MUTYH c.1276C>T, p.(Arg426Cys)

Reasoning

BS3 requires well-established functional studies showing no damaging effect on protein function. PMID:25820570 assayed 47 germline MUTYH variants in a MutY-disrupted E. coli complementation system that reconstitutes the core MUTYH function (base excision repair at 8-oxoG:A mismatches; exogenous wild-type MUTYH suppressed the rifampicin-resistant mutation rate from 137 to 9.67 per 10^8). Using cut-offs of 1.7-fold (retained vs partially defective) and 4.8-fold (partially defective vs defective) anchored on the established pathogenic variants p.Y179C and p.G396D and on the benign/common variants p.V22M, p.Q338H and p.S515F, p.R426C was classified as functionally retained (below the 1.7-fold cut-off), grouping with the benign/common variants. The same study detected no reduction in protein expression and no change in nuclear localisation across the 47 variants, so the retained activity is not an artefact of abundance or mislocalisation, and its results agreed with earlier in vitro glycosylase assays for the seven overlapping variants. The numbering offset was verified (+14 residues relative to legacy U63329 numbering; see PS3 rationale), confirming the assayed p.R426C is this variant. BS3 is met but is assigned supporting rather than strong strength for four evidence-based reasons: (i) the authors describe the cut-offs as 'tentatively set for convenience' and state the clinical application may be limited by the difficulty of establishing an appropriate cut-off; (ii) the same 'retained' group contains p.G286E, which in vitro glycosylase assays and a knock-in mouse show to be defective, so this assay is known to produce false retained calls; (iii) the system is bacterial and no formal ClinGen SVI PS3/BS3 calibration of this assay is available, so a strong-strength assignment is not benchmarked; and (iv) other clinical submitters read the same data as 'inconclusive' rather than as clear benign functional evidence. The verdict (no damaging effect demonstrated by the only available, biologically relevant, internally controlled assay) is well supported; only the strength assignment is a judgement call, which is why this criterion is flagged for human review.

Rule

Generic ACMG/AMP 2015 BS3 (well-established functional studies show no damaging effect on protein function or splicing), applied at supporting strength because the assay's cut-offs are described as tentative and the assay has a documented false retained call

Evidence considered

• PMID:25820570 (E. coli CC104mutY complementation assay): p.R426C listed among the 17 functionally retained variants, with mutation rate below the 1.7-fold retained/partially-defective cut-off; 13 variants were defective and 17 partially defective.
• PMID:25820570 assay controls and calibration: p.Y179C (defective, 4.8-fold) and p.G396D (partially defective, 1.7-fold) as pathogenic anchors, p.V22M (1.2-fold), p.Q338H (0.7-fold) and p.S515F (1.0-fold) as benign/common-population anchors; wild-type MUTYH 9.67 per 10^8 versus empty vector 137 per 10^8.
• PMID:25820570 direct quote bearing on strength: 'However, the clinical application of our results might be limited by the difficulty in establishing an appropriate cut-off value, as we could not estimate how intermediate or subtle functional defects would contribute to the pathogenesis of MAP.'
• PMID:25820570 direct quote documenting a known false retained call, relevant to downgrading strength: 'The reason for the discrepancy in p.G286E is uncertain, because both an in vitro glycosylase assay and analysis of a knock-in mouse harboring the equivalent variant have shown that this variant is defective; however, it was found to be retained in our study.'
• PMID:25820570 protein-stability and localisation arms: minimal differences among the 47 variants in FLAG-tagged MUTYH protein level in HCT116 cells and nuclear localisation preserved for all variants (EGFP-fusion, isoform 4), so the retained BER activity is not attributable to altered expression or distribution.
• PMID:25820570 concordance: results agreed with previously published in vitro glycosylase and E. coli assays for overlapping variants (including retained calls for p.Q338H and p.Q338R and defective calls for p.Y179C, p.R241W, p.G396D and p.P405L).
• Numbering alignment: the paper's reference numbering matches the modern MUTYH reference (p.Y179C, p.G396D, p.Q338H, p.S515F versus legacy p.Tyr165Cys, p.Gly382Asp, p.Gln324His, p.Ser501Phe; uniform +14-residue offset), confirming the assayed p.R426C corresponds to NM_001128425.2:c.1276C>T p.(Arg426Cys).
• Applied the generic ACMG/AMP 2015 BS3 definition (well-established functional studies show no damaging effect on protein function or splicing) at supporting strength; the governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis MUTYH CSPEC v1.0 framework was retrieved as an unstructured ruleset with an empty criteria payload and provides no gene-specific BS3 rule or strength calibration.

Still missing

• Strength is not formally validated: no ClinGen SVI PS3/BS3 calibration (odds-of-pathogenicity) exists for this complementation assay, and the authors describe the 1.7-fold/4.8-fold cut-offs as tentatively set; strong strength could be argued if the governing InSiGHT MUTYH VCEP specification defines this assay class as high-strength evidence.
• The exact rifampicin-resistant mutation-rate ratio for p.R426C is not present in the extracted tabular data (Table 1 was not captured as text); the retained classification and its position below the 1.7-fold cut-off are, however, stated explicitly in the results text.
• The assay is bacterial, so human-specific effects (e.g. protein interactions, isoform-specific behaviour) are not fully represented; no orthogonal human-cell or in vitro glycosylase assay of this variant was available.

Sources

Reasoning

Framework first: the governing specification for this gene is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534). It was retrieved only as an unstructured ruleset with an empty criteria payload (framework_complete=false, rule_payload={}) and supplies no PS1 rule, so the generic ACMG/AMP 2015 PS1 definition applies (PMID:25741868). PS1 is met only when a DIFFERENT nucleotide change produces the SAME amino-acid change and that amino-acid change has been established as pathogenic. No such variant exists here. NM_001128425.2:c.1276C>T (NP_001121897.1:p.(Arg426Cys), MUTYH exon 13) is the only substitution reported at codon 426: ClinVar VCV000041753 (Variation ID 41753) holds a single variant record, with conflicting classifications (14 laboratory submissions Uncertain significance, 11 Likely benign/Likely Benign) and no expert-panel submission, so the amino-acid change p.Arg426Cys is not established pathogenic. The legacy namesake used throughout the literature, p.Arg412Cys (c.1234C>T, U63329 numbering), is the same nucleotide substitution under a fixed 14-codon offset, not an independent codon-426 alteration: PMID:16134147 describes it as a novel monoallelic MYH variant in classical FAP patient GD108, and PMID:14579148 reports 'R412C (1234C>T) in exon 13 (patient 405)' - the same change. PMID:16557584's spectrum of 21 MUTYH mutations contains no additional codon-426 variant. Because no distinct established-pathogenic variant encodes p.Arg426Cys, PS1 is not met.

Rule

PS1 requires a different nucleotide change encoding the same amino-acid change (p.Arg426Cys) that has been established as pathogenic (Richards et al. 2015, PMID:25741868); no such variant was identified.

Evidence considered

• Variant identity: NM_001128425.2:c.1276C>T encodes NP_001121897.1:p.(Arg426Cys) in MUTYH exon 13; the equivalent legacy nomenclature c.1234C>T / p.Arg412Cys (U63329) is what the older literature and the ClinVar alias list use for the same substitution.
• PS1 requires a different nucleotide change that encodes the same amino-acid change already established as pathogenic (Richards et al. 2015, PMID:25741868).
• Only one variant is recorded at MUTYH codon 426 - the queried change itself (ClinVar VCV000041753, Variation ID 41753): 14 laboratory submissions classify it Uncertain significance and 11 classify it Likely benign/Likely Benign, with no expert-panel submission, so p.Arg426Cys is not an established pathogenic amino-acid change.
• PMID:16134147 reports p.Arg412Cys (legacy c.1234C>T) as a novel monoallelic MYH variant in classical FAP patient GD108 - the same nucleotide substitution as the query, not a second, independent codon-426 change.
• PMID:14579148 reports 'R412C (1234C>T) in exon 13 (patient 405)' - again the same substitution under legacy nomenclature, so it too is not an independent codon-426 alteration.
• PMID:16557584 lists 21 different MUTYH mutations (Table II) and contains no additional codon-426 variant.
• The governing MUTYH InSiGHT VCEP v1.0 specification contains no parsed PS1 criterion, so the generic ACMG/AMP rules were applied.

Still missing

• The governing MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved only as an unstructured ruleset with an empty criteria payload, so no gene-specific PS1 rule (e.g. a curated list of established pathogenic amino-acid changes) was available; the generic ACMG/AMP 2015 definition was applied instead.
• No systematic ClinVar search for an alternative nucleotide change encoding p.Arg426Cys was run beyond the records already present in this case bundle; the conclusion rests on the single ClinVar record for this variant and on the three fetched literature sources that sequenced the MUTYH coding region.

Sources

Reasoning

PS3 requires well-established variant-specific functional evidence of a damaging effect on MUTYH (base-excision repair of 8-oxoG:A mismatches). The only variant-level functional study available for this variant is the E. coli CC104mutY complementation assay of 47 germline MUTYH variants (PMID:25820570), which measures rifampicin-resistant mutation frequency relative to wild-type MUTYH (9.67 per 10^8) against cut-offs of 1.7-fold (retained vs partially defective) and 4.8-fold (partially defective vs defective) anchored on the well-characterised pathogenic variants p.Y179C (4.8-fold, defective) and p.G396D (1.7-fold, partially defective) and the benign/common variants p.V22M, p.Q338H and p.S515F (retained). p.R426C was classified as functionally retained - mutation rate below the 1.7-fold cut-off - in the same group as those benign/common variants, i.e. the assay shows retained, not abolished, BER function. The same study found no significant difference in protein expression (western blot, HCT116 cells) and no disturbance of nuclear localisation for any of the 47 variants, so neither reduced protein abundance nor mislocalisation provides an alternative mechanism of damage. Numbering was verified to ensure the assay tested this variant: the paper's reference (NM_001048171.1) uses the same numbering as the modern MUTYH reference for the shared control variants (p.Y179C, p.G396D, p.Q338H, p.S515F), whose legacy U63329/NM_012222.2 equivalents are p.Tyr165Cys, p.Gly382Asp, p.Gln324His and p.Ser501Phe - a uniform +14-residue offset - so the paper's p.R426C is this variant (NM_001128425.2:c.1276C>T, p.(Arg426Cys); legacy c.1234C>T, p.Arg412Cys). No other functional data exist for this variant: OncoKB reports no variant-specific curated functional evidence, COSMIC and Cancer Hotspots contain no record, and no other full text examined assays p.R426C. Several ClinVar submissions cite this same assay under PS3, but their own criterion text states that the variant 'may not impact protein function' (PMID:25820570) or that the study shows an 'inconclusive effect' on protein function; retained function cannot be used as support for a damaging-effect criterion, so that usage was not adopted. With the sole calibrated assay reporting retained function and no evidence of a damaging effect, PS3 is not met.

Rule

Generic ACMG/AMP 2015 PS3 (well-established functional studies support a damaging effect on the gene or gene product); no gene-specific PS3 rule is extractable from the governing InSiGHT MUTYH CSPEC v1.0 specification.

Evidence considered

• PMID:25820570 (E. coli CC104mutY complementation assay, 47 germline MUTYH variants): wild-type MUTYH suppressed the rifampicin-resistant mutation rate to 9.67 per 10^8 versus 137 per 10^8 with empty vector; the retained/partially-defective cut-off was set at 1.7-fold and the partially-defective/defective cut-off at 4.8-fold, anchored on p.Y179C (4.8-fold, defective), p.G396D (1.7-fold, partially defective), p.V22M (1.2-fold), p.Q338H (0.7-fold) and p.S515F (1.0-fold).
• PMID:25820570 direct quote: 'According to this categorization, 17 variants (p.V22M, p.G25D, p.D105N, p.I223V, p.V246F, p.G286E, p.Q338H, p.Q338R, p.Q414R, p.L420M, p.R426C, p.R437Q, p.A473T, p.S515F, p.P516L, p.L529M, and p.R534Q) were functionally retained' - p.R426C sits with the benign/common variants rather than with the 13 functionally defective variants.
• PMID:25820570 also reports that protein expression levels did not differ significantly among the 47 variants (western blot in HCT116 cells) and that all variants, including those in the C-terminal nuclear localisation region, retained nuclear localisation of isoform 4, excluding abundance loss and mislocalisation as mechanisms.
• Numbering alignment check: the paper's control variants (p.Y179C, p.G396D, p.Q338H, p.S515F) carry the modern numbering, whose legacy U63329 equivalents are p.Tyr165Cys, p.Gly382Asp, p.Gln324His and p.Ser501Phe (uniform +14-residue offset), confirming that the assayed p.R426C is NM_001128425.2 p.(Arg426Cys), i.e. the legacy p.Arg412Cys reported in PMID:16134147.
• OncoKB returned no variant-specific reviewed functional evidence for MUTYH R426C (gene-level context only); COSMIC reports no record and Cancer Hotspots finds no statistically significant hotspot, so no additional functional evidence of a damaging effect exists.
• ClinVar submissions for this variant were consulted at criterion level: a major laboratory submission lists PS3 alongside the statement that 'in vitro functional studies provide som e evidence that the ... arg426cys variant may not impact protein function (komine 2015)', and another submitter records that 'functional studies demonstrated that this variant has an inconclusive effect on protein function (pmid: 25820570 (2015))'. Both describe retained/inconclusive rather than damaging function, so neither supports PS3.
• Applied the generic ACMG/AMP 2015 PS3 definition (well-established functional studies support a damaging effect) because the governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis MUTYH CSPEC v1.0 framework was retrieved for this case as an unstructured ruleset with an empty criteria payload and supplies no gene-specific PS3 rule.

Still missing

• No functional assay of this variant demonstrates a damaging effect; PS3 is not met (rather than not assessed) because a variant-specific calibrated assay result exists and points to retained function.
• One ClinVar submitter refers to a yeast complementation assay, but no citable publication or dataset was supplied and that submission was flagged as having no validated PMID trail, so the claim could not be evaluated.
• No orthogonal assay of this variant (e.g. in vitro 8-oxoG:A glycosylase activity) is available in the case materials, so the absence of damaging functional evidence rests on a single bacterial complementation system.

Sources

Reasoning

PS4 requires that the prevalence of this exact variant in affected individuals be significantly increased relative to controls (Richards et al. 2015, PMID:25741868). The variant is NM_001128425.2:c.1276C>T, p.(Arg426Cys) in MUTYH (legacy MYH numbering c.1234C>T, p.Arg412Cys). No case-control enrichment dataset for this allele was identified. The only report of this exact allele is PMID:16134147, where it was detected as a monoallelic (heterozygous) germline change in a single APC-mutation-negative Italian polyposis patient (GD108, classical FAP with >100 polyps) out of 60 unrelated adenomatous polyposis patients, and was absent from 158 control chromosomes (allelic frequency 0; 95% CI 0-0.0237). One carrier is not a statistically significant case enrichment, and no variant-specific odds ratio or relative risk was computed for p.Arg412Cys. The relative risk of 3.82 (95% CI 2.78-5.25) reported in that same paper applies to monoallelic MYH mutations as a class (11 carriers), not to this variant, and cannot be transferred to it. The variant does not appear among the MUTYH mutations reported in the 329-patient APC-negative polyposis series (PMID:16557584) or in the lung-carcinoma cohort (PMID:14579148). No numeric threshold governs this verdict: generic ACMG/AMP PS4 is a qualitative criterion, and the ClinGen InSiGHT MUTYH specification, although identified (cspec, doc 1742141534), did not yield retrievable criteria-level content (framework_complete=false), so no VCEP-specific PS4 odds-ratio cutoff exists for this case and no >= / <= inequality against a numeric cutoff was evaluated. PS4 is not met.

Rule

ACMG/AMP 2015 PS4 (PMID:25741868); generic fallback, no usable VCEP-specific numeric threshold

Evidence considered

• ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specification for MUTYH v1.0 was identified as the governing framework (cspec, doc 1742141534, svi_url https://cspec.genome.network/cspec/ui/svi/doc/1742141534), but its criteria-level content was not retrievable in this case (framework_complete=false, empty criteria list), so generic ACMG/AMP 2015 (PMID:25741868) governs PS4.
• PMID:16134147 reports p.Arg412Cys (legacy U63329 numbering of c.1276C>T/p.Arg426Cys) as a novel monoallelic variant in patient GD108 (Italian cohort of 60 adenomatous polyposis patients), absent from 158 control chromosomes, with no case-control enrichment statistic for this allele.
• PMID:16134147 states monoallelic MYH mutations are unlikely to have played a determinant role in recessive MUTYH-associated polyposis, with a class-level relative risk of 3.82 (95% CI 2.78-5.25) for monoallelic mutations in the series.
• PMID:16557584 did not report this allele among the 21 MUTYH mutations found in 329 unselected APC-mutation-negative polyposis patients.
• PMID:14579148 (lung carcinoma cohort, 276 cases/106 controls) did not report this allele.
• ClinVar VCV000041753 provides classification counts only (Uncertain significance 14 labs; Likely benign 9 + 2 labs; additional single-submitter Likely benign calls), which is not case-control enrichment evidence and must not be used to infer PS4.
• No numeric odds-ratio threshold applies: generic PS4 is qualitative and no MUTYH-VCEP numeric PS4 cutoff was retrievable, so no >= or <= comparison was performed.

Still missing

• No variant-specific case-control enrichment study (with an odds ratio or relative risk for c.1276C>T/p.Arg426Cys) was available in the case evidence; databases give only population frequency, not affected-vs-control enrichment.
• Literature triage flagged candidate PS4 papers (PMID:23035301, PMID:19531215, PMID:20687945, PMID:22703879, PMID:23788249, PMID:26389505, PMID:27854360) that were not retrieved as full text; none of the retrieved titles is a variant-specific case-control study for this allele.

Sources

Reasoning

Framework first: the MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved with an empty criteria payload and no PM1 rule, and vcep_materials.json's domain_tables key holds no entry for MUTYH ({}), so no VCEP-approved list of critical functional domains exists for this gene in this case. The generic ACMG/AMP 2015 PM1 definition therefore applies (PMID:25741868): a mutational hotspot and/or critical, well-established functional domain WITHOUT benign variation. Both prongs fail. (1) Hotspot: the Cancer Hotspots resource (cancerhotspots.org) returned no row for the query 'MUTYH R426' ('No matching records found', filtered from 1,220 hotspot mutations), and COSMIC returned no result for 'MUTYH c.1276C>T'; Arg426 is not a statistically significant single-residue hotspot. (2) Domain: the available sources actively conflict about whether Arg426 sits in a functionally critical domain - PMID:16134147 places the equivalent p.Arg412Cys in the 'NUDIX domain of the MYH protein' (the same paper places the pathogenic p.Gly382Asp in the NUDIX domain) and a ClinVar submitter annotates the change as 'located in the NUDIX hydrolase domain (IPR000086)', whereas another ClinVar submitter states the residue lies in 'a domain of the MUTYH protein that is not known to be functional' and PMID:25820570 reports that functionally retained variants were distributed throughout the whole gene. (3) Decisively, the 'without benign variation' condition fails at this residue: the change is present in gnomAD v2.1 at AF 0.000832 (235/282614 alleles, 1 homozygote; non-Finnish European AF 0.001457), 11 laboratory submissions classify it Likely benign/Likely Benign, it is functionally retained in the E. coli complementation assay (PMID:25820570), and ClinVar submitters note 'the p.Arg426 residue is not conserved in mammals'. PM1 is not met.

Rule

PM1 requires a mutational hotspot and/or critical, well-established functional domain without benign variation (Richards et al. 2015, PMID:25741868); Arg426 is not a cancer hotspot and this residue carries benign variation, so PM1 is not met.

Evidence considered

• PM1 requires location in a mutational hotspot and/or a critical, well-established functional domain without benign variation (Richards et al. 2015, PMID:25741868).
• Hotspot test: Cancer Hotspots (cancerhotspots.org), query 'MUTYH R426', returned 'No matching records found' (filtered from 1,220 total hotspot mutations) - no statistically significant single-residue hotspot at Arg426 (screenshot: screenshots/hotspots.png; search recorded in evidence.json as search_status=no_result).
• Somatic-cancer test: COSMIC query 'MUTYH c.1276C>T' returned no results ('Your search term "MUTYH c.1276C>T" did not return any results'; screenshot: screenshots/cosmic.png).
• No VCEP domain table is available: vcep_materials.json's domain_tables is empty ({}), so the InSiGHT VCEP's list of approved critical functional domains for MUTYH could not be applied and no approved-domain check against Arg426 was possible.
• Domain placement is contested: PMID:16134147 states that 'the other two novel missense variants (p.Leu374Pro and p.Arg412Cys) are located in the NUDIX domain of the MYH protein' and that the pathogenic p.Gly382Asp is also in the NUDIX domain; one ClinVar submitter annotates the change as 'located in the NUDIX hydrolase domain (IPR000086)'; by contrast another ClinVar submitter writes that 'the p.Arg426Cys change affects a poorly conserved amino acid residue located in a domain of the MUTYH protein that is not known to be functional'.
• PMID:25820570 reports that functionally retained variants were 'distributed throughout the whole gene, whereas defective ones clustered in the N-terminal catalytic domain and C-terminal MutT-like domain', i.e. this residue's retention status does not demonstrate a critical-domain effect.
• The 'without benign variation' condition fails at this residue: gnomAD v2.1 AF 0.000832 (235/282614 alleles, best subpopulation non-Finnish European AF 0.001457, 1 homozygote, grpmax FAF 0.001238); ClinVar submissions include 9 Likely benign and 2 Likely Benign classifications versus 14 Uncertain significance, with no expert-panel submission.
• Functional data point the same way: PMID:25820570 placed p.R426C among 17 variants that were functionally retained in the E. coli MutY-complementation assay, alongside benign-like alleles such as p.V22M, p.Q338H and p.S515F, with no difference in protein expression/stability or nuclear localization.
• Conservation is also low: ClinVar submitter comments note 'The p.Arg426 residue is not conserved in mammals' and that the change 'affects a poorly conserved amino acid residue'.
• The governing MUTYH InSiGHT VCEP v1.0 specification contains no parsed PM1 criterion and no domain table, so the generic ACMG/AMP rules were applied.

Still missing

• No VCEP domain table is available for MUTYH: vcep_materials.json's domain_tables key is empty ({}), so the authoritative InSiGHT VCEP list of approved critical functional domains could not be checked residue-by-residue against Arg426; the domain question had to be resolved from conflicting submitter statements and primary literature instead.
• The Cancer Hotspots and COSMIC results are present in evidence.json but are not source_registry keys, so they are documented in evidence_used and the saved screenshots rather than cited in evidence_refs.
• The available sources disagree on whether Arg426 lies in the NUDIX hydrolase domain (IPR000086) or in a domain not known to be functional; this was not resolved independently and does not change the outcome because the 'without benign variation' condition fails at this residue regardless.

Sources

Reasoning

PM2 (supporting) requires the variant to be rare in population databases; the applied threshold is <=0.0001 (SVI recommendation to use PM2 at supporting strength; ACMG/AMP 2015). The variant is more common than this in every available dataset. gnomAD v2.1 all-comers: total AF 0.000831523 (235/282,614 alleles, 1 homozygote), grpmax FAF 0.00123834, European (non-Finnish) AF 0.00145696. gnomAD v4.1 all-comers: total AF 0.0013085 (2,112/1,614,058 alleles, 1 homozygote), grpmax FAF 0.00160542, European (non-Finnish) AF 0.00166688. The v2.1 exome-only AF (0.000815979) and v4.1 exome-only AF (0.00136129) are likewise above threshold. These values exceed the 0.0001 cut-off by roughly 8- to 16-fold, so PM2 is not met at any strength. The gnomAD-Canada v1.0 dataset returned no record (lookup timed out), so it could not contribute, but a rare-variant claim is not rescued by a missing dataset. The governing ClinGen InSiGHT MUTYH CSPEC v1.0 framework was retrieved without structured criteria, so the generic ACMG/AMP threshold applies; a gene-specific PM2 cut-off cannot be confirmed, but for it to change this verdict it would have to exceed 0.00167 (the highest observed population frequency), which is implausible for a rarity criterion. MUTYH-associated polyposis is autosomal recessive, so the disease allele frequency rather than carrier frequency is the relevant comparison, and the variant still exceeds the generic rarity cut-off by an order of magnitude.

Rule

Generic PM2 (supporting): allele frequency <= 0.0001 (SVI recommendation to apply PM2 at supporting strength; PMID:25741868).

Evidence considered

• gnomAD v2.1 all-comers: total AF 0.000831523 (235/282,614 alleles, 1 homozygote); grpmax FAF 0.00123834; exome AF 0.000815979 (205/251,232 alleles); European (non-Finnish) AF 0.00145696.
• gnomAD v4.1 all-comers: total AF 0.0013085 (2,112/1,614,058 alleles, 1 homozygote); grpmax FAF 0.00160542; exome AF 0.00136129 (1,990/1,461,850 alleles); European (non-Finnish) AF 0.00166688.
• Applied the generic SVI/ACMG PM2 supporting rarity threshold of <= 0.0001.
• The governing ClinGen InSiGHT MUTYH CSPEC v1.0 framework (document 1742141534) was retrieved with an empty criteria payload, so it supplies no gene-specific PM2 threshold.
• gnomAD-Canada v1.0 (HostSeq genomes) returned no record for this variant (lookup timed out), so no additional frequency data were available from that source.
• PMID:16134147 reports this variant (legacy nomenclature c.1234C>T / p.Arg412Cys) absent from 158 control chromosomes, but that control cohort is far too small to affect the gnomAD-based rarity assessment.

Still missing

• No gene-specific (InSiGHT MUTYH) PM2 threshold is available because the governing CSPEC framework was retrieved with an empty criteria payload; the generic <=0.0001 cut-off was applied.
• gnomAD-Canada v1.0 returned no record (timeout) and could not be used.

Sources

Reasoning

PM3 (moderate pathogenic) requires that, for a recessive disorder, the variant be detected in trans with a pathogenic variant, with phase established by testing parents or offspring (ACMG/AMP 2015, PMID:25741868). MUTYH causes MUTYH-associated polyposis (MAP), an autosomal recessive condition (MONDO:0012041; preferred mode of inheritance per the InSiGHT MUTYH specification v1.0), so PM3 is the applicable allelic pathogenic criterion. No source in this case documents a proband carrying c.1276C>T in trans with a confirmed pathogenic MUTYH variant. The only primary reports available place the variant on a single allele: Aceto 2005 (PMID:16134147) lists patient GD108 in Table 2 under 'Patients with monoallelic variants' as [c.1234C>T]+[c.=] / [p.Arg412Cys]+[p.=] (legacy MYH U63329 numbering, equivalent to c.1276C>T / p.Arg426Cys under NM_001128425.2), and Aretz 2006 (PMID:16557584) lists R412C in Table II among 'Rare variants (identified in monoallelic state only)' at 1/658 alleles. ClinVar submissions are concordant: the Laboratory for Molecular Medicine record (SCV000711723) states that all individuals reported in the literature were heterozygous and did not carry a second MUTYH variant, and the University of Chicago record (SCV002067654) likewise describes the variant in the heterozygous state only. One ClinVar submission (LabCorp, SCV000697674) does assert that the variant has been reported with other pathogenic MUTYH variants in biallelic patients, citing Lopez-Villar 2010, De Rycke 2017 and Yurgelun 2017, but it provides no phase data, none of those primary reports were retrieved for this case, and the same submission concludes that the data do not allow any conclusion about variant significance before classifying the variant Likely benign. The ACMG guideline additionally notes that when a variant is present in the general population a statistical approach is needed to control for random co-occurrence; this variant is not rare (gnomAD v2.1 AF 0.000831523, 235/282614 alleles; gnomAD v4.1 AF 0.0013085, 2112/1614058 alleles; one homozygote in each release), so co-occurrence in cancer cohorts alone would not establish trans phase. PM3 is therefore not met. Flagged for human review because the unrebutted LabCorp assertion of biallelic occurrence conflicts with the primary and expert-laboratory evidence and has not been resolved.

Rule

Generic ACMG/AMP 2015 PM3 (moderate pathogenic): for recessive disorders, detected in trans with a pathogenic variant; phase determined by testing parents or offspring (PMID:25741868).

Evidence considered

• MUTYH-associated polyposis (MONDO:0012041) is an autosomal recessive disorder (preferred mode of inheritance per the ClinGen InSiGHT MUTYH specification v1.0), so PM3 rather than a dominant-phase criterion is the applicable allelic pathogenic evidence.
• Aceto 2005 (PMID:16134147), Table 2, patient GD108: [c.1234C>T]+[c.=] / [p.Arg412Cys]+[p.=], listed under 'Patients with monoallelic variants'; the variant was the only MYH change detected in that classical FAP patient, so no second allele was present to establish trans phase.
• Aretz 2006 (PMID:16557584), Table II: 'Rare variants (identified in monoallelic state only) ... 13 c.1234C>T R412C 1/658 (0.15)', with the Results text grouping R412C among '2 missense variants at unconserved sites' detected in monoallelic state only.
• Legacy-to-MANE nomenclature mapping: both primary papers use GenBank U63329 (Al-Tassan) numbering, in which the variant is c.1234C>T / p.Arg412Cys; the fixed 42-nucleotide / 14-codon offset (legacy G382D c.1145G>A equals MANE c.1187G>A p.Gly396Asp) makes p.Arg412Cys identical to p.Arg426Cys, and ClinVar lists R412C among the alternate protein names for variation 41753.
• ClinVar (variation 41753), submission SCV000711723 (Laboratory for Molecular Medicine, Mass General Brigham): 'All individuals reported in the literature were heterozygous and did not carry a second MUTYH variant.'
• ClinVar submission SCV000697674 (LabCorp) claims the variant 'has been reported with other pathogenic MUTYH variants in biallelic patients affected with synchronous/metachronous polyps (Lopez-Villar_2010) and colorectal cancer (e.g. De Rycke 2017, Yurgelun 2017)' but supplies no phase data and states 'These data do not allow any conclusion about variant significance.'
• ClinVar submission SCV002067654 (Genetic Services Laboratory, University of Chicago) reports the variant 'in the heterozygous state in multiple individuals with colorectal cancer', i.e. with no second-allele data.
• Population frequency relevant to the ACMG caveat on random co-occurrence: gnomAD v2.1 AF 0.000831523 (235/282614 alleles, 1 homozygote) and gnomAD v4.1 AF 0.0013085 (2112/1614058 alleles, 1 homozygote); the ACMG guideline states that for a variant present in the general population a statistical approach is needed to control for random co-occurrence when inferring trans phase.
• Applied the generic ACMG/AMP 2015 PM3 definition, which requires detection in trans with a pathogenic variant and testing of parents or offspring to determine phase; the governing ClinGen InSiGHT MUTYH CSPEC v1.0 framework (document 1742141534) was retrieved without structured criteria, so it supplies no gene-specific PM3 rule.

Still missing

• No phase-resolved proband data (parental or offspring testing) showing c.1276C>T in trans with a pathogenic MUTYH variant exist in the retrieved sources.
• The primary biallelic-co-occurrence reports cited by one ClinVar submitter (Lopez-Villar 2010; De Rycke 2017; Yurgelun 2017) were not retrieved and could not be verified or rebutted.
• No MUTYH-specific PM3 rule is available because the governing InSiGHT MUTYH CSPEC v1.0 framework was retrieved with an empty criteria payload; the generic ACMG/AMP criterion text was applied.

Sources

Reasoning

Framework first: the MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved with an empty criteria payload and no PM5 rule, so the generic ACMG/AMP 2015 PM5 definition applies (PMID:25741868): a novel missense change at an amino-acid residue where a DIFFERENT missense change has been established as pathogenic. The residue here is Arg426. No different pathogenic missense at Arg426 was identified. The case's own pm5_candidates artifact returned total_candidates_seen=0 and same_residue_candidates=0 and explicitly flagged that classic same-residue harvesting could not be completed safely. ClinVar VCV000041753 (Variation ID 41753) contains only the queried Arg426Cys substitution at codon 426. None of the three fetched sources that sequenced the MUTYH coding region reports another codon-426 change: PMID:16557584 (21 mutations, Table II), PMID:16134147 (four novel missense variants - p.Arg231His, p.Arg260Trp, p.Leu374Pro and p.Arg412Cys, the last being the queried substitution under legacy nomenclature), and PMID:14579148 (four rare missense variants R412C, C276W, P502L, R520Q plus the common polymorphisms V22M, Q324H and S501F). A ClinVar submitter remark that 'there are no benign variants within 3 amino acid positions of the variant p.Arg426Cys' speaks to the absence of benign neighbours, not to the presence of a pathogenic same-residue comparator, and cannot support PM5. PM5 is not met.

Rule

PM5 requires a different missense change at the same residue (Arg426) that has been established as pathogenic (Richards et al. 2015, PMID:25741868); no such comparator variant exists, so PM5 is not met.

Evidence considered

• PM5 requires a different missense change at the same amino-acid residue that has been established as pathogenic (Richards et al. 2015, PMID:25741868).
• The residue under assessment is Arg426 of NP_001121897.1 (MUTYH codon 426, exon 13).
• The pm5_candidates artifact for this case returned eligible_for_classic_pm5_search=false, total_candidates_seen=0 and same_residue_candidates=0, i.e. no same-residue comparator variant was harvested.
• ClinVar Variation ID 41753 (VCV000041753) contains only the queried Arg426Cys substitution; no other variant at codon 426 is recorded there.
• PMID:16557584's mutation spectrum (Table II: Y165C, G382D, R231H, P391L, V479F, P143L, R168H, R260W, P281L, R83X, Q196X, Q377X, Q324X, splice and frameshift alleles) contains no codon-426 change.
• PMID:16134147 reports four novel MYH missense variants (p.Arg231His, p.Arg260Trp, p.Leu374Pro, p.Arg412Cys) - the last being the queried substitution under legacy nomenclature - and no other Arg426 change.
• PMID:14579148 reports four rare missense variants (R412C, C276W, P502L, R520Q) plus the common coding polymorphisms V22M, Q324H and S501F; R412C is the queried substitution under legacy nomenclature, not a second codon-426 variant.
• A ClinVar submitter's statement that 'There are no benign variants within 3 amino acid positions of the variant p.Arg426Cys' describes the absence of benign neighbouring variants and provides no evidence of an established pathogenic same-residue comparator.
• The governing MUTYH InSiGHT VCEP v1.0 specification contains no parsed PM5 criterion, so the generic ACMG/AMP rules were applied.

Still missing

• The governing MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved with an empty criteria payload, so no gene-specific PM5 rule (or approved same-residue comparator list) was available; the generic ACMG/AMP 2015 definition was applied instead.
• Same-residue comparator harvesting was not completed automatically: pm5_candidates.json recorded eligible_for_classic_pm5_search=false and 0 candidates, so the negative result rests on the single ClinVar record for this variant plus the three fetched literature sources that surveyed the MUTYH coding sequence, not on an exhaustive codon-426 query.

Sources

Reasoning

Framework first: the MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved with an empty criteria payload and no PP2 rule, so the generic ACMG/AMP 2015 PP2 definition applies (PMID:25741868). PP2 has two conjunctive requirements: (i) missense variants are a common mechanism of disease in the gene, and (ii) the gene has a low rate of benign missense variation. MUTYH satisfies (i): MUTYH-associated polyposis is autosomal recessive and caused by biallelic missense alleles, the two most prevalent being p.Tyr179Cys and p.Gly396Asp (PMID:25820570), and PMID:16557584's spectrum consists largely of missense changes at conserved sites. Requirement (ii) is not satisfied. MUTYH carries well-established common benign missense variation: p.Val22Met, p.Gln324His and p.Ser501Phe are described as common coding polymorphisms (PMID:14579148), and PMID:16134147 reports '2 MYH polymorphisms (p.Val22Met, p.His324Gln) at equal frequency in cases and controls'. Functionally, PMID:25820570 found 17 of 47 tested germline MUTYH missense variants to be functionally retained - including p.Val22Met, p.Gln338His and p.Ser501Phe - i.e. a large measured fraction of rare missense variation is benign. The queried change sits in the same benign direction: gnomAD v2.1 AF 0.000832 with one homozygote, functionally retained (PMID:25820570), and classified Likely benign/Likely Benign by 11 laboratory submissions. With a substantial burden of established benign missense variation, PP2's 'low rate of benign missense variation' precondition fails and PP2 is not met.

Rule

PP2 requires both a low rate of benign missense variation and missense variants as a common disease mechanism (Richards et al. 2015, PMID:25741868); MUTYH has established common benign missense polymorphisms, so the first requirement fails and PP2 is not met.

Evidence considered

• PP2 requires a 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 (Richards et al. 2015, PMID:25741868).
• Requirement (i) is satisfied: MUTYH-associated polyposis (MONDO:0012041, autosomal recessive) is caused by biallelic missense alleles, and the two most prevalent pathogenic MUTYH variants, p.Tyr179Cys and p.Gly396Asp, are missense (PMID:25820570).
• PMID:16557584 documents 21 MUTYH mutations in APC-mutation-negative polyposis patients and states that 'All but one (V479F) of the missense variants were located at highly conserved sites, occurred together with another mutation of assumed pathogenic relevance, and none was detected in 232 chromosomes of normal controls' - i.e. missense changes are a recognized disease mechanism in this gene.
• Requirement (ii) fails: PMID:16134147 reports '2 MYH polymorphisms (p.Val22Met, p.His324Gln) at equal frequency in cases and controls', and PMID:14579148 lists V22M, Q324H and S501F as the 'common coding polymorphisms' of MYH - established common benign missense variation in this gene.
• PMID:25820570 classified 17 of 47 germline MUTYH missense variants as functionally retained (p.V22M, p.G25D, p.D105N, p.I223V, p.V246F, p.G286E, p.Q338H, p.Q338R, p.Q414R, p.L420M, p.R426C, p.R437Q, p.A473T, p.S515F, p.P516L, p.L529M, p.R534Q), i.e. a large measured fraction of rare missense variation in MUTYH is benign.
• The queried variant itself behaves as benign missense variation: gnomAD v2.1 AF 0.000832 with 1 homozygote (best subpopulation non-Finnish European AF 0.001457), functionally retained in the E. coli complementation assay (PMID:25820570), and 11 laboratory submissions classify it Likely benign/Likely Benign.
• The governing MUTYH InSiGHT VCEP v1.0 specification contains no parsed PP2 criterion, so the generic ACMG/AMP rules were applied.

Still missing

• The governing MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved with an empty criteria payload, so no gene-specific PP2 rule or approved PP2 gene list was available; the generic ACMG/AMP 2015 definition was applied instead.
• No ClinGen-approved quantitative threshold for 'low rate of benign missense variation' exists for this gene in the available sources; the judgement therefore rests on the documented common benign missense polymorphisms (p.Val22Met, p.Gln324His, p.Ser501Phe) and on the 17 of 47 functionally retained missense variants in PMID:25820570.

Sources

Reasoning

Scope check first: NM_001128425.2:c.1276C>T is a missense substitution (NP_001121897.1:p.(Arg426Cys)), so PP3/BP4 are evaluated on the REVEL missense path only. The SpliceAI path (intronic/synonymous/splice-region variants) does not govern a missense substitution, and its score is therefore not used here as support for or against PP3. The governing specification was checked first: the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534) was retrieved, but its criteria payload is empty (no PP3/BP4 rule or gene-specific in-silico lookup table), so the generic ClinGen SVI REVEL calibration applies. REVEL = 0.615. This is below the PP3 supporting threshold of >= 0.644 (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997) and above the BP4 supporting threshold of <= 0.29, placing the variant in the indeterminate middle zone in which no PP3 weight is earned at any strength (supporting 0.644 / moderate 0.773 / strong 0.932). BayesDel = -0.00912838 was retrieved but has no established generic ACMG-strength calibration and was not used for PP3. A legacy-nomenclature in-silico finding for the equivalent substitution, SIFT 'not tolerated' for p.Arg412Cys (PMID:16134147), is an uncalibrated predictor outside the ClinGen SVI calibration and cannot substitute for a qualifying REVEL score. PP3 is not met.

Rule

PP3 requires a qualifying missense predictor score on the REVEL path: >= 0.644 (supporting), >= 0.773 (moderate), >= 0.932 (strong) per ClinGen SVI REVEL calibration, PMID:36413997; not met at 0.615.

Evidence considered

• Variant consequence is missense: NM_001128425.2:c.1276C>T -> NP_001121897.1:p.(Arg426Cys), autosomal-recessive MUTYH-associated polyposis (familial adenomatous polyposis 2).
• Because the variant is missense, the REVEL (missense protein-impact) path governs PP3/BP4 and the SpliceAI path is not applicable to it.
• REVEL score = 0.615 (local REVEL v1.3 lookup; chr1:45331467 G>A, GRCh38 coordinates of the same variant).
• Threshold applied: REVEL >= 0.644 for PP3 supporting, >= 0.773 moderate, >= 0.932 strong (ClinGen SVI REVEL calibration, Pejaver et al. 2022, Am J Hum Genet, PMID:36413997). 0.615 is below all three.
• REVEL 0.615 sits above the BP4 supporting cut-off (<= 0.29), i.e. in the indeterminate middle range where neither PP3 nor BP4 is met.
• BayesDel score = -0.00912838 was retrieved; no generic ACMG-strength calibration is established for BayesDel, so it was treated as not_available and contributed no weight.
• SpliceAI max delta = 0.011 (DS_AG 0.007, DS_AL 0.002, DS_DG 0.011, DS_DL 0.001; Pangolin SG 0.013) was retrieved but is not used: a splice prediction is not evidence about tolerance of an amino-acid substitution and is not the governing path for a missense variant's PP3/BP4.
• PMID:16134147 reports an uncalibrated SIFT prediction of 'not tolerated' for the equivalent legacy-named substitution p.Arg412Cys (c.1234C>T, U63329 numbering), together with absence from 158 control chromosomes and no predicted splice effect by SpliceSitefinder/BDGP/GENSCAN; this is a different, uncalibrated predictor and was not used to assign PP3.
• The governing MUTYH InSIGHT VCEP v1.0 specification contains no parsed PP3/BP4 criterion, so the generic ACMG/AMP computational-evidence rules were applied.

Still missing

• The governing MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved only as an unstructured ruleset with an empty criteria payload, so no gene-specific PP3 threshold or PP3 lookup table was available; generic ClinGen SVI REVEL calibration was used instead.
• BayesDel (-0.00912838) is available but has no established generic ACMG-strength PP3 calibration and could not contribute.

Sources

Reasoning

PP4 requires that the patient's phenotype or family history be highly specific for a disease with a single genetic etiology (Richards et al. 2015, PMID:25741868). The only case-level phenotype linked to this exact variant (NM_001128425.2:c.1276C>T, p.Arg426Cys) is patient GD108 in PMID:16134147: a heterozygous (monoallelic) MYH carrier with classical FAP (>100 polyps) and vertical disease transmission, ascertained in a screen of APC-mutation-negative polyposis patients. MUTYH-associated polyposis is autosomal recessive and characteristically attenuated: in PMID:16557584, 70 of 71 patients with biallelic MUTYH mutations presented with an attenuated or atypical phenotype, whereas >100 polyps with vertical transmission is the classic autosomal dominant APC/FAP presentation. A single heterozygous carrier whose presentation is atypical for MAP does not establish phenotype specificity for this variant, and the authors of PMID:16134147 themselves concluded that monoallelic MYH mutations are unlikely to be causative in the recessive model. PP4 is not met. No numeric threshold governs PP4 in the available framework, so no >= / <= comparison was evaluated.

Rule

ACMG/AMP 2015 PP4 (PMID:25741868); generic fallback

Evidence considered

• ClinGen InSiGHT MUTYH v1.0 specification identified as the governing framework (cspec, doc 1742141534) but with no retrievable criteria-level content (framework_complete=false); generic ACMG/AMP 2015 (PMID:25741868) therefore governs PP4.
• PMID:16134147: the exact variant (as legacy p.Arg412Cys / c.1234C>T) was found monoallelic in patient GD108, an Italian classical FAP patient with >100 polyps and vertical disease transmission, among APC-mutation-negative polyposis patients.
• PMID:16134147 conclusion that monoallelic MYH mutations are unlikely to play a determinant role in the recessive MUTYH-associated polyposis.
• PMID:16557584: 70 of 71 patients with biallelic MUTYH mutations had an attenuated (80%) or atypical (18%) phenotype, indicating classical >100-polyp FAP is not the typical MAP phenotype.
• This variant's occurrence in the general population (gnomAD v2.1 AF ~0.083%, including one homozygote) is inconsistent with a highly specific, fully penetrant phenotype association.

Still missing

• Only one affected individual carrying this exact allele has a described phenotype; no independent case series links this allele to a phenotype specific for MUTYH-associated polyposis.

Sources

Reasoning

PP5 applies only when the exact variant has been classified Pathogenic or Likely pathogenic by a ClinVar expert panel (ClinGen Variant Curation Expert Panel). The exact allele here is NM_001128425.2:c.1276C>T, p.(Arg426Cys); ClinVar records it as VCV000041753 (variation ID 41753), titled NM_001048174.2(MUTYH):c.1192C>T (p.Arg398Cys), which is the same genomic/protein change on an alternative transcript. That record has no expert-panel submission (evidence.json source_data.expert_panels is empty; clinvar_submission_audit.json expert_panel_submissions = 0); its review status is 'criteria provided, conflicting classifications' and its overall level is 1 star, with 27 submissions from 25 submitters split between Uncertain significance (14 laboratories), Likely benign (9 + 2 laboratories) and several additional single-submitter laboratory calls. Ordinary laboratory submissions, aggregate ClinVar labels and non-expert assertions must never trigger PP5, and no expert-panel Pathogenic/Likely pathogenic classification exists for this exact variant. PP5 is not met. No numeric threshold is involved in this criterion.

Rule

Exact-variant ClinVar expert-panel (ClinGen VCEP) Pathogenic/Likely pathogenic classification required; laboratory submissions excluded

Evidence considered

• ClinVar VCV000041753 (variation ID 41753; NM_001048174.2:c.1192C>T, p.Arg398Cys; same allele as NM_001128425.2:c.1276C>T, p.Arg426Cys) has no expert-panel submissions (expert_panels empty; expert_panel_submissions = 0) and a review status of 'criteria provided, conflicting classifications' (1 star).
• ClinVar classification counts for the exact variant: Uncertain significance (14 clinical laboratories), Likely benign (9), Likely Benign (2), plus further single-submitter Likely benign calls (ARUP, GeneDx, Mendelics, PreventionGenetics, All of Us, CeGaT, Labcorp) - none of these is a ClinGen expert-panel assertion.
• The ClinGen InSiGHT MUTYH specification was identified as the disease/gene framework (cspec, doc 1742141534); no ClinGen expert-panel classification of this variant via a VCEP is recorded in ClinVar, and the framework's criteria-level content was not retrievable in this case.

Sources

Reasoning

BA1 (stand-alone benign) requires an allele frequency >=0.05 (ACMG/AMP 2015). The variant is far below this in every available dataset. gnomAD v4.1 all-comers: total AF 0.0013085 (2,112/1,614,058 alleles, 1 homozygote), population-max (grpmax) FAF 0.00160542, European (non-Finnish) AF 0.00166688 (1,967/1,180,046 alleles). gnomAD v2.1 all-comers: total AF 0.000831523 (235/282,614 alleles, 1 homozygote), grpmax FAF 0.00123834, European (non-Finnish) AF 0.00145696. The highest frequency observed in any single population (NFE 0.00166688, v4.1) is still roughly 30-fold below the 0.05 stand-alone threshold, so BA1 is not met. MUTYH causes MUTYH-associated polyposis (MAP), an autosomal recessive condition (MONDO:0012041); the governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis MUTYH CSPEC v1.0 framework was retrieved for this case but carries no structured criterion thresholds, so the generic ACMG/AMP threshold is the applicable rule and no gene-specific value that could alter the verdict exists. The non-cancer/exome-only gnomAD subsets are not specified by any available governing rule, so the all-comers totals were used as the default; they would not change the outcome, since even the exome-only AFs (v2.1 0.000815979; v4.1 0.00136129) remain orders of magnitude below 0.05.

Rule

Generic ACMG/AMP 2015 BA1 (stand-alone benign): allele frequency >= 0.05 (PMID:25741868).

Evidence considered

• gnomAD v4.1 all-comers: total AF 0.0013085 (2,112/1,614,058 alleles, 1 homozygote); grpmax FAF 0.00160542; European (non-Finnish) AF 0.00166688 (1,967/1,180,046 alleles).
• gnomAD v2.1 all-comers: total AF 0.000831523 (235/282,614 alleles, 1 homozygote); grpmax FAF 0.00123834; European (non-Finnish) AF 0.00145696 (188/129,036 alleles, 1 homozygote); exome AF 0.000815979, genome AF 0.000955962.
• Applied the generic ACMG/AMP 2015 stand-alone benign threshold BA1 >= 0.05.
• The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis MUTYH CSPEC v1.0 framework (document 1742141534) was retrieved for this case but contains an unstructured ruleset with an empty criteria payload, so it supplies no gene-specific BA1 threshold and the generic ACMG/AMP default applies.
• gnomAD non-cancer subsets (GNOMAD_V2_1_NON_CANCER, GNOMAD_V3_1_NON_CANCER) were not retrieved for this case and are not required by any available governing MUTYH rule, so the all-comers totals were used as the default.

Sources

Reasoning

BS1 (strong benign) requires an allele frequency greater than expected for the disorder; the generic SVI default is >=0.01. The variant falls well short of this in every dataset: gnomAD v4.1 all-comers total AF 0.0013085 (2,112/1,614,058 alleles) with grpmax FAF 0.00160542 and European (non-Finnish) AF 0.00166688; gnomAD v2.1 all-comers total AF 0.000831523 (235/282,614 alleles) with grpmax FAF 0.00123834 and European (non-Finnish) AF 0.00145696. The maximum observed population frequency (NFE 0.00166688) is about 6-fold below the 0.01 threshold, so BS1 is not met. A per-gene BS1 derivation (Whiffin et al. 2017, PMID:28518168) is preferred over the generic default, but the governing ClinGen InSiGHT MUTYH CSPEC v1.0 framework was retrieved without structured criteria and provides no MUTYH-specific BS1 threshold, so the generic value was used. MUTYH-associated polyposis is autosomal recessive; the carrier frequency (as opposed to the disease allele frequency) could in principle justify a higher gene-specific BS1 cut-off for a recessive condition, but the variant's frequency (0.08-0.13% overall, up to 0.17% in NFE) remains below 1% even on that footing, so no recessive-specific adjustment changes the verdict.

Rule

Generic BS1 (strong benign): allele frequency >= 0.01; per-gene derivation preferred (PMID:28518168).

Evidence considered

• gnomAD v2.1 all-comers: total AF 0.000831523 (235/282,614 alleles); grpmax FAF 0.00123834; European (non-Finnish) AF 0.00145696.
• gnomAD v4.1 all-comers: total AF 0.0013085 (2,112/1,614,058 alleles); grpmax FAF 0.00160542; European (non-Finnish) AF 0.00166688.
• Applied the generic BS1 strong-benign allele-frequency default of >= 0.01 (per-gene derivation preferred; Whiffin et al. 2017, PMID:28518168).
• The governing ClinGen InSiGHT MUTYH CSPEC v1.0 framework (document 1742141534) was retrieved with an empty criteria payload, so it supplies no MUTYH-specific BS1 threshold.
• MUTYH-associated polyposis is autosomal recessive, but no available governing rule specifies a recessive-adjusted BS1 frequency.

Still missing

• No gene-specific (InSiGHT MUTYH) BS1 threshold is available because the governing CSPEC framework was retrieved with an empty criteria payload; the generic 0.01 cut-off was applied.

Sources

Reasoning

BS2 requires the variant to be observed in a healthy adult individual for a recessive (homozygous) disorder, with full penetrance expected at an early age. MUTYH causes MUTYH-associated polyposis (MAP), an autosomal recessive condition that is incompletely penetrant and typically adult-onset: biallelic patients present predominantly with an attenuated or atypical phenotype (PMID:16557584), and biallelic MUTYH carriage confers a substantially increased but far from fully penetrant lifetime colorectal cancer risk. The criterion's precondition of full, early-onset penetrance is therefore not satisfied for this gene. In addition, gnomAD reports only a single homozygote (v2.1: 1 homozygote, European non-Finnish; v4.1: 1 homozygote, genomes/NFE) out of 282,614 (v2.1) and 1,614,058 (v4.1) alleles, so there is no robust observation of an unaffected adult homozygote; gnomAD homozygotes have unknown health/diagnosis status and, given the late onset of MAP, may reflect undiagnosed affected individuals. BS2 is therefore not met. The criterion is flagged for human review because interpretation of population homozygotes for incompletely penetrant recessive conditions is a recognised judgement call and some frameworks accept such observations at reduced strength; the governing InSiGHT MUTYH CSPEC v1.0 framework was retrieved without structured criteria and provides no gene-specific BS2 rule to resolve this.

Rule

Generic ACMG/AMP 2015 BS2 (strong benign): observed in a healthy adult individual for a recessive (homozygous) disorder with full penetrance expected at an early age (PMID:25741868).

Evidence considered

• gnomAD v2.1 and v4.1 each report a single homozygote for this variant (v2.1 total 1/282,614 alleles, European non-Finnish; v4.1 total 1/1,614,058 alleles, genomes/NFE), with no cohort-level health or diagnostic annotation.
• MUTYH-associated polyposis is an autosomal recessive, incompletely penetrant, typically adult-onset condition; biallelic patients present predominantly with attenuated (80%) or atypical (18%) phenotypes (PMID:16557584).
• Applied the generic ACMG/AMP 2015 BS2 criterion, which requires observation in a healthy adult with full penetrance expected at an early age.
• The governing ClinGen InSiGHT MUTYH CSPEC v1.0 framework (document 1742141534) was retrieved with an empty criteria payload, so it supplies no gene-specific BS2 rule.

Still missing

• Health and diagnostic status of the gnomAD homozygote(s) is not reported; gnomAD homozygotes may include undiagnosed affected adults given the late onset of MAP.
• No MUTYH-specific BS2 rule is available from the governing CSPEC framework (empty criteria payload), so the generic ACMG/AMP criterion text was applied.

Sources

Reasoning

BP2 (supporting benign) is met when a variant is 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 (ACMG/AMP 2015, PMID:25741868). MUTYH causes autosomal recessive MUTYH-associated polyposis, so the first clause does not apply to this gene and the operative clause is the cis observation, which the ACMG guideline explicitly describes as supporting evidence for a benign role when two variants are found in a recessive gene. No source in this case reports c.1276C>T in cis with a pathogenic MUTYH variant. The primary reports instead show the variant as the only MYH change on its allele: Aceto 2005 (PMID:16134147) lists patient GD108 as [c.1234C>T]+[c.=] / [p.Arg412Cys]+[p.=] under 'Patients with monoallelic variants', and Aretz 2006 (PMID:16557584) Table II lists R412C (the legacy U63329 name for this variant) under 'Rare variants (identified in monoallelic state only)' at 1/658 alleles. ClinVar submissions describe heterozygous carriers without a second MUTYH variant (for example SCV000711723: all literature individuals heterozygous, no second MUTYH variant; SCV002067654: reported in the heterozygous state), and the only co-occurrence claim, from LabCorp (SCV000697674), is of biallelic (i.e. trans) occurrence, which would be PM3-type evidence rather than cis evidence, and is unverified. Because no cis phase data exist and the dominant-gene clause is inapplicable, BP2 is not met.

Rule

Generic ACMG/AMP 2015 BP2 (supporting benign): 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 (PMID:25741868).

Evidence considered

• BP2 in the ACMG/AMP 2015 framework reads: 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; the guideline's cis/trans section further states that finding the second variant in cis is supporting evidence for a benign role.
• MUTYH-associated polyposis is autosomal recessive (MONDO:0012041), so the BP2 clause covering trans occurrence with a pathogenic variant for a fully penetrant dominant disorder does not apply to this gene.
• Aceto 2005 (PMID:16134147), Table 2, patient GD108: [c.1234C>T]+[c.=] / [p.Arg412Cys]+[p.=], under 'Patients with monoallelic variants' - the variant was the only MYH change on that allele, so no cis-with-pathogenic configuration is reported.
• Aretz 2006 (PMID:16557584), Table II: R412C (legacy U63329 name for c.1276C>T / p.Arg426Cys) listed under 'Rare variants (identified in monoallelic state only)' at 1/658 alleles; no cis or biallelic observation is reported.
• ClinVar submissions SCV000711723, SCV002067654 and SCV000592715 describe heterozygous carriers with no second MUTYH variant on the same allele.
• The only co-occurrence evidence in ClinVar (SCV000697674, LabCorp) describes biallelic patients, i.e. a trans configuration, which is PM3-type evidence rather than a cis observation supporting BP2, and it is unverified and contradicted by SCV000711723.
• No source retrieved for this case reports the variant in cis with a pathogenic MUTYH variant, so no BP2-supporting observation exists.

Still missing

• No parental or cis-phase testing is available for any carrier, so an in-cis-with-pathogenic observation has not been made; none is reported in the retrieved literature or ClinVar submissions.
• No MUTYH-specific BP2 rule is available because the governing InSiGHT MUTYH CSPEC v1.0 framework was retrieved with an empty criteria payload; the generic ACMG/AMP criterion text was applied.

Sources

Reasoning

Scope check first: NM_001128425.2:c.1276C>T is a missense substitution (NP_001121897.1:p.(Arg426Cys)), so BP4 is evaluated on the REVEL missense path only. The SpliceAI result (max delta 0.011) is deliberately not substituted for BP4: a clean splice prediction says nothing about whether the amino-acid substitution is tolerated, and BP4 cannot be reached by crossing to the other predictor path. The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534) was checked first but contains no BP4 rule, so the generic ClinGen SVI REVEL calibration applies. REVEL = 0.615, which is far above the BP4 supporting threshold of <= 0.29 and also above the moderate (<= 0.183) and strong (<= 0.016) cut-offs (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997). The score does not support a benign computational prediction at any strength, and it simultaneously falls short of the PP3 supporting threshold, so the computational evidence is indeterminate rather than benign. BayesDel = -0.00912838 has no established generic ACMG-strength calibration and was not used. BP4 is not met.

Rule

BP4 requires a qualifying benign-range missense predictor score on the REVEL path: <= 0.29 (supporting), <= 0.183 (moderate), <= 0.016 (strong) per ClinGen SVI REVEL calibration, PMID:36413997; not met at 0.615.

Evidence considered

• Variant consequence is missense: NM_001128425.2:c.1276C>T -> NP_001121897.1:p.(Arg426Cys); BP4 was assessed on the REVEL missense path only.
• REVEL score = 0.615 from the local REVEL v1.3 lookup for the same variant (chr1:45331467 G>A, GRCh38).
• Threshold applied: REVEL <= 0.29 for BP4 supporting, <= 0.183 moderate, <= 0.016 strong (ClinGen SVI REVEL calibration, Pejaver et al. 2022, Am J Hum Genet, PMID:36413997). 0.615 exceeds all three cut-offs.
• SpliceAI max delta = 0.011 was retrieved but is not BP4 support for a missense variant: the splice-impact path does not govern a missense substitution and a low splice delta is not evidence that the amino-acid change is tolerated.
• BayesDel score = -0.00912838 was retrieved; with no established generic ACMG-strength calibration it was treated as not_available and contributed no BP4 weight.
• The governing MUTYH InSiGHT VCEP v1.0 specification contains no parsed BP4 criterion, so the generic ACMG/AMP computational-evidence rules were applied.
• REVEL 0.615 is inside the indeterminate middle range (above 0.29 but below 0.644), so it supports neither PP3 nor BP4.

Still missing

• The governing MUTYH InSiGHT VCEP v1.0 specification (CSPEC doc 1742141534) was retrieved only as an unstructured ruleset with an empty criteria payload, so no gene-specific BP4 threshold or benign-range lookup was available; generic ClinGen SVI REVEL calibration was used instead.

Sources

Reasoning

BP5 applies when the variant is found in a case in which an alternate molecular basis for the disease has been identified (Richards et al. 2015, PMID:25741868). The only case reported to carry this exact variant is patient GD108 in PMID:16134147, and that individual was APC-mutation-negative: the study screened the MYH gene precisely in the 29 polyposis patients in whom no APC truncating mutation was detectable, and GD108 carried only the heterozygous legacy p.Arg412Cys (c.1234C>T; = NM_001128425.2:c.1276C>T, p.Arg426Cys) change. No alternate molecular basis for that patient's polyposis is documented in the available evidence, so there is no 'variant in a case with an alternate cause' observation to support BP5. No numeric likelihood-ratio-style threshold applies to this assessment: generic ACMG/AMP BP5 is a qualitative criterion, and no InSiGHT MUTYH VCEP-specific numeric BP5 cutoff of either comparison direction (>= or <=) was retrievable from the governing framework, so no inequality was evaluated and no value could have been compared in the wrong direction. BP5 is not met.

Rule

ACMG/AMP 2015 BP5 (PMID:25741868); qualitative criterion, no numeric threshold available

Evidence considered

• PMID:16134147 analysed MYH coding sequence and intron-exon borders in the 29 Italian polyposis patients without a detectable APC truncating mutation; patient GD108, the carrier of the exact variant (legacy p.Arg412Cys / c.1234C>T), had no identified APC mutation and is listed as monoallelic for MYH.
• PMID:16134147 places monoallelic MYH variants in a separate 'patients with monoallelic variants' group and concludes they are unlikely to be determinant in this recessive condition - consistent with no alternate molecular basis being identified for GD108.
• ClinGen InSiGHT MUTYH v1.0 specification (cspec, doc 1742141534) was identified as the governing framework but its criteria-level text was not retrievable (framework_complete=false); generic ACMG/AMP 2015 (PMID:25741868) therefore governs BP5.
• BP5 has no numeric threshold in the available framework: this is a qualitative criterion, and no MUTYH-VCEP likelihood-ratio-style BP5 cutoff was available to compare against, so no >= or <= operator was applied.

Still missing

• Alternate-basis data are limited to the one reported carrier (PMID:16134147); no other case carrying this allele documents a co-occurring pathogenic variant in another polyposis gene.

Sources

Reasoning

BP6 applies only when the exact variant has been classified Benign or Likely benign by a ClinVar expert panel (ClinGen Variant Curation Expert Panel). The exact allele is NM_001128425.2:c.1276C>T, p.(Arg426Cys), recorded in ClinVar as VCV000041753 (variation ID 41753), titled NM_001048174.2(MUTYH):c.1192C>T (p.Arg398Cys) - the same allele on an alternative transcript. That record has no expert-panel submission (evidence.json source_data.expert_panels is empty; clinvar_submission_audit.json expert_panel_submissions = 0), with review status 'criteria provided, conflicting classifications' (1 star). The numerous Likely benign calls (9 + 2 laboratories in the aggregate summary, plus single-submitter Likely benign submissions from ARUP, GeneDx, Mendelics, PreventionGenetics, All of Us, CeGaT and Labcorp) are ordinary laboratory submissions and must never trigger BP6 under the rule that only an exact-variant expert-panel Benign/Likely benign classification qualifies. No expert-panel benign classification exists for this variant, so BP6 is not met. No numeric threshold is involved in this criterion.

Rule

Exact-variant ClinVar expert-panel (ClinGen VCEP) Benign/Likely benign classification required; laboratory submissions excluded

Evidence considered

• ClinVar VCV000041753 (variation ID 41753; NM_001048174.2:c.1192C>T, p.Arg398Cys; same allele as NM_001128425.2:c.1276C>T, p.Arg426Cys) shows expert_panel_submissions = 0 and review status 'criteria provided, conflicting classifications' (1 star) with 26-27 laboratory submissions.
• All Likely benign assertions on this record come from individual clinical laboratories (e.g. Ambry Genetics, Color Health, GeneDx, ARUP, Labcorp, Mendelics, PreventionGenetics, All of Us, CeGaT), not from a ClinGen expert panel, so none can trigger BP6.
• The ClinGen InSiGHT MUTYH specification was identified (cspec, doc 1742141534) as the gene's expert-panel framework, but no expert-panel classification of this variant is recorded in ClinVar and the framework's criteria-level content was not retrievable in this case.

Sources

Reasoning

PS2 (generic ACMG/AMP 2015) requires a confirmed de novo occurrence in a patient with the disease, with both maternity and paternity established. This curation is variant-level: there is no proband record, no parental/trio testing, and no statement of de novo origin anywhere in the available evidence. The only clinical report of this variant, PMID:16134147, describes it as a heterozygous (monoallelic) germline change in patient GD108, an Italian classical FAP patient with >100 polyps and a positive family history, i.e. an inherited rather than de novo observation, and no parental testing is reported. The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH (v1.0, CSPEC doc 1742141534, ruleset 1742141543) publishes no criteria codes at all (status 'Pilot Rules In Prep', 4/24/2025), so no gene-specific PS2 modification is available and the generic ACMG/AMP definition applies. Because confirmed parentage is required and unavailable, the criterion cannot be evaluated and is recorded as not assessed rather than failed.

Rule

Generic ACMG/AMP 2015 PS2: de novo (maternity and paternity confirmed) in a patient with the disease and no family history. No published InSiGHT MUTYH VCEP v1.0 criteria exist, so the generic definition applies.

Evidence considered

• Reviewed the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534, ruleset 1742141543): the document contains gene/disease/MOI metadata only and no published criteria codes, with status 'Pilot Rules In Prep' dated 4/24/2025, so no gene-specific PS2 rule exists and the generic ACMG/AMP 2015 definition of PS2 was applied.
• No proband, trio, or parental-testing data are present for this variant; the evidence set contains no de novo assertion and no maternity/paternity confirmation.
• PMID:16134147 is the only source that reports this exact variant in a patient (legacy numbering c.1234C>T / p.Arg412Cys = NM_001128425.2 c.1276C>T / p.Arg426Cys); it was detected as a monoallelic (heterozygous) germline change in patient GD108 with a positive family history, which is inconsistent with a confirmed de novo event.
• PMID:25741868 supplies the generic ACMG/AMP 2015 PS2 definition used here (de novo with confirmed maternity and paternity in a patient with the disease and no family history).

Still missing

• No proband-level clinical record for this variant (variant-level curation only).
• No trio or parental testing to establish maternity and paternity and confirm a de novo occurrence.
• No explicit statement of de novo origin in any clinical report; the single published carrier (PMID:16134147, patient GD108) is a heterozygous case with a positive family history.

Sources

Reasoning

PM6 (generic ACMG/AMP 2015) requires an assumed de novo occurrence in a patient, i.e. a de novo event reported without confirmation of maternity and paternity. No de novo occurrence of this variant is reported in any source examined: PMID:16134147, the only report of this variant in a patient, documents a heterozygous carrier (GD108) with a positive family history and does not state a de novo origin, and no other source in the evidence set asserts a de novo event. The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534) has no published criteria codes, so no gene-specific PM6 modification exists and the generic ACMG/AMP definition applies. With no de novo observation in any proband, PM6 cannot be evaluated and is recorded as not assessed.

Rule

Generic ACMG/AMP 2015 PM6: assumed de novo without confirmation of paternity and maternity. No published InSiGHT MUTYH VCEP v1.0 criteria exist, so the generic definition applies.

Evidence considered

• Reviewed the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534): no criteria codes are published (status 'Pilot Rules In Prep', 4/24/2025), so the generic ACMG/AMP 2015 PM6 definition was applied.
• No de novo occurrence of this variant is reported anywhere in the available evidence; the single published carrier (PMID:16134147, patient GD108) is a heterozygous case with a positive family history and no statement of a de novo event.
• PMID:25741868 supplies the generic ACMG/AMP 2015 PM6 definition used here (assumed de novo without confirmation of paternity and maternity).

Still missing

• No proband-level report asserting a de novo occurrence of this variant.
• No parental testing information that could support even an unconfirmed (assumed) de novo event.
• No proband or pedigree data in this case (variant-level curation only).

Sources

Reasoning

PP1 requires co-segregation of the variant with disease in multiple affected family members of a gene definitively known to cause the disease. No such pedigree exists in the evidence. PMID:16134147 reports this variant once, in patient GD108 (Italian classical FAP, >100 polyps, monoallelic), with a family-history notation of vertical transmission, but no relatives were genotyped, so this is family-history information, not co-segregation; the paper's explicit statement that monoallelic MYH changes are unlikely to be determinant events in the recessive MUTYH-associated polyposis also argues against treating the single carrier as a segregating allele. PMID:16557584 characterises MUTYH-associated polyposis as autosomal recessive with biallelic families but does not report this variant. The InSiGHT MUTYH VCEP specification v1.0 (CSPEC doc 1742141534) publishes no criteria codes, so the generic ACMG/AMP PP1 definition applies. With no segregation study available, PP1 is not assessed.

Rule

Generic ACMG/AMP 2015 PP1: co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. No published InSiGHT MUTYH VCEP v1.0 criteria exist, so the generic definition applies.

Evidence considered

• Reviewed the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534): no criteria codes are published (status 'Pilot Rules In Prep', 4/24/2025), so the generic ACMG/AMP 2015 PP1 definition was applied.
• PMID:16134147 reports the variant (legacy c.1234C>T / p.Arg412Cys = NM_001128425.2 c.1276C>T / p.Arg426Cys) once, as a monoallelic change in patient GD108, an Italian classical FAP patient with >100 polyps and a family-history notation of vertical transmission; no relatives were genotyped, so no co-segregation could be assessed.
• PMID:16557584 characterises MUTYH-associated polyposis as autosomal recessive with biallelic mutations in index patients and affected relatives, but this variant is not reported in that cohort, so it contributes inheritance context only and no segregation data.
• PMID:25741868 supplies the generic ACMG/AMP 2015 PP1 definition used here (co-segregation with disease in multiple affected family members).

Still missing

• No family in which this variant was genotyped in multiple affected relatives.
• No genotype data for relatives of the one published carrier (PMID:16134147, patient GD108); only a family-history notation of vertical transmission is available.
• No meioses counted in either direction.

Sources

Reasoning

BS4 requires demonstrable lack of segregation of the variant with disease in affected members of a family. No family with multiple affected members genotyped for this variant is available in the evidence: PMID:16134147 reports the variant in a single heterozygous FAP patient (GD108) with a positive family history of vertical transmission rather than any genotyped non-segregating pedigree, and no source describes an affected relative who carries the variant but lacks disease, or an affected relative who lacks the variant. PMID:16557584 provides autosomal-recessive inheritance context for MUTYH-associated polyposis but does not report this variant. The InSiGHT MUTYH VCEP specification v1.0 (CSPEC doc 1742141534) publishes no criteria codes, so the generic ACMG/AMP BS4 definition applies. With no segregation data in either direction, BS4 is not assessed rather than met.

Rule

Generic ACMG/AMP 2015 BS4: lack of segregation in affected members of a family. No published InSiGHT MUTYH VCEP v1.0 criteria exist, so the generic definition applies.

Evidence considered

• Reviewed the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP specification for MUTYH v1.0 (CSPEC doc 1742141534): no criteria codes are published (status 'Pilot Rules In Prep', 4/24/2025), so the generic ACMG/AMP 2015 BS4 definition was applied.
• PMID:16134147 reports the variant once, as a monoallelic change in classical FAP patient GD108 with a positive family history; no relatives were genotyped, so neither segregation nor non-segregation can be shown.
• PMID:16557584 describes autosomal-recessive MUTYH-associated polyposis with biallelic families but does not report this variant; no non-segregation data are provided for it.
• PMID:25741868 supplies the generic ACMG/AMP 2015 BS4 definition used here (lack of segregation in affected members of a family).

Still missing

• No genotyped multiply-affected family showing that the variant fails to segregate with disease.
• No genotype data for any relative of the single published carrier (PMID:16134147, patient GD108).
• No meioses counted in either direction.

Sources