MUTYH c.74G>A, p.(Gly25Asp)

Reasoning

The governing InSiGHT MUTYH framework is present but contains no usable population-specific BS1 rule, so the supplied generic BS1 threshold applies. The highest observed allele frequency is 0.0130313 (1.30313%) in the gnomAD v2.1 East Asian subgroup and 0.0113403 (1.13403%) in gnomAD v4.1 East Asian individuals, both exceeding the generic BS1 threshold of 0.01 (1%). The all-comers frequencies are 0.00105347 and 0.000441106, respectively, illustrating a strong ancestry effect; the criterion is met because the maximum observed ancestry frequency exceeds the stated threshold. The variant is also reported in control cohorts, including the p.P18L-p.G25D haplotype in 3 of 96 Korean controls and the c.53C>T/c.74G>A haplotype in 3 of 343 Chinese controls, although these older haplotype observations are not used as the primary threshold calculation.

Rule

{'source': 'generic_svi_default', 'threshold': 0.01, 'comparison': '>=', 'unit': 'allele frequency', 'population_selection': 'highest observed ancestry frequency'}

Evidence considered

• The InSiGHT MUTYH specification is identified, but its retrieved ruleset has no structured BS1 population threshold; the supplied generic ACMG/ClinGen threshold is therefore used.
• gnomAD v2.1 reports the highest East Asian AF as 0.0130313 (260/19952), while gnomAD v4.1 reports 0.0113403 (509/44884); both exceed 0.01.
• The all-comers AF is lower in both datasets: 0.00105347 in gnomAD v2.1 and 0.000441106 in gnomAD v4.1, demonstrating that ancestry-specific frequency is decisive here.
• PMID:17703316 reports the p.P18L-p.G25D haplotype in three of 96 normal Korean controls, and PMID:18811933 reports the c.53C>T/c.74G>A haplotype in three of 343 Chinese controls; these observations provide independent population-frequency context but are not substituted for gnomAD thresholding.
• The supplied generic BS1 threshold is AF >=0.01 (1%), with per-gene derivation preferred, as attributed to Whiffin et al. 2017 (PMID:28518168).

Sources

Reasoning

BS3 supporting is met. The validated MUTYH functional study directly evaluated p.G25D in a biologically relevant BER complementation model using MutY-deficient E. coli, with empty-vector and wild-type controls and nine independent cultures. The variant's mutation rate was below the assay's 1.7-fold threshold for functional retention relative to wild type, and p.G25D was classified as functionally retained. Independent mammalian-cell immunofluorescence also showed normal mitochondrial localization of isolated p.Gly25Asp. Supporting strength is appropriate because the main assay is heterologous and the authors describe the cutoffs as tentative, while the localization result assesses only one aspect of function.

Evidence considered

• Komine et al. evaluated 47 MUTYH variants in a MutY-deficient E. coli BER complementation assay, with rifampicin-resistant mutation rate as the functional readout, nine independent overnight cultures, an empty-vector negative control, and wild-type MUTYH comparator.
• The published calibration categorized mutation rates less than 1.7-fold above wild type as functionally retained; p.G25D was explicitly categorized as functionally retained.
• The study also reported minimal differences in protein expression among tested variants and nuclear localization of the tested nuclear isoform, providing assay-context controls, but these measures do not replace the BER readout.
• The authors cautioned that the assay cutoffs were tentatively selected and that clinical application may be limited for intermediate or subtle functional defects; therefore BS3 is not upgraded beyond supporting.
• A separate cos-7-cell immunofluorescence experiment found isolated p.Gly25Asp localized to mitochondria similarly to wild-type hMYH, supporting absence of a localization defect for the isolated variant.

Sources

Reasoning

The variant is missense, NM_001128425.2:c.74G>A (p.Gly25Asp), so BP4 must be evaluated using REVEL only; SpliceAI and BayesDel are not applicable to this BP4 assessment. REVEL is 0.111, meeting the generic ClinGen SVI REVEL BP4 supporting threshold of <=0.29 (PMID:36413997). The MUTYH VCEP framework contains no specific BP4 assignment. Therefore BP4 is met at supporting strength.

Rule

Missense variant; REVEL <=0.29 supports BP4, per the supplied ClinGen SVI calibration (PMID:36413997).

Evidence considered

• The MUTYH InSiGHT VCEP framework was checked first; its available ruleset contains no specific BP4 assignment, so the supplied generic calibration applies.
• The variant consequence is missense, so REVEL is the sole applicable computational path; SpliceAI is not used for BP4.
• REVEL score: 0.111. The supplied ClinGen SVI calibration sets BP4 supporting at <=0.29 (Pejaver et al. 2022, PMID:36413997).

Sources

Reasoning

The variant is MUTYH p.Gly25Asp (G25D). Publications report this exact amino-acid change, but none establishes a pathogenic comparator for the same amino-acid substitution: ClinVar is conflicting without an expert-panel submission, and the available reports describe clinical observations or functional results that do not establish pathogenicity. Therefore PS1 is not met.

Rule

PS1 requires the same amino-acid change as an established pathogenic variant; reports of the same change without a reliable pathogenic classification do not satisfy PS1.

Evidence considered

• The case variant is NP_001121897.1:p.(Gly25Asp) (G25D).
• PMID:18422726 reports p.G25D in a Japanese patient but states that no functional analysis was performed and that possible functional alteration required further study.
• PMID:17703316 reports p.G25D in cis with p.P18L in one patient and three controls, without establishing the variant as pathogenic.
• PMID:18811933 reports p.Gly25Asp in a haplotype and shows isolated p.Gly25Asp mitochondrial localization similar to wild type, not a pathogenic classification.
• PMID:25820570 classifies p.G25D as functionally retained in a MutY-deficient E. coli complementation assay.
• ClinVar shows conflicting submissions with no expert-panel submission; this does not provide a reliable pathogenic comparator for PS1.

Sources

Reasoning

PS3 is not met. The most informative variant-specific functional study used a MutY-deficient E. coli complementation assay with nine independent overnight cultures, an empty-vector control, and wild-type MUTYH control. p.G25D had a mutation rate below the study's 1.7-fold threshold for functional retention relative to wild type and was classified as functionally retained, not defective. A separate mammalian-cell localization study found isolated p.Gly25Asp localized like wild-type protein, although the c.53C>T/c.74G>A haplotype showed dual localization. These results do not provide evidence of abnormal function for p.Gly25Asp sufficient for PS3.

Evidence considered

• Komine et al. tested p.G25D in a MutY-deficient E. coli complementation assay measuring rifampicin-resistant mutation rates, using nine independent cultures, an empty-vector control, and wild-type MUTYH control.
• The study defined variants with mutation rates less than 1.7-fold higher than wild type as functionally retained; p.G25D was included in the functionally retained group rather than the partially defective or defective groups.
• The study authors noted that the 1.7-fold and 4.8-fold cutoffs were set from selected variants and were tentative, so the result is strong evidence against a demonstrable assay defect but not evidence supporting PS3.
• In cos-7-cell immunofluorescence experiments, isolated p.Gly25Asp retained mitochondrial localization similar to wild-type hMYH; the combined p.Pro18Leu/p.Gly25Asp haplotype, not isolated p.Gly25Asp, showed dual nuclear and mitochondrial localization.

Sources

Reasoning

Generic PS4 requires a statistically supported excess of the exact variant in affected individuals compared with controls. PMID:18811933 reported the linked c.53C>T/c.74G>A haplotype in 6/138 sporadic colorectal-cancer cases (4.35%) versus 3/343 controls (0.87%), but this does not establish enrichment for isolated c.74G>A because the cases and controls were evaluated for the linked haplotype. PMID:17703316 also found the p.P18L-p.G25D cis combination in one affected individual and three controls, and PMID:18422726 reported p.G25D in one affected patient without a matched control comparison. The available evidence therefore does not support PS4 for the isolated variant.

Rule

Generic PS4: prevalence of the exact variant is significantly increased in affected individuals compared with controls; linked haplotypes cannot be treated as isolated-variant enrichment.

Evidence considered

• PMID:18811933 reports the c.53C>T/c.74G>A haplotype in 6/138 sporadic colorectal-cancer cases and 3/343 controls; the comparison is for the linked haplotype rather than isolated c.74G>A.
• PMID:17703316 reports the p.P18L-p.G25D cis combination in one FAP patient and three normal controls.
• PMID:18422726 reports p.G25D in one Japanese adenomatous-polyposis patient but does not provide a matched case-control enrichment analysis for the exact variant.

Still missing

• No adequately powered case-control analysis of isolated NM_001128425.2:c.74G>A was identified.

Sources

Reasoning

The governing InSiGHT MUTYH specification is present, but it supplies no structured PM1 rule and vcep_materials.json has an empty domain_tables object. The variant is not in a statistically significant hotspot. No approved critical functional domain or hotspot evidence places residue 25 in a PM1 region, so PM1 is not met.

Rule

PM1 requires a well-established critical functional domain or mutational hotspot with no benign variation; authoritative VCEP domain-table entries take precedence when present.

Evidence considered

• The applicable framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis MUTYH specification, version 1.0.
• The specification materials contain no structured PM1 rule, and vcep_materials.json contains no MUTYH domain-table entries to assess against residue 25.
• The case hotspot assessment reports that p.G25D does not lie in a statistically significant hotspot.
• Because no approved critical functional domain or hotspot evidence covers residue 25, the PM1 requirement for a well-established critical region is not satisfied.

Sources

Reasoning

The governing InSiGHT MUTYH framework is present but contains no usable population-specific PM2 rule, so the supplied generic PM2 supporting threshold applies. The all-comers AF is 0.00105347 in gnomAD v2.1 and 0.000441106 in gnomAD v4.1, both above the PM2 threshold of 0.0001 (0.01%). The highest East Asian frequencies are still higher at 0.0130313 and 0.0113403. Thus the variant is not sufficiently rare for PM2, and the observed homozygotes further argue against applying rarity evidence.

Rule

{'source': 'generic_clingen_svi_default', 'threshold': 0.0001, 'comparison': '<=', 'unit': 'allele frequency', 'population_selection': 'all-comers default unless governing specification requires a different source'}

Evidence considered

• The InSiGHT MUTYH specification is identified, but its retrieved ruleset has no structured PM2 population threshold; the supplied generic PM2 threshold is therefore used.
• gnomAD v2.1 reports an all-comers AF of 0.00105347 (298/282876), and gnomAD v4.1 reports an all-comers AF of 0.000441106 (712/1614126).
• Both all-comers frequencies exceed the supplied PM2 threshold of 0.0001; the East Asian subgroup frequencies are substantially higher at 0.0130313 in v2.1 and 0.0113403 in v4.1.
• The supplied generic ClinGen SVI PM2 recommendation is AF <=0.0001 (0.01%), attributed in the calibration block to ACMG/AMP guidance (PMID:25741868).

Sources

Reasoning

The variant is p.Gly25Asp at residue 25. The reviewed evidence reports G25D itself but identifies no different missense substitution at Gly25 with an established pathogenic or likely pathogenic classification. The available PM5 candidate artifact also contains zero same-residue candidates, so PM5 is not met.

Rule

PM5 requires a different missense change at the same residue that is established pathogenic or likely pathogenic; the target variant itself cannot serve as its PM5 comparator.

Evidence considered

• The target residue is MUTYH Gly25 and the observed substitution is Gly25Asp.
• PMID:18422726, PMID:17703316, and PMID:18811933 report the target G25D change, not a different missense change at residue 25 with established pathogenicity.
• ClinVar evidence available for the target record is conflicting and has no expert-panel submission; it does not establish an alternate same-residue pathogenic comparator.
• The case PM5 candidate record reports zero same-residue candidates and does not establish classic PM5 eligibility.

Sources

Reasoning

MUTYH-associated polyposis is established as an autosomal-recessive disorder involving loss of MUTYH function, while the reviewed literature documents numerous missense variants and specifically evaluates G25D. The available evidence does not establish that pathogenic MUTYH variation is predominantly missense with a low benign missense rate, so generic PP2 is not met.

Rule

PP2 requires a missense-driven gene-disease mechanism with a low benign missense rate; gene-level missense observations alone are insufficient.

Evidence considered

• The applicable MUTYH specification identifies familial adenomatous polyposis 2 with autosomal-recessive inheritance, but provides no gene-specific PP2 rule in the available structured materials.
• PMID:25820570 states that more than 200 MUTYH missense variants have been detected and evaluates 47 missense variants, including p.G25D; this documents missense variation but does not establish a predominantly missense disease mechanism or a low benign missense rate.
• PMID:18422726 reports multiple MUTYH variants and explicitly notes that G25D required further functional study, rather than supporting a missense-enriched pathogenic mechanism.

Sources

Reasoning

The variant is missense, NM_001128425.2:c.74G>A (p.Gly25Asp), so PP3 must be evaluated using REVEL only; SpliceAI and BayesDel are not applicable to this PP3 assessment. REVEL is 0.111, below the generic ClinGen SVI REVEL PP3 supporting threshold of 0.644 (PMID:36413997), and the MUTYH VCEP framework contains no specific PP3 assignment. Therefore PP3 is not met.

Rule

Missense variant; REVEL >=0.644 is required for PP3 supporting, per the supplied ClinGen SVI calibration (PMID:36413997).

Evidence considered

• The MUTYH InSiGHT VCEP framework was checked first; its available ruleset contains no specific PP3 assignment, so the supplied generic calibration applies.
• The variant consequence is missense, so REVEL is the sole applicable computational path; SpliceAI is not used for PP3.
• REVEL score: 0.111. The supplied ClinGen SVI calibration sets PP3 supporting at >=0.644 (Pejaver et al. 2022, PMID:36413997).

Sources

Reasoning

PP4 requires a highly specific phenotype or family history that is strongly characteristic of the disease associated with the variant. The available reports describe adenomatous polyposis, colorectal cancer, and related findings in isolated cases, but p.G25D was also observed in unaffected controls in cis with p.P18L (PMID:17703316), and the c.74G>A-containing haplotype was studied in sporadic colorectal cancer rather than a uniquely specific MUTYH-associated phenotype (PMID:18811933). These observations do not provide phenotype specificity sufficient for PP4.

Rule

Generic PP4: the patient's phenotype or family history is highly specific for a disease associated with the gene and variant; nonspecific colorectal cancer or polyposis alone is insufficient.

Evidence considered

• PMID:17703316 reports one FAP patient with the p.P18L-p.G25D cis combination and three normal controls with the same combination.
• PMID:18422726 reports one patient with adenomatous polyposis and colorectal carcinoma carrying p.G25D among multiple MUTYH variants, without demonstrating phenotype specificity for p.G25D.
• PMID:18811933 evaluates a linked c.53C>T/c.74G>A haplotype in sporadic colorectal cancer and controls, not a distinctive isolated-variant phenotype.

Still missing

• No uniquely characteristic phenotype or family history tied specifically to isolated p.Gly25Asp was documented.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel assertion of Pathogenic or Likely pathogenic. The ClinVar audit identifies zero expert-panel submissions for this exact variant; available assertions are ordinary laboratory submissions, including Benign, Likely benign, and Uncertain significance. Therefore PP5 is not met.

Rule

PP5 applies only to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic; ordinary submissions and aggregate labels do not qualify.

Evidence considered

• The exact-variant ClinVar audit reports expert_panel_submissions = 0 and lists only ordinary single-submitter assertions, with classifications including Benign, Likely benign, and Uncertain significance.
• Ordinary laboratory submissions, aggregate labels, and non-expert assertions were excluded from PP5 under the specified rule.

Still missing

• No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion is available.

Sources

Reasoning

The governing InSiGHT MUTYH framework is present but contains no usable population-specific BA1 rule, so the supplied generic ACMG stand-alone threshold applies. The highest observed population frequency is 0.0130313 (1.30313%) in the gnomAD v2.1 East Asian subgroup; the gnomAD v4.1 East Asian frequency is 0.0113403 (1.13403%), and neither reaches the generic BA1 threshold of 0.05 (5%). The all-comers frequencies are lower: 0.00105347 in gnomAD v2.1 and 0.000441106 in gnomAD v4.1. Therefore BA1 is not met.

Rule

{'source': 'generic_acmg_amp', 'threshold': 0.05, 'comparison': '>=', 'unit': 'allele frequency', 'population_selection': 'highest observed ancestry frequency'}

Evidence considered

• The InSiGHT MUTYH specification is identified, but its retrieved ruleset has no structured BA1 population threshold; the supplied generic ACMG threshold is therefore used.
• gnomAD v2.1 reports an all-comers AF of 0.00105347 (298/282876) and a highest East Asian subgroup AF of 0.0130313 (260/19952).
• gnomAD v4.1 reports an all-comers AF of 0.000441106 (712/1614126) and a highest East Asian subgroup AF of 0.0113403 (509/44884).
• The generic ACMG/AMP BA1 threshold is AF >=0.05 (5%), as specified in the supplied calibration block and attributed to ACMG/AMP 2015 (PMID:25741868).

Sources

Reasoning

MUTYH-associated polyposis has an established loss-of-function component, but the reviewed MUTYH literature documents substantial missense variation and functional evaluation of missense disease candidates, including G25D. The available evidence does not support the stronger BP1 premise that disease-causing variation in MUTYH is primarily truncating with missense variation generally benign; BP1 is therefore not met.

Rule

BP1 requires a gene-disease context in which pathogenic variants are primarily truncating and missense variants are generally not a disease mechanism; this premise is not established for MUTYH here.

Evidence considered

• The applicable MUTYH specification identifies autosomal-recessive familial adenomatous polyposis 2 but provides no structured BP1 rule in the available materials.
• PMID:25820570 states that more than 200 MUTYH missense variants have been detected and experimentally evaluates 47 missense variants, including p.G25D.
• PMID:18422726 reports missense MUTYH variants in affected patients and notes that the functional effect of G25D required further study.
• PMID:18811933 reports a MUTYH missense haplotype and performs cellular localization experiments on p.Gly25Asp, demonstrating that missense variation is biologically studied in this gene.
• Accordingly, the available evidence does not justify the BP1 assumption that missense variants in MUTYH are generally benign because the gene is primarily truncating.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel assertion of Benign or Likely benign. The ClinVar audit identifies zero expert-panel submissions for this exact variant; the available Benign and Likely benign assertions are from individual laboratories and are not expert-panel assertions. Therefore BP6 is not met.

Rule

BP6 applies only to an exact-variant ClinVar expert-panel classification of Benign or Likely benign; ordinary submissions and aggregate labels do not qualify.

Evidence considered

• The exact-variant ClinVar audit reports expert_panel_submissions = 0 and identifies the Benign and Likely benign assertions as single-submitter laboratory records.
• Ordinary laboratory submissions, aggregate labels, and non-expert assertions were excluded from BP6 under the specified rule.

Still missing

• No exact-variant ClinVar expert-panel Benign or Likely benign assertion is available.

Sources

Reasoning

The applicable InSiGHT MUTYH specification is present but provides no criterion-specific rules. Generic ACMG/AMP PS2 requires a documented de novo occurrence in the proband with confirmed maternity and paternity, but the available evidence contains no proband-parent genotypes, parental testing, or de novo assertion for NM_001128425.2:c.74G>A (p.Gly25Asp). The published case reports describe patients carrying p.G25D but do not establish a de novo event.

Rule

Generic ACMG/AMP PS2; no applicable criterion-specific MUTYH VCEP rule was available.

Evidence considered

• The MUTYH InSiGHT specification identifies autosomal-recessive familial adenomatous polyposis 2 but contains no criterion-specific PS2 rule payload.
• No case-level parental testing or confirmed de novo status is reported for NM_001128425.2:c.74G>A (p.Gly25Asp).
• PMID:18422726 reports p.G25D in a Japanese patient with adenomatous polyposis, but does not report parental testing or a de novo determination.
• PMID:17703316 reports p.P18L-p.G25D in one Korean patient and does not report parental testing or a de novo determination.

Still missing

• Documented proband genotype and phenotype
• Confirmed maternity and paternity
• Testing results for both biological parents
• Explicit de novo interpretation with assay and laboratory details

Sources

Reasoning

The applicable MUTYH specification is present but provides no criterion-level PM3 rule, so generic ACMG/AMP PM3 is used. MUTYH is autosomal recessive. PMID:18422726 reports p.G25D in a patient described as having compound heterozygous MUTYH mutations, but lists four heterozygous variants (P18L, G25D, 1389G>C, and Q324H) without establishing which partner variant was in trans with p.G25D or demonstrating that the partner was pathogenic. PMID:17703316 instead establishes p.P18L and p.G25D in cis. Therefore, affected-proband observation alone does not establish the required p.G25D-in-trans-with-a-pathogenic-variant observation, and PM3 cannot be assigned without definitive phase and pathogenicity of the partner allele.

Rule

Generic ACMG/AMP PM3: pathogenic or likely pathogenic variant observed in trans with the variant under assessment in an affected individual with a recessive disorder; definitive phase and partner pathogenicity are required.

Evidence considered

• The MUTYH framework specifies autosomal recessive inheritance but contains no criterion-level PM3 rule, so generic ACMG/AMP PM3 was applied.
• PMID:18422726 reports p.G25D in one Japanese patient described as having compound heterozygous mutations P18L, G25D, 1389G>C, and Q324H; the report does not resolve which variants were in trans with p.G25D or establish a pathogenic partner allele.
• PMID:17703316 demonstrates that p.P18L and p.G25D were in cis in a Korean patient and in three controls, which does not establish p.G25D in trans with a pathogenic allele.

Still missing

• Definitive phase showing p.G25D in trans with a pathogenic or likely pathogenic MUTYH variant in an affected individual.
• Pathogenicity assessment of the specific partner allele in the reported compound-heterozygous patient.

Sources

Reasoning

The applicable InSiGHT MUTYH specification is present but provides no criterion-specific rules. Generic ACMG/AMP PM6 concerns a presumed de novo occurrence without confirmed maternity and paternity, but no parental genotypes, family testing, or documented presumed de novo interpretation is available for NM_001128425.2:c.74G>A (p.Gly25Asp). The published patient reports do not establish de novo status.

Rule

Generic ACMG/AMP PM6; no applicable criterion-specific MUTYH VCEP rule was available.

Evidence considered

• The MUTYH InSiGHT specification contains no criterion-specific PM6 rule payload.
• No presumed de novo interpretation, parental testing, or family genotyping is reported for NM_001128425.2:c.74G>A (p.Gly25Asp).
• PMID:18422726 and PMID:17703316 report affected individuals carrying p.G25D but provide no evidence that the variant arose de novo.

Still missing

• Parental testing or other evidence establishing presumed de novo origin
• Proband and parental phenotype documentation
• Laboratory details supporting the de novo inference

Sources

Reasoning

The applicable InSiGHT MUTYH specification is present but provides no criterion-specific rules. Generic ACMG/AMP PP1 requires cosegregation of the variant with disease in affected family members, evaluated across informative meioses. The available evidence documents isolated patients or variant-containing haplotypes, but no affected relatives, unaffected tested relatives, genotype-phenotype concordance, informative meioses, or segregation statistics for NM_001128425.2:c.74G>A (p.Gly25Asp).

Rule

Generic ACMG/AMP PP1; no applicable criterion-specific MUTYH VCEP rule was available.

Evidence considered

• The MUTYH InSiGHT specification contains no criterion-specific PP1 rule payload.
• PMID:18422726 reports p.G25D in one patient and notes no family history of colorectal adenomatous polyposis, but provides no relative genotypes or segregation analysis.
• PMID:17703316 reports p.P18L-p.G25D in one patient and three controls with phase confirmation, but does not report familial segregation or informative meioses.
• PMID:25820570 explicitly provides no patient-level clinical or segregation findings specific to p.G25D.

Still missing

• Pedigree and phenotype data for relatives
• Genotypes of affected and unaffected relatives
• Number of informative meioses
• Segregation analysis accounting for autosomal-recessive inheritance

Sources

Reasoning

gnomAD reports four homozygotes in v2.1 and seven homozygotes in v4.1, including East Asian homozygotes, but these databases do not establish that the individuals were healthy, unaffected adults assessed for MUTYH-associated polyposis or that disease penetrance was sufficient for BS2. The variant occurs in an autosomal-recessive, adult-onset cancer-predisposition context, so homozygote counts alone cannot satisfy the healthy-person requirement. No governing MUTYH-specific BS2 rule or phenotype-confirmed homozygote evidence was available.

Rule

{'source': 'generic_acmg_amp', 'requirement': 'observation in healthy individuals, including homozygotes when applicable', 'population_selection': 'phenotype-confirmed unaffected adults'}

Evidence considered

• gnomAD v2.1 reports four total homozygotes, including four East Asian homozygotes; gnomAD v4.1 reports seven total homozygotes, including seven East Asian homozygotes.
• The available gnomAD evidence provides genotype counts but no individual-level phenotype, age, clinical ascertainment, or penetrance information sufficient to establish unaffected healthy adults.
• The supplied ACMG/AMP framework describes BS2 as observation in healthy individuals and does not authorize treating an unphenotyped reference-population homozygote as definitively healthy for an adult-onset recessive cancer-predisposition disorder.

Still missing

• Phenotype-confirmed healthy adult status and age of the reported homozygotes are unavailable.
• A MUTYH-specific BS2 rule addressing adult-onset disease penetrance is unavailable in the retrieved framework.

Sources

Reasoning

The applicable InSiGHT MUTYH specification is present but provides no criterion-specific rules. Generic ACMG/AMP BS4 requires lack of segregation in affected family members, with adequate clinical ascertainment and informative testing. No affected-family cohort, tested relatives, discordant genotypes, or non-segregation analysis is documented for NM_001128425.2:c.74G>A (p.Gly25Asp).

Rule

Generic ACMG/AMP BS4; no applicable criterion-specific MUTYH VCEP rule was available.

Evidence considered

• The MUTYH InSiGHT specification contains no criterion-specific BS4 rule payload.
• No adequately phenotyped and genotyped affected relatives are reported for this variant.
• The available reports describe individual patients or control observations rather than documented non-segregation within families.

Still missing

• Affected-family-member testing
• Clinical ascertainment of relatives
• Documented discordant genotype-phenotype observations
• Assessment of phenocopies and reduced penetrance

Sources

Reasoning

The applicable MUTYH specification is present but provides no criterion-level BP2 rule, so generic ACMG/AMP BP2 is used. MUTYH is autosomal recessive. PMID:17703316 establishes p.G25D in cis with p.P18L in one affected individual and three controls, but the source does not establish p.P18L as pathogenic or likely pathogenic; therefore the observation cannot satisfy the recessive-disease BP2 cis requirement. PMID:18422726 reports a compound-heterozygous context but does not provide evidence that p.G25D is in cis with a pathogenic variant. BP2 remains unassessed pending pathogenicity confirmation of the cis partner and complete phase-resolved evidence.

Rule

Generic ACMG/AMP BP2: for a recessive disorder, the variant is observed in cis with a pathogenic or likely pathogenic variant; the cis partner must itself meet that pathogenicity requirement.

Evidence considered

• The MUTYH framework specifies autosomal recessive inheritance but contains no criterion-level BP2 rule, so generic ACMG/AMP BP2 was applied.
• PMID:17703316 used cloning and sequencing to show p.P18L and p.G25D on the same allele; the paper does not establish p.P18L as pathogenic or likely pathogenic, and the same cis haplotype occurred in three controls.
• PMID:18422726 does not provide phase-resolved evidence that p.G25D was in cis with a pathogenic MUTYH variant.

Still missing

• Pathogenicity or likely pathogenicity of the p.P18L allele in the documented cis haplotype.
• Independent confirmation that the relevant cis partner satisfies the BP2 pathogenic-variant requirement.

Sources

Reasoning

BP5 requires the variant to be found in a patient with a convincing alternative molecular explanation for the same phenotype. The reports describe additional MUTYH changes in patients carrying p.G25D, including a cis p.P18L combination and other variants in one compound-heterozygous patient, but the available evidence does not establish any of those alternatives as a convincing pathogenic explanation for the reported phenotype. BP5 cannot be assigned from these observations alone.

Rule

Generic BP5: apply only when a convincing pathogenic alternative variant explains the patient's phenotype; co-occurrence of additional unestablished variants is insufficient.

Evidence considered

• PMID:17703316 reports p.P18L in cis with p.G25D in one FAP patient and three controls, but does not establish p.P18L as a convincing pathogenic alternative explanation.
• PMID:18422726 reports p.G25D with P18L, Q324H, and 1389G>C in one patient, but does not establish which additional variant, if any, explains the phenotype or prove a convincing alternative diagnosis.

Still missing

• The clinical phase, pathogenicity, and phenotype-explanatory role of the additional variants were not sufficiently established.

Sources