MUTYH c.452A>G, p.Tyr151Cys

Reasoning

The variant is NP_001041639.1:p.(Tyr151Cys), also reported as MYH Tyr165Cys (494A>G) because of a 14-residue numbering difference. PMID:11818965 reports this same amino-acid substitution in affected siblings with biallelic MUTYH variants and provides functional glycosylase evidence; the alternate historical notation is concordant with the current transcript-level p.(Y151C).

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• Al-Tassan et al. 2002 (PMID:11818965), Results paragraph describing MYH variants: Tyr165Cys was reported as an adenine-to-guanine substitution at nucleotide 494 in exon 7; the extraction maps this historical numbering to NP_001041639.1:p.(Y151C).
• The same paper reports Tyr165Cys in three affected siblings and functional glycosylase testing of the corresponding substitution, supporting that this is an established disease-associated amino-acid change rather than a splice-only observation.

Sources

Reasoning

PS3 is met at strong strength. The variant NM_001048174.2:c.452A>G (p.(Y151C)) is reported in the functional literature under the historical MUTYH Y165C/Tyr165Cys nomenclature. Multiple independent, biologically relevant assays with wild-type and deficient controls show impaired MUTYH function: the equivalent bacterial MutY Tyr82Cys substitution had approximately 98% reduced adenine-removal activity; recombinant Y165C had approximately threefold lower adenine-excision and approximately twofold lower product-release rates and failed bacterial complementation, producing a mutation frequency similar to the deficient strain; and mammalian-cell assays showed absent detectable glycosylase activity, impaired oxidative-DNA repair, increased 8-oxodG, and oxidative-stress hypersensitivity. The concordant results across in vitro enzymatic, bacterial complementation, and mammalian-cell assays are well-established functional evidence supportive of a damaging effect.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• Al-Tassan et al. 2002 (PMID:11818965), Results/Fig. 5: the historical Tyr165Cys allele corresponding to p.(Y151C) was evaluated in site-directed mutagenesis and single-turnover glycosylase assays; the equivalent E. coli MutY Tyr82Cys substitution showed approximately 98% reduced adenine-removal activity.
• Ali et al. 2008 (PMID:18534194), glycosylase and DNA-binding assays: the historical Y165C MUTYH protein generated no detectable products under the assay conditions, supporting loss of enzymatic function.
• Kundu et al. 2009 (PMID:19836313), Tables 1-2 and Results sections 3.4-3.6: Y165C showed approximately threefold lower adenine-excision rate, approximately twofold lower product-release rate (0.006 ± 0.001 versus 0.011 ± 0.006 min−1), and bacterial complementation produced mutation frequency 23, similar to the deficient strain and approximately tenfold above wild type.
• Molatore et al. 2009 (PMID:19953527), mammalian-cell and purified-protein assays: Y165C lacked detectable 8-oxodG:A glycosylase activity, impaired oxidative-DNA repair, increased genomic 8-oxodG, and caused hypersensitivity to KBrO3.
• The papers explicitly explain that Y165C/Tyr165Cys uses an alternate 14-residue MUTYH protein numbering and corresponds to the case variant p.(Y151C).

Sources

Reasoning

PM3 is met for this recessive MUTYH disorder. The reported c.452A>G/p.(Y151C) allele corresponds to the paper's Tyr165Cys notation and was observed in compound heterozygosity with Gly382Asp in three affected siblings with multiple colorectal adenomas and carcinoma. The compound-heterozygous configuration establishes the alleles were in trans, and Gly382Asp was the second MUTYH disease allele in the affected probands. This is direct affected-proband phase evidence rather than an inference from the variant's overall classification.

Rule

For recessive disorders, detected in trans with a pathogenic variant ... This requires testing of parents (or offspring) to determine phase.

Evidence considered

• Al-Tassan et al. 2002 (PMID:11818965), Results, family N: the paper identified Tyr165Cys (the alternate numbering corresponding to p.(Y151C)) and Gly382Asp, and reported that the three affected siblings were compound heterozygotes for these mutations.
• The same family had three affected siblings with multiple colorectal adenomas and carcinoma; unaffected relatives were either heterozygous for one variant or normal, providing family-based phase and affected-proband context.
• The paper also reported reduced functional activity for the MYH variants, supporting Gly382Asp as the pathogenic partner allele rather than an unclassified polymorphism.

Sources

Reasoning

The variant is reported as MYH/MUTYH Tyr165Cys (494A>G), corresponding to the case variant c.452A>G/p.(Y151C) under the transcript and numbering used here. In family N, it occurred in trans with Gly382Asp in three siblings affected by multiple colorectal adenomas and carcinoma; unaffected relatives carried only one variant or neither variant. This is co-segregation with disease in multiple affected family members in a gene definitively associated with MUTYH-associated polyposis. Supporting strength is applied because the evidence is from one reported family and the disease is autosomal recessive.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.

Evidence considered

• Al-Tassan et al. 2002, PMID:11818965, Results and Fig. 3: family N had Tyr165Cys (494A>G; corresponding to c.452A>G/p.(Y151C)) in trans with Gly382Asp in three siblings affected by multiple colorectal adenomas and carcinoma; unaffected relatives were heterozygous for one variant or had neither variant.

Sources

Reasoning

The variant is a missense substitution, p.(Tyr151Cys), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for PP3. REVEL is 0.963, meeting the generic ClinGen SVI strong PP3 threshold of >= 0.932 from the Pejaver et al. 2022 calibration (PMID:36413997).

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (strong): >= 0.932 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Local REVEL predictor lookup: MUTYH NM_001048174.2:c.452A>G, p.(Tyr151Cys), REVEL score 0.963.
• Generic threshold supplied for this interpretation: PP3 strong requires REVEL >= 0.932, based on the ClinGen SVI REVEL calibration by Pejaver et al. 2022 (PMID:36413997).
• Path selection: a missense variant uses REVEL only; the available SpliceAI score and BayesDel score were not counted for PP3.

Sources

Reasoning

PM2 is not met. The generic ClinGen SVI-based supporting threshold is <=0.0001. The variant is observed in gnomAD v2.1 non-cancer exomes at AF=0.0015364 (364/236,918 alleles; homozygotes=0), in gnomAD v4.1 all-comers at AF=0.001921714 (3,102/1,614,184 alleles; homozygotes=5), and in gnomAD v3.1 non-cancer genomes at AF=0.00154809 (229/147,924 alleles; homozygotes=2). These frequencies are all above 0.0001, so the variant is not absent or at an extremely low frequency under the supplied PM2 threshold.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• Generic PM2 calibration: <=0.0001, the supplied ClinGen SVI recommendation to downgrade PM2 to Supporting (PMID:25741868).
• gnomAD v2.1 non-cancer exomes: AF=0.0015364, 364/236,918 alleles, homozygotes=0; FILTERING grpmax FAF=0.00236984.
• gnomAD v4.1 all-comers: AF=0.001921714, 3,102/1,614,184 alleles, homozygotes=5; FILTERING grpmax FAF=0.00225897.
• gnomAD v3.1 non-cancer genomes: AF=0.00154809, 229/147,924 alleles, homozygotes=2; FILTERING grpmax FAF=0.0020322.

Sources

Reasoning

PMID:11818965 describes multiple colorectal adenomas and carcinoma in affected family members carrying the variant in trans with another MUTYH variant. This phenotype is compatible with MUTYH-associated polyposis, but multiple colorectal adenomas and carcinoma are not highly specific for a disease with a single genetic etiology because other hereditary polyposis and colorectal-cancer genes can produce the same phenotype. The available evidence therefore does not meet generic PP4.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• Al-Tassan et al. 2002, PMID:11818965: family N was affected by multiple colorectal adenomas and carcinoma, with the variant observed in trans with Gly382Asp in three affected siblings.

Sources

Reasoning

The exact ClinVar record is classified as Pathogenic/Likely pathogenic, but the record has no expert-panel submissions; it consists of ordinary laboratory and other non-expert assertions. Generic PP5 is therefore not triggered.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 5293, exact NM_001048174.2(MUTYH):c.452A>G (p.Tyr151Cys): Pathogenic/Likely pathogenic aggregate classification, with 0 expert-panel submissions and ordinary laboratory submissions only.

Sources

Reasoning

BA1 is not met. The governing generic threshold is >=0.05, whereas the appropriate FILTERING frequency is gnomAD v2.1 non-cancer exome grpmax FAF=0.00236984 and the all-comers gnomAD v4.1 grpmax FAF=0.00225897; both are far below 5%. The gnomAD v4.1 population with the highest point estimate is European (non-Finnish), AF=0.00233214 from 2,752/1,180,030 alleles, and therefore does not override the lower grpmax FAF. The variant also has a strong pathogenic ClinVar consensus (58 pathogenic clinical laboratories and 2 likely pathogenic laboratories), so a default-frequency BA1 stand-alone benign call would be discordant with the available disease evidence.

Rule

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

Evidence considered

• Generic BA1 calibration: >= 0.05, ACMG/AMP 2015 stand-alone benign allele-frequency threshold (PMID:25741868).
• gnomAD v2.1 non-cancer exomes: AF=0.0015364, 364/236,918 alleles, homozygotes=0; FILTERING grpmax FAF=0.00236984.
• gnomAD v4.1 all-comers: AF=0.001921714, 3,102/1,614,184 alleles, homozygotes=5; FILTERING grpmax FAF=0.00225897; highest point-estimate population European (non-Finnish), AF=0.00233214 from 2,752/1,180,030 alleles.
• ClinVar variation 5293: Pathogenic consensus with 58 clinical laboratories, plus 2 likely pathogenic and 2 additional pathogenic submissions; review status criteria provided, multiple submitters, no conflicts.

Sources

Reasoning

BS1 is not met on the available population-frequency evidence. The generic default threshold is >=0.01, and the appropriate FILTERING grpmax FAF is 0.00236984 in gnomAD v2.1 non-cancer exomes and 0.00225897 in gnomAD v4.1 all-comers, both below 1%. The variant is associated with a recessive MUTYH disorder and has a strong pathogenic ClinVar consensus; no per-allele maximum-credible-frequency calculation with explicit prevalence, penetrance, and allelic-heterogeneity inputs supports applying BS1 despite the lower observed FAF.

Rule

Allele frequency is greater than expected for the disorder.

Evidence considered

• Generic BS1 calibration: >= 0.01; per-gene derivation is preferred (Whiffin et al. 2017, PMID:28518168).
• gnomAD v2.1 non-cancer exomes: FILTERING grpmax FAF=0.00236984, based on 364/236,918 exome alleles overall; highest point-estimate population European (non-Finnish), AF=0.00257322 from 304/118,140 alleles.
• gnomAD v4.1 all-comers: FILTERING grpmax FAF=0.00225897; highest point-estimate population European (non-Finnish), AF=0.00233214 from 2,752/1,180,030 alleles.
• The governing framework identifies MUTYH-related familial adenomatous polyposis 2 as autosomal recessive, and ClinVar reports a pathogenic consensus rather than a benign frequency-based consensus.

Sources

Reasoning

BS3 is not met. The available variant-specific functional studies do not show no damaging effect; instead, they consistently demonstrate impaired MUTYH function, including absent or markedly reduced glycosylase activity, defective bacterial complementation, impaired oxidative-DNA repair, increased 8-oxodG, and oxidative-stress hypersensitivity. Therefore, the evidence is directionally incompatible with BS3.

Rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Evidence considered

• Al-Tassan et al. 2002 (PMID:11818965), functional glycosylase assays: the historical Tyr165Cys/Y151Cys-equivalent substitution showed approximately 98% reduced adenine-removal activity.
• Ali et al. 2008 (PMID:18534194), recombinant-protein assay: Y165C generated no detectable glycosylase products under the reported conditions.
• Kundu et al. 2009 (PMID:19836313), enzymatic and bacterial-complementation assays: Y165C had compromised adenine glycosylase activity and mutation frequency similar to the mutY/mutM-deficient strain.
• Molatore et al. 2009 (PMID:19953527), mammalian-cell and purified-protein assays: Y165C lacked detectable 8-oxodG:A glycosylase activity and impaired oxidative-DNA repair.

Sources

Reasoning

The available family evidence does not show lack of segregation. Instead, the variant is reported in trans with Gly382Asp in three affected siblings, while unaffected relatives carried only one variant or neither variant, which is compatible with segregation of the recessive disease genotype.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• Al-Tassan et al. 2002, PMID:11818965, family N segregation analysis: three affected siblings carried Tyr165Cys in trans with Gly382Asp; unaffected relatives carried one variant or neither variant, with no reported affected non-carrier.

Sources

Reasoning

BP2 is not met. MUTYH-associated polyposis is an autosomal recessive disorder in this case, so the BP2 trans pathway, which is limited to a fully penetrant dominant gene/disorder, does not apply. The available family report documents the variant in trans with Gly382Asp, not in cis with a pathogenic variant, and no cis observation for c.452A>G/p.(Y151C) is reported.

Rule

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.

Evidence considered

• The case framework identifies MUTYH-associated polyposis as autosomal recessive.
• Al-Tassan et al. 2002 (PMID:11818965) reported the variant's alternate Tyr165Cys notation in trans/compound heterozygosity with Gly382Asp in affected siblings; it did not report cis configuration with a pathogenic variant.

Still missing

• No report of c.452A>G/p.(Y151C) in cis with a pathogenic MUTYH variant was identified.

Sources

Reasoning

The variant is a missense substitution, p.(Tyr151Cys), so the governing generic rule selects the REVEL path only; SpliceAI cannot substitute for a non-supportive REVEL result. REVEL is 0.963, which is above the BP4 supporting cutoff of <= 0.29, so BP4 is not met. BayesDel has no established generic ACMG-strength calibration and is not used.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Local REVEL predictor lookup: MUTYH NM_001048174.2:c.452A>G, p.(Tyr151Cys), REVEL score 0.963.
• Generic threshold supplied for this interpretation: BP4 supporting requires REVEL <= 0.29, based on the ClinGen SVI REVEL calibration by Pejaver et al. 2022 (PMID:36413997).
• Path selection: a missense variant uses REVEL only; the available SpliceAI score was not used to create BP4 support, and BayesDel has no generic ACMG-strength calibration.

Sources

Reasoning

The reviewed evidence does not report this variant in a case with an established alternate molecular basis for the disease. The family report describes affected individuals with biallelic MUTYH variants, not an alternate molecular diagnosis, so generic BP5 is not met.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• PMID:11818965 reports the variant in trans with another MUTYH variant in affected family members; this is a second MUTYH allele, not an alternate molecular basis for the disease.

Sources

Reasoning

The exact ClinVar record has no expert-panel submission reporting this variant as benign or likely benign. Its aggregate classification is Pathogenic/Likely pathogenic from ordinary submissions, which cannot trigger BP6 under the required generic rule.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 5293, exact NM_001048174.2(MUTYH):c.452A>G (p.Tyr151Cys): aggregate Pathogenic/Likely pathogenic classification and 0 expert-panel submissions; no qualifying expert-panel benign assertion is present.

Sources

Reasoning

No case-specific evidence establishes that the variant arose de novo. The available family report describes affected siblings and familial segregation, but does not document confirmed maternity and paternity for the proband or absence of the variant in both parents.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Still missing

• Confirmed maternity and paternity testing for the proband is not documented.
• The variant status of both biological parents is not documented for a de novo assessment.

Reasoning

PMID:11818965 reports the exact variant under the equivalent notation MYH Tyr165Cys/c.494A>G (corresponding to p.(Y151C)): all three affected siblings in family N carried it, each variant was found once among 100 British controls, and the paper reports an odds ratio of approximately 50:1 assuming full penetrance in compound heterozygotes. This is a case-versus-control comparison and the reported OR satisfies the required direction, 50 > 5, but the paper does not provide a 95% confidence interval; the zero affected-noncarrier cell also prevents deriving a standard uncorrected finite OR/CI from the reported counts. The ACMG/AMP PS4 threshold therefore cannot be fully evaluated. The literature_pass packet has no ai_classified_papers requiring additional PS4 verification.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.

Evidence considered

• Al-Tassan et al. 2002, PMID:11818965: family N had three affected siblings carrying MYH Tyr165Cys in trans with Gly382Asp; the variant was found once among 100 British controls without colorectal adenoma or carcinoma.
• The paper explicitly reports odds ratio≈50:1 assuming full penetrance in compound heterozygotes. The governing PS4 operator is >5.0, so the explicit comparison is 50 > 5.0? yes. However, no 95% confidence interval is reported, and the affected noncarrier cell is zero, so the required confidence-interval condition cannot be verified.

Still missing

• An independent, adequately sized case-control cohort or complete 2x2 counts with a valid confidence interval is needed for formal PS4 assessment.

Sources

Reasoning

The MUTYH VCEP is listed without released criteria, and vcep_materials.json contains no domain-table entry for MUTYH. The available evidence records no statistically significant hotspot for Y151 and does not establish that residue 151 lies in a critical, well-established functional domain without benign variation. A complete domain or hotspot assessment is therefore unavailable under the generic rule.

Rule

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.

Evidence considered

• vcep_materials.json: domain_tables is empty for MUTYH, and the listed InSiGHT specification has no released criteria; generic ACMG/AMP therefore governs.
• Cancer Hotspots result for MUTYH Y151: no statistically significant hotspot row was found.
• No supplied source establishes residue 151 as a critical, well-established functional domain lacking benign variation.

Still missing

• A validated MUTYH critical-domain or hotspot source with residue boundaries and evidence of absent benign variation is required.

Sources

Reasoning

The evidence reviewed confirms the Tyr151Cys substitution but does not identify a different missense change at residue 151 that has been established as pathogenic. The PM5 candidate collection reports zero same-residue candidates, but it is explicitly non-confirmatory and cannot establish that the residue-level search was complete.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• pm5_candidates.json: total_candidates_seen=0 and same_residue_candidates=0, with the artifact warning that classic PM5 semantics could not be confirmed safely.
• PMID:11818965 reports Tyr165Cys, which is the same Tyr151Cys substitution under alternate numbering, not a different missense substitution at the residue; therefore it cannot independently establish PM5.

Still missing

• A complete, validated search for pathogenic alternative missense substitutions at MUTYH residue 151 is required.

Sources

Reasoning

No case-specific evidence establishes an assumed de novo event. The available report describes a familial variant in affected siblings and does not provide a proband-level de novo observation or parental testing information.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Still missing

• A proband-level de novo observation is not documented.
• Parental testing information is not documented.

Reasoning

The supplied evidence documents that MUTYH disease involves pathogenic missense variants and that Tyr151Cys has functional effects, but it does not provide a gene-level missense constraint or benign-missense-rate assessment and does not establish that missense variants are a common disease mechanism relative to other variant classes. The PP2 prerequisites therefore cannot be verified.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• PMID:19836313 reports functional impairment for several MUTYH missense variants, including Y165C, but does not quantify the gene's benign missense rate or establish missense as a common disease mechanism.
• PMID:19953527 reports functional effects for Y165C in cellular and biochemical assays, but likewise does not provide the gene-level missense-rate and mechanism-frequency data required by PP2.
• gnomAD v4.1 reports the case variant frequency (AF 0.00192171; 3102/1614184 alleles) but does not establish the required gene-level benign missense rate.

Still missing

• A validated gene-level assessment of benign missense variation and the relative frequency of missense disease mechanism in MUTYH is required.

Sources

Reasoning

BS2 cannot be established from the available data. gnomAD v4.1 reports 5 homozygotes overall, including 3 in the European (non-Finnish) population, and gnomAD v3.1 non-cancer genomes reports 2 homozygotes. However, these aggregate database counts do not identify individual subjects as healthy adults, do not provide age or phenotype follow-up, and do not demonstrate absence of the expected early-onset phenotype. The non-cancer label alone is insufficient to satisfy the healthy-adult requirement for a fully penetrant recessive disorder.

Rule

Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

Evidence considered

• gnomAD v4.1 all-comers reports 5 homozygotes overall and 3 homozygotes among European (non-Finnish) individuals; the aggregate record does not provide individual age, clinical status, or phenotype follow-up.
• gnomAD v3.1 non-cancer genomes reports 2 homozygotes among 147,924 alleles; the non-cancer cohort label is not equivalent to documented healthy-adult status.
• The disorder context is autosomal recessive MUTYH-related familial adenomatous polyposis 2, but the evidence does not establish that the observed homozygotes were healthy adults with full penetrance expected at an early age.

Still missing

• Individual-level phenotype and age data for the reported homozygotes are unavailable; non-cancer cohort status does not establish healthy-adult status or absence of disease.

Sources

Reasoning

The available MUTYH literature shows both truncating and missense disease-associated variants, including functionally abnormal missense alleles, but does not establish that disease in this gene is caused primarily by truncating variants. The comparative variant-spectrum prerequisite for BP1 is therefore unresolved.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• PMID:16557584 describes biallelic MUTYH disease variants across the coding region and reports recurrent missense variants Y165C and G382D, so it does not establish a primarily truncating disease spectrum.
• PMID:19836313 and PMID:19953527 provide functional evidence for disease-associated MUTYH missense variants, further preventing a conclusion that truncating variants are primarily responsible without a complete comparative spectrum analysis.

Still missing

• A validated MUTYH disease-variant spectrum demonstrating that truncating variants predominate is required.

Sources