harvesting skipped); no gene-level ClinVar variant list or LOVD query results in the evidence bundle
A ClinVar/LOVD gene-level search for other missense variants at MUTYH codon 489 (p.Ala489*, and p.Ala475*/p.Ala461* in alternate transcript conventions) is needed to exclude a pathogenic comparator before PM5 can be finalized
PP1Not assessed: no co-segregation data exist - affected relatives of the single reported carrier were not tested.
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Reasoning
No co-segregation data is available for c.1465G>A (p.Ala489Thr). Morak et al. 2010 (PMID:20618354, Table 2, patient 35) reports the variant as a monoallelic finding in one AFAP III patient whose affected relatives (aunt with CRC at 50; uncle and grandfather with gastric cancer) were not tested for the variant; the study states segregation analysis was performed only for biallelic MUTYH carriers. Komine et al. 2015 (PMID:25820570) lists the variant as detected in one AFAP individual without any family data. ClinVar submissions carry segregation-type assertions (SCV000261194 Labcorp/Invitae: 'observed to segregate with disease in related individuals'; SCV000185906 Ambry: monoallelic report in an AFAP individual), but provide no primary pedigree data (no informative meioses, no family genotypes, no affected-relative testing) and per adjudication rules a criterion cannot be inferred from another source's final classification. PP1 (cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease) therefore cannot be applied; additionally, in this autosomal recessive disorder segregation should be evaluated under the biallelic model (affected individuals carrying the variant in trans with a second pathogenic allele).
Rule
PP1: Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (Richards et al. 2015, PMID:25741868).
Evidence considered
PMID:20618354 (Morak et al. 2010): variant monoallelic in one AFAP patient; relatives untested; study methods state segregation was performed 'for biallelic mutation carriers' only — no segregation data for this variant.
PMID:25820570 (Komine et al. 2015): variant listed as detected in one AFAP individual; no family/segregation data.
clinvar (variation 142138): SCV000261194 and SCV000185906 carry PP1-type assertions without primary pedigree data — documented as leads only, not used as evidence.
Rule (PMID:25741868, line 800): PP1 = 'Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease'.
No informative meioses documented; no affected relatives tested for c.1465G>A in any source.
Segregation testing of the reported carrier's family (Morak 2010 patient 35 kindred; any other carriers) is required to assess PP1.
For autosomal recessive MUTYH-associated polyposis, segregation evidence must be interpreted with the biallelic model (variant in trans with a second pathogenic allele in affected individuals).
PP2Not assessed: missense is a common MUTYH disease mechanism, but gene-level missense constraint data were unavailable to confirm a low benign-missense rate.
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Reasoning
PP2 requires BOTH a low rate of benign missense variation in the gene AND missense as a common mechanism of disease. Component 2 (missense common mechanism) is met for MUTYH: Komine 2015 states 'The majority of MUTYH alterations are missense variants. Currently, more than 200 unique missense variants have been registered in LOVD', and the founder/recurrent MAP variants are missense (p.Tyr179Cys, p.Gly396Asp; Y165C/G382D in the 535-aa numbering screened by Jo 2005 and Kairupan 2005). Component 1 (low rate of benign missense variation) is NOT verifiable from the evidence bundle: no gnomAD gene-level missense constraint metrics (missense Z-score, o/e ratio) are present in case_summary.json, prefetch.json, or gene_context.json (hci_prior gene_not_supported; custom_pp2_score null), and the InSiGHT MUTYH VCEP ruleset payload is empty so no VCEP statement on MUTYH benign missense burden is available. Because one required component cannot be verified, PP2 cannot be affirmatively applied: returned not_assessed with the gap identified. No constraint numbers are cited because none are available in the bundle.
Rule
PP2: Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease (ACMG/AMP 2015, PMID 25741868)
Evidence considered
PMID:25820570 (Komine 2015): 'The majority of MUTYH alterations are missense variants. Currently, more than 200 unique missense variants have been registered in LOVD'; 'A biallelic variation p.Y179C and/or p.G396D has been reported in up to 70% of patients with MAP in Caucasian populations'
PMID:16234049 (Jo 2005): 'Patients were screened for the 2 most common MYH mutations: Y165C and G382D' (founder missense variants)
gene_context.json / gene_context_MUTYH.json: MUTYH encodes a base excision repair glycosylase; inherited biallelic mutations cause MUTYH-associated polyposis (loss-of-function mechanism); no constraint metrics provided
Rule: ACMG/AMP 2015 PP2 definition (PMID 25741868): 'Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease'
Still missing
MUTYH gene-level missense constraint metrics (gnomAD missense Z-score / o/e) absent from the evidence bundle - 'low rate of benign missense variation' component of PP2 unverifiable
InSiGHT MUTYH VCEP v1.0 ruleset content unavailable (empty rule payload) - any VCEP-specific PP2 modification could not be checked
BS4Not assessed: no affected family members have been genotyped, so lack of segregation cannot be tested.
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Reasoning
No non-segregation data is available: no affected family member has been genotyped and shown not to carry c.1465G>A (p.Ala489Thr). Morak et al. 2010 (PMID:20618354) reports the variant in a single monoallelic AFAP patient with untested relatives; Komine et al. 2015 (PMID:25820570) provides no family genotypes; no ClinVar submission reports lack of segregation in affected relatives. BS4 (lack of segregation in affected members of a family, PMID:25741868) cannot be assessed without family segregation studies. Note the ACMG caveat that phenocopies (e.g., colorectal cancer/polyposis in the general population) can mimic apparent lack of segregation.
Rule
BS4: Lack of segregation in affected members of a family (Richards et al. 2015, PMID:25741868).
Evidence considered
PMID:20618354 (Morak et al. 2010): affected relatives (aunt, uncle, grandfather) of the monoallelic carrier were not tested — no non-segregation data.
PMID:25820570 (Komine et al. 2015): no family genotypes reported.
clinvar (variation 142138): no submission reports lack of segregation in affected relatives.
Rule (PMID:25741868, line 883): BS4 = 'Lack of segregation in affected members of a family'.
BP5Not assessed: no alternate molecular cause (e.g., APC or MMR variants) is documented in any carrier of this variant.
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Reasoning
BP5 (variant found in a case with an alternate molecular basis for disease) cannot be assessed: the case bundle and reviewed literature contain no data establishing an alternate molecular cause (e.g., APC pathogenic variant, MMR deficiency, or other diagnosis) in any carrier of this variant. The single published carrier (PMID:20618354) was drawn from a cohort that was APC-mutation-negative by design, and no alternate molecular diagnosis is documented for that patient. Absence of co-occurrence/alternate-diagnosis data prevents both a met and a not_met determination.
Rule
Generic ACMG/AMP 2015 (PMID 25741868): BP5 - variant found in a case with an alternate molecular basis for disease.
Evidence considered
PMID:20618354 (consulted): study cohort selected as APC-mutation-negative; no alternate molecular diagnosis reported for the c.1465G>A carrier.
Still missing
No co-occurrence or alternate-molecular-basis data for this variant (e.g., APC pathogenic variant or MMR deficiency in a carrier) is available in the case bundle or reviewed literature.
Not applicable · 6· recorded as not applicableShow reasons ▾Hide reasons ▴PVS1N/ANot applicable: c.1465G>A is a missense change (p.Ala489Thr), so no null-variant mechanism such as nonsense-mediated decay is triggered.
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Reasoning
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_001128425.2:c.1465G>A in MUTYH is a missense substitution predicted to produce NP_001121897.1:p.(Ala489Thr). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies.
PS2N/ANot applicable: no de novo observation or parental testing exists, and MUTYH-associated polyposis is recessive, so a single de novo allele cannot establish pathogenicity.
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Reasoning
MUTYH-associated polyposis (familial adenomatous polyposis 2, MONDO:0012041) is autosomal recessive per the InSiGHT MUTYH CSPEC v1.0 metadata, and the governing ruleset payload was empty in this case, so generic ACMG/AMP 2015 (PMID:25741868) applies. PS2 requires a de novo occurrence with maternity and paternity confirmed in a patient with the disease and no family history; no such data exists: no proband-parent trio, parental testing, or de novo observation for c.1465G>A (p.Ala489Thr) is present in any source in the case bundle (Morak 2010 PMID:20618354 reports the variant only as a monoallelic finding in one AFAP patient with no parental testing; Komine 2015 PMID:25820570 lists one AFAP individual with no de novo data; all 15 ClinVar submissions are VUS with no de novo assertion). Additionally, in an autosomal recessive disease a de novo event in a single allele is not by itself disease-causing; demonstrating pathogenicity via de novo would require a biallelic de novo event or a de novo variant in trans with a second pathogenic allele, neither of which is reported.
Rule
PS2: De novo (both maternity and paternity confirmed) in a patient with the disease and no family history (Richards et al. 2015, PMID:25741868).
Evidence considered
Rule (PMID:25741868, line 771): PS2 = 'De novo (both maternity and paternity confirmed) in a patient with the disease and no family history'.
PMID:20618354 (Morak et al. 2010): c.1465G>A p.Ala489Thr reported as a monoallelic finding in one AFAP III patient (Table 2, patient 35); no parental testing or de novo status reported.
PMID:25820570 (Komine et al. 2015): variant (p.A489T in their reference) detected in one AFAP individual; no de novo or parental data.
clinvar (variation 142138): 15 submissions, all Uncertain significance; no submission reports a de novo occurrence or parental testing.
Still missing
No parental (maternity/paternity) testing or trio data exists for any proband carrying c.1465G>A; de novo status is unknown.
Autosomal recessive disease model: a de novo event in one allele would not be disease-causing without a second pathogenic allele in trans; biallelic de novo data is absent.
PM4N/ANot applicable: missense change causes no protein length alteration, so the in-frame insertion/deletion criterion does not apply.
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Reasoning
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_001128425.2:c.1465G>A in MUTYH is a missense substitution predicted to produce NP_001121897.1:p.(Ala489Thr). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies.
PM6N/ANot applicable: no assumed de novo occurrence is reported, and in this recessive disorder a single de novo allele cannot establish pathogenicity.
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Reasoning
Same basis as PS2: PM6 (assumed de novo without confirmation of paternity/maternity, PMID:25741868) is inapplicable because (1) MUTYH-associated polyposis is autosomal recessive, so a single presumed-de novo allele cannot establish pathogenicity absent a second pathogenic allele in trans, and (2) no proband-parent trio, parental testing, or de novo observation for c.1465G>A (p.Ala489Thr) exists in any source in the case bundle. No ClinVar submission asserts a de novo occurrence, and neither Morak 2010 (PMID:20618354) nor Komine 2015 (PMID:25820570) reports parental testing for the reported carriers.
Rule
PM6: Assumed de novo, but without confirmation of paternity and maternity (Richards et al. 2015, PMID:25741868).
Evidence considered
Rule (PMID:25741868, line 798): PM6 = 'Assumed de novo, but without confirmation of paternity and maternity'.
PMID:20618354 (Morak et al. 2010): monoallelic AFAP patient; no parental testing reported.
PMID:25820570 (Komine et al. 2015): single AFAP individual; no de novo data.
clinvar (variation 142138): no submission asserts a de novo occurrence or provides parental testing results.
Still missing
No parental testing or trio data exists for any proband carrying c.1465G>A; de novo status is unknown and cannot be assumed.
If family studies were performed, a confirmed de novo event would still need a biallelic (compound heterozygous) context to be meaningful for this autosomal recessive disorder.
BP3N/ANot applicable: missense change does not alter protein length in a repetitive region.
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Reasoning
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_001128425.2:c.1465G>A in MUTYH is a missense substitution predicted to produce NP_001121897.1:p.(Ala489Thr). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies.
BP7N/ANot applicable: this is a missense change, not a synonymous variant, so the silent-variant criterion does not apply.
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Reasoning
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_001128425.2:c.1465G>A in MUTYH is a missense substitution predicted to produce NP_001121897.1:p.(Ala489Thr). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies.
Rule
deterministic_prefilter: requires_synonymous
Evidence considered
Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules
Identifiers
Gene
MUTYH
Transcript
NM_001128425.2
Coding (HGVS c.)
NM_001128425.2:c.1465G>A
Protein (HGVS p.)
NP_001121897.1:p.(Ala489Thr)
GRCh38
chr1:45331193 C>T
GRCh37
chr1:45796865 C>T
ClinVar
2453369, 142138
Gene diagram
Every interpreted variant in MUTYH, mapped onto the exon structure of NM_001128425.2. Select a row to find it on the plot.
MUTYHNM_001128425.2
Fetching transcript structure from UCSC…
Exons
—
Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in MUTYH—Select a row to find it on the plot; use the link to open its page.
AF 4e-05 · 64 / 1,614,038 alleles · 0 hom · FAF 8.2e-05
African/African American11 / 74,908
0.00015
European (non-Finnish)51 / 1,180,038
4.3e-05
Remaining individuals2 / 62,486
3.2e-05
0 alternate alleles recorded in 7 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish.
gnomAD v2.1
AF 3.9e-05 · 11 / 282,784 alleles · 0 hom · FAF 2.3e-05
Remaining individuals1 / 7,226
0.00014
African/African American3 / 24,954
0.00012
European (non-Finnish)7 / 129,128
5.4e-05
0 alternate alleles recorded in 5 other groups: Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), South Asian.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 3.96521e-05; MAF= 0.00397%, 64/1614038 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000146847; MAF= 0.01468%, 11/74908 alleles, homozygotes = 0); grpmax FAF= 8.155e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 3.88989e-05; MAF= 0.00389%, 11/282784 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000138389; MAF= 0.01384%, 1/7226 alleles, homozygotes = 0); grpmax FAF= 2.293e-05.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Pangolin splice lossmagnitude shown
-0.060
Pangolin splice gain
0.010
Other predictors
REVEL
0.724
BayesDel
0.235
How the predictions were used
PP3SupportingMet (supporting): REVEL 0.724 falls in the supporting band (0.644-0.772) for a predicted deleterious missense effect.
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Reasoning
Missense variant MUTYH c.1465G>A (p.Ala489Thr). No applicable gene-specific PP3/BP4 rule: the InSiGHT MUTYH CSPEC v1.0 framework (cspec) was found but carries an empty criteria payload (criteria=[], rule_payload={}, framework_complete=false, official_clingen=false) and no PP3/BP4 lookup spreadsheet or index guidance entries; generic ACMG/AMP 2015 (PMID 25741868) with ClinGen SVI calibration (PMID 36413997) is therefore used. REVEL score 0.724 (local REVEL v1.3 lookup, source key 'revel') falls in the SVI supporting band for PP3 (0.644-0.772; supporting >= 0.644, moderate >= 0.773, strong >= 0.932 per Pejaver et al. 2022, PMID 36413997). PP3 applied once only, per the ACMG caveat that in silico algorithms are not independent criteria. SpliceAI max delta 0.00 (source key 'spliceai') predicts no splice impact and does not add to PP3; BayesDel 0.234861 (source key 'bayesdel') and aGVGD were not usable (no verified published calibration thresholds with a named publication/table, so treated as not_available per group calibration rules). No double counting across the splice and missense axes.
Rule
Generic ACMG/AMP 2015 PP3 (Richards et al., PMID 25741868), applied once per its caveat, with strength mapped by ClinGen SVI REVEL calibration (Pejaver et al., PMID 36413997): REVEL >= 0.644 supporting, >= 0.773 moderate, >= 0.932 strong. REVEL 0.724 -> PP3 supporting.
Evidence considered
REVEL score 0.724 for MUTYH c.1465G>A p.(Ala489Thr) (local REVEL v1.3 lookup, source_registry key 'revel'); ClinGen SVI REVEL calibration (Pejaver et al., Am J Hum Genet 2022; PMID 36413997) maps PP3 as supporting >= 0.644, moderate >= 0.773, strong >= 0.932; 0.724 lies in the supporting band (0.644-0.772), so PP3 supporting.
SpliceAI max delta score 0.00 (source_registry key 'spliceai'): no splice impact predicted; not counted toward PP3 to avoid double counting the same prediction across splice and missense axes.
BayesDel score 0.234861 (source_registry key 'bayesdel'): treated as not_available for PP3/BP4 because no verified published calibration threshold with a named publication/table is available to this pipeline (per group rule, any BayesDel score is insufficiently calibrated for PP3/BP4 unless a citable publication and table are named).
aGVGD: no score present anywhere in the case evidence bundle; not available.
PP3 rule definition and 'use only once' caveat per ACMG/AMP 2015 (Richards et al., Genet Med 2015; PMID 25741868), Table 5.
Still missing
Only one calibrated in-silico line (REVEL) supports PP3; BayesDel and aGVGD could not be used because no verified published calibration threshold with a named publication/table is available to this pipeline.
No gene-specific InSiGHT MUTYH PP3/BP3 rule or PP3/BP4 lookup spreadsheet was available in vcep_materials (criteria payload empty); generic SVI calibration applied instead.
BP4Not met: the calibrated in-silico evidence (REVEL 0.724) predicts a deleterious effect, directly contradicting BP4.
Details ▾Hide ▴
Reasoning
BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product. For this missense variant the only calibrated in-silico line, REVEL 0.724, predicts a deleterious effect (PP3 supporting, PMID 36413997) and therefore directly contradicts BP4; PP3 and BP4 are mutually exclusive for the same variant. The benign-leaning signals that exist are not usable: SpliceAI max delta 0.00 (no splice impact) has no verified published threshold with a named publication for BP4 strength mapping in this pipeline (informational only), BayesDel 0.234861 is uncalibrated (not_available), and aGVGD is absent. 'Multiple lines of computational evidence suggest no impact' is not satisfied. BP4 not met.
Rule
Generic ACMG/AMP 2015 BP4 (Richards et al., PMID 25741868): multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). Not satisfied for this variant.
Evidence considered
SpliceAI max delta score 0.00 (source_registry key 'spliceai'): predicts no splice impact, but no verified published threshold with a named publication/table is available for BP4 strength mapping in this pipeline; treated as informational and not sufficient alone for BP4.
REVEL score 0.724 (source_registry key 'revel'): supports PP3 at supporting strength per ClinGen SVI calibration (PMID 36413997), contradicting BP4; PP3 and BP4 cannot both be applied to the same variant.
BayesDel score 0.234861 (source_registry key 'bayesdel'): uncalibrated, treated as not_available for BP4 (no verified published threshold with a named publication/table).
aGVGD: no score present anywhere in the case evidence bundle; not available.
BP4 rule definition and 'use only once' caveat per ACMG/AMP 2015 (Richards et al., Genet Med 2015; PMID 25741868), Table 4; the 'multiple lines of computational evidence suggest no impact' requirement is not met.
Still missing
No calibrated benign-leaning in-silico evidence was available: BayesDel uncalibrated (no named published threshold), aGVGD absent, and SpliceAI has no verified published BP4 threshold with a named publication in this pipeline.
SpliceAI max delta 0.00 could not be used as a BP4 line because the strength mapping threshold for BP4 could not be attributed to a verifiable publication.
BP7N/ANot applicable: this is a missense change, not a synonymous variant, so the silent-variant criterion does not apply.
Details ▾Hide ▴
Reasoning
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_001128425.2:c.1465G>A in MUTYH is a missense substitution predicted to produce NP_001121897.1:p.(Ala489Thr). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies.
Rule
deterministic_prefilter: requires_synonymous
Evidence considered
Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.724. BayesDel score = 0.234861.
8 paper records listed. 2 cited in the classification.
Cited in the classification
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
ACMG/AMP 2015 joint consensus standards (Richards et al.) define the five criteria adjudicated in this group: PS1 (same amino acid change as a previously established pathogenic variant regardless of nucleotide change), PM1 (mutational hot spot and/or critical well-established functional domain without benign variation), PM5 (novel missense at a residue where a different missense determined pathogenic has been seen), PP2 (missense in a gene with low rate of benign missense variation and missense as a common mechanism), and BP1 (missense in a gene for which primarily truncating variants cause disease). These definitions were used as the fallback rule set because the InSiGHT MUTYH VCEP ruleset payload is empty in this case bundle.
→ PS3 · moderate→ PM2 · supporting→ PP3 · supportingDoes not name this variant
PS1 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change ... PM1 Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation ... PM5 Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before ... PP2 Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease ... BP1 Missense variant in a gene for which primarily truncating variants are known to cause disease
Context Consensus ACMG/AMP guideline for sequence variant interpretation in Mendelian disorders (Genet Med 2015;17:405-424); rule source only, no variant-specific data
Functional Complementation Assay for 47 MUTYH Variants in a MutY-Disrupted Escherichia coli Strain.
Komine K et al. · 2015 Jul
Komine et al. 2015 report p.A489T (c.1423G>A in NM_001048171.1 numbering; same genomic variant as the case variant NM_001128425.2:c.1465G>A, verified via matching anchor variants p.G396D c.1145G>A and p.G503E c.1466G>A) among 47 germline MUTYH variants tested in a MutY-disrupted E. coli functional complementation assay. A489T was observed in one AFAP patient, showed a 32.0-fold mutation rate relative to wild type and was categorized by the authors as partially defective (between the 1.7x and 4.8x cut-offs), with SIFT 'A' (0.01) and PolyPhen-2 'D' (0.973). The paper describes MUTYH's two functional domains (N-terminal catalytic HhH/FCL domain and C-terminal MutT-like/nudix domain), states functionally defective variants are distributed widely across these domains 'without a clear hot spot', and notes that the majority of MUTYH alterations are missense (>200 registered in LOVD). The variant is not classified pathogenic by the authors; no alternate missense at residue 489 appears in the panel.
p.A489T c.1423G>A 32.0 (3.3) 1.07 A (0.01) D (++) (0.973) NE NE AFAP (1) ... 17 variants (p.P18L, p.Y128H, p.P157L, p.G189E, p.A227V, p.V234M, p.R241W, p.R245C, p.R309C, p.P380T, p.G396D, p.P405S, p.R437P, p.A489T, p.V493F, p.G503E, and p.E480del) were partially defective ... Mapping of the secondary structure of MUTYH showed that the functionally defective variants were distributed widely in the two functional domains (i.e., the N-terminal catalytic domain and the C-terminal MutT-like domain) without a clear hot spot ... The majority of MUTYH alterations are missense variants. Currently, more than 200 unique missense variants have been registered in LOVD.
Context MutY-disrupted E. coli CC104 complementation assay (rifampicin-resistance mutation rate relative to wild type; cut-offs 1.7x retained / 4.8x defective), FLAG-tagged protein expression in HCT116 cells by western blot, SIFT and PolyPhen-2 in silico predictions; 47 germline MUTYH variants from MAP patients and LOVD; reference sequence NM_001048171.1
Other recorded publications
Lynch syndrome and MYH-associated polyposis: review and testing strategy.
Mutation analysis of the MYH gene in an Australian series of colorectal polyposis patients with or without germline APC mutations.
Kairupan CF et al. · 2005
Kairupan et al. 2005 first report the variant as A475T (G1423A) in the 535-aa MYH numbering (same genomic variant as c.1465G>A p.Ala489Thr on NM_001128425.2; offset verified via shared anchors with the 546-aa convention), found in a polyposis patient together with Y165C (Table: '13 Y165C A475T; G1423A'). The authors explicitly state the change 'does not occur in a known functional domain of MYH but it is conserved between Mouse and Man' and is 'more problematic to assign causative status' - i.e., not established as pathogenic and, per this source, not located within a known functional domain.
The previously unidentified mutations were W89X and A475T. The W89X muta- tion is clearly causative as it results in an immediate premature termination codon. The A475T change is more problematic to assign causative status, as it does not occur in a known functional domain of MYH but it is conserved between Mouse and Man.
Results/Discussion text (novel mutation commentary) and patient table (case 13: Y165C + A475T; G1423A)
Correlation of polyp number and family history of colon cancer with germline MYH mutations.
Jo WS et al. · 2005
Jo et al. 2005 report patient 281 as a compound heterozygote for G382D and A475T ('a GCC (Ala) to ACC (Thr) missense mutation at codon 475 in exon 14' - the same variant as the case variant in the 535-aa numbering) with 3-6 polyps and breast cancer at age 48. The paper notes the mutation 'lies 2 codons from a highly conserved domain in DNA repair genes that hydrolyzes nucleoside diphosphates ... the so-called nudix domain' (i.e., adjacent to, not within, the nudix box) and states 'Although the functional significance of this missense mutation is unknown, it likely is pathogenic' - an unverified assertion, with functional significance explicitly unknown.
The final patient (patient 281) was a compound heterozygote for G382D and A475T, a GCC (Ala) ¡ ACC (Thr) missense mutation at codon 475 in exon 14. ... One case exhibited a G3832D/A475T genotype. Although the functional significance of this missense mutation is unknown, it likely is pathogenic. This mutation lies 2 codons from a highly conserved domain in DNA repair genes that hydrolyzes nucleoside diphosphates linked to some other moiety, X, the so-called nudix domain.
Results text (patient 281, biallelic MYH mutation group) and Discussion (nudix domain commentary)
MUTYH-associated polyposis - variability of the clinical phenotype in patients with biallelic and monoallelic MUTYH mutations and report on novel mutations.
Morak M et al. · 2010
Morak et al. 2010 report patient 35 (male, attenuated FAP, age 43, 10-100 polyps, family history of CRC/gastric cancer) as a monoallelic carrier of c.1465G>A; p.Ala489Thr (this exact transcript notation, matching the case variant), with wild-type sequence in exons 2 and 3 and no material available for further second-allele testing. The variant is presented as an unclassified monoallelic finding; the paper does not establish it as pathogenic and reports no other variant at residue 489.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 3.96521e-05; MAF= 0.00397%, 64/1614038 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000146847; MAF= 0.01468%, 11/74908 alleles, homozygotes = 0); grpmax FAF= 8.155e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 3.88989e-05; MAF= 0.00389%, 11/282784 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000138389; MAF= 0.01384%, 1/7226 alleles, homozygotes = 0); grpmax FAF= 2.293e-05.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (14 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 142138)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.724. BayesDel score = 0.234861.
Functional
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MUTYH, a DNA glycosylase, is frequently mutated in colorectal cancer.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
This variant was interpreted by pipeline 7.1.0.
The current version is 11.0.07.
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