APC c.4237A>G, p.(Met1413Val)

Reasoning

The governing APC InSiGHT VCEP specifies BS1 Strong at gnomAD Popmax filtering AF >= 0.00001. gnomAD v4.1 reports Popmax filtering AF 0.00023147, exceeding the threshold; gnomAD v2.1 independently reports 0.00020478.

Rule

APC InSiGHT VCEP v2.1 BS1 Strong: gnomAD Popmax Filtering AF >= 0.00001.

Evidence considered

• The APC InSiGHT VCEP version 2.1 specifies BS1 Strong as gnomAD Popmax Filtering Allele Frequency >= 0.001% (0.00001).
• gnomAD v4.1 reports Popmax filtering AF 0.00023147, based on the joint dataset; this exceeds 0.00001. gnomAD v2.1 also reports grpmax FAF 0.00020478.

Sources

Reasoning

The APC VCEP applies BP1 to APC missense variants except those located in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035. This variant is p.Met1413Val at codon 1413, outside that exception, so BP1 Supporting is met.

Rule

BP1 Supporting is applicable to APC missense variants except missense variants located in the first 15-amino-acid repeat of the beta-catenin-binding domain (codons 1021-1035).

Evidence considered

• The APC VCEP BP1 rule is applicable to APC missense variants except those in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035.
• The assessed protein change is p.Met1413Val, placing the residue at codon 1413, outside the codon 1021-1035 exception.

Sources

Reasoning

PVS1 is not met. NM_001127510.3:c.4237A>G produces the missense substitution NP_001120982.1:p.(Met1413Val), not a predicted loss-of-function null consequence such as nonsense, frameshift, or canonical splice disruption. The APC InSiGHT VCEP specification establishes APC loss of function as a disease mechanism and provides a PVS1 decision tree for null variants, but this missense variant does not enter that tree; therefore no PVS1 strength is assigned. The exact M1413V substitution was reported in a study of APC missense variation, supporting its missense consequence rather than a truncating or splice-altering effect.

Rule

APC InSiGHT VCEP PVS1 specification: PVS1 applies to null variants in APC, with strength determined by the modified APC PVS1 decision tree; this missense variant is outside the eligible null-variant categories.

Evidence considered

• The APC InSiGHT VCEP specification states that APC loss of function is a known disease mechanism and provides PVS1 guidance for null variants through its modified decision tree.
• The case consequence is NM_001127510.3:c.4237A>G with protein change NP_001120982.1:p.(Met1413Val), a missense substitution; it is not a nonsense, frameshift, or canonical ±1,2 splice variant.
• PMID:20233475 reports M1413V as an APC missense change identified in patients and relatives, with no evidence that it creates a premature termination or splice consequence.

Sources

Reasoning

The APC VCEP permits PS1 for the same amino-acid change when a previously established pathogenic or likely pathogenic missense variant exists. The variant is p.Met1413Val, but the governing APC framework identifies only p.Asn1026Ser and p.Ser1028Arg as established likely pathogenic missense variants and states that no missense variant has been classified as pathogenic on current evidence. The directly relevant literature reports M1413V in a polyposis patient and healthy controls, including unaffected relatives, and does not establish it as pathogenic.

Rule

The previously established variant was classified as Pathogenic or Likely Pathogenic according to the APC-specific modifications; for missense variants, the assessed variant must result in the same amino-acid change.

Evidence considered

• The APC VCEP PS1 rule requires the same amino-acid change as a previously established pathogenic or likely pathogenic variant; it names c.3077A>G p.(Asn1026Ser) and c.3084T>A p.(Ser1028Arg) as the only established likely pathogenic missense variants and states that no APC missense variant has been classified as pathogenic on current evidence.
• M1413V was reported in one patient and three unrelated healthy controls; the publication did not provide variant-specific functional or segregation evidence establishing pathogenicity.
• A second publication reported M1413V in two patients, including one with unaffected relatives carrying the same combination and another with a separate premature-termination mutation, and stated that the missense changes could not be unequivocally associated with altered APC function or polyposis risk.

Sources

Reasoning

The APC VCEP specifies PS4 using phenotype points: the governing rules state "≥ 16 phenotype points" for Very Strong, "4-15.5 phenotype points" for Strong, "2-3.5 phenotype points" for Moderate, and "1-1.5 phenotype point" for Supporting, with phenotype curation governed by Table 1. The most directly relevant exact-protein-variant report found M1413V in one non-FAP, non-MUTYH-associated polyposis patient and in three unrelated healthy controls; the report provides no variant-specific segregation or case-control enrichment estimate. The 11–99 adenoma category does not establish a single Table 1 point value for the individual, and the observation in three healthy controls weighs against a specific disease association. Accordingly, no valid phenotype-point total reaches a VCEP PS4 threshold. The source's generic case-control statement uses OR >5.0 with a confidence interval excluding 1.0, but no OR or confidence interval was reported here; no numeric inequality can therefore be formed for that alternative route.

Rule

APC VCEP PS4: ≥ 16 phenotype points = Very Strong; 4-15.5 phenotype points = Strong; 2-3.5 phenotype points = Moderate; 1-1.5 phenotype point = Supporting. For case-control evidence, the governing source describes OR >5.0 with a confidence interval excluding 1.0.

Evidence considered

• The APC VCEP PS4 rule assigns Very Strong at ≥16 phenotype points, Strong at 4–15.5, Moderate at 2–3.5, and Supporting at 1–1.5 phenotype points; Table 1 defines the phenotype scoring.
• PMID:18199528 reports M1413V in one non-FAP, non-MUTYH-associated polyposis patient with 11–99 colorectal adenomas and in three unrelated healthy controls.
• PMID:20233475 reports M1413V in two patients; one had the change with D1822V and unaffected relatives shared the combination, while the other had a separate APC premature-termination mutation.
• The available exact-variant reports provide no odds ratio, relative risk, confidence interval, or unambiguous VCEP phenotype-point total.

Still missing

• A VCEP-scored phenotype-point total for each exact-variant proband is not available.
• No exact-variant case-control odds ratio, relative risk, or confidence interval is available.

Sources

Reasoning

The governing APC InSiGHT VCEP specifies PM2 Supporting as allele frequency <= 0.000003 when allele count is >1, or <0.00001 when allele count is <=1. gnomAD v4.1 reports 350/1,614,118 alleles (AF 0.000216837), and gnomAD v2.1 reports 56/282,408 alleles (AF 0.000198295), so the variant is far above the APC rarity thresholds. No APC VCEP instruction requires a non-cancer subset, so all-comers totals are the governing default.

Rule

APC InSiGHT VCEP v2.1 PM2 Supporting: AF <= 0.000003 if allele count >1, or AF <0.00001 if allele count <=1.

Evidence considered

• The APC InSiGHT VCEP version 2.1 specifies PM2 Supporting as AF <= 0.000003 when allele count is >1, or AF <0.00001 when allele count is <=1.
• gnomAD v4.1 reports total AF 0.000216837, with 350 of 1,614,118 alleles and 0 homozygotes; this exceeds the applicable 0.000003 threshold.
• gnomAD v2.1 reports total AF 0.000198295, with 56 of 282,408 alleles and 0 homozygotes; this also exceeds the applicable 0.000003 threshold.
• The APC VCEP specification does not require a non-cancer or exome-only population source for PM2, so the all-comers gnomAD totals are used.

Sources

Reasoning

The variant is missense (p.(Met1413Val)), so PP3 must use the missense REVEL path only. REVEL is 0.587, below the generic ClinGen SVI supporting threshold of 0.644 from Pejaver et al. 2022 (PMID:36413997), and therefore does not meet PP3. The SpliceAI result is not used to support PP3 for a missense variant.

Rule

Missense variant: evaluate PP3 using REVEL only; supporting requires REVEL >=0.644 under the supplied generic calibration. APC VCEP framework: PP3 supporting.

Evidence considered

• The APC ClinGen InSiGHT VCEP framework specifies PP3 as supporting for applicable computational evidence, but this missense assessment uses the required REVEL path only.
• REVEL score is 0.587; the supplied ClinGen SVI calibration defines missense PP3 supporting at >=0.644 (Pejaver et al. 2022, PMID:36413997).
• SpliceAI is not used for missense PP3 because the criterion must be evaluated from the single consequence-matched predictor path.

Sources

Reasoning

The governing APC InSiGHT VCEP specifies BA1 at gnomAD Popmax filtering AF >= 0.001. gnomAD v4.1 reports a Popmax filtering AF of 0.00023147, and gnomAD v2.1 reports 0.00020478; neither reaches the APC stand-alone benign threshold.

Rule

APC InSiGHT VCEP v2.1 BA1: gnomAD Popmax Filtering AF >= 0.001.

Evidence considered

• The APC InSiGHT VCEP version 2.1 specifies BA1 as gnomAD Popmax Filtering Allele Frequency >= 0.1% (0.001).
• gnomAD v4.1 reports Popmax filtering AF 0.00023147 (joint grpmax FAF); gnomAD v2.1 reports grpmax FAF 0.00020478. Both are below 0.001.

Sources

Reasoning

The APC InSiGHT VCEP requires at least 2 homozygous observations for BS2 Strong or at least 3 healthy-individual points for BS2 Supporting. gnomAD v4.1 and v2.1 each report 0 homozygotes. PMID:18199528 reports M1413V in three healthy controls, but APC VCEP scoring assigns 0.5 points to a healthy-control observation, totaling 1.5 points, below the supporting threshold. PMID:20233475 reports one homozygous patient and the same combination in unaffected relatives, without documenting at least two qualifying homozygous observations.

Rule

APC InSiGHT VCEP v2.1 BS2: Strong requires >=10 healthy-individual points or >=2 homozygous observations; Supporting requires >=3 healthy-individual points.

Evidence considered

• The APC InSiGHT VCEP version 2.1 specifies BS2 Strong for >=2 homozygous observations or >=10 healthy-individual points, and BS2 Supporting for >=3 healthy-individual points; a healthy control defined by control/non-cancer/normal/unaffected terminology contributes 0.5 points.
• gnomAD v4.1 reports 0 homozygotes and gnomAD v2.1 reports 0 homozygotes for this variant.
• PMID:18199528 reports M1413V in three unrelated healthy controls. Applying the APC VCEP value of 0.5 points per healthy-control observation gives 1.5 points, below the 3-point BS2 Supporting threshold.
• PMID:20233475 reports M1413V homozygous in one patient and the same M1413V/D1822V combination in unaffected relatives, but does not document at least two qualifying homozygous observations with sufficient clinical detail for the APC BS2 rule.

Sources

Reasoning

The APC VCEP permits BP5 at Supporting only for an alternate genetic basis of a colorectal polyposis phenotype, specifically a (Likely) Pathogenic variant in another adenomatous polyposis gene such as POLD1, POLE, MUTYH, NTHL1, MSH3, or specified mismatch-repair genes. The case evidence identifies no such pathogenic variant. The separate premature-termination variant reported in PMID:20233475 was in APC itself, not another gene, and does not satisfy the BP5 rule.

Rule

APC VCEP BP5: Supporting, only applicable for an alternate genetic basis of the colorectal polyposis phenotype; the instructions specify (Likely) Pathogenic variants in another adenomatous polyposis gene.

Evidence considered

• The APC VCEP BP5 rule requires an alternate genetic basis of colorectal polyposis, specifically a (Likely) Pathogenic variant in another adenomatous polyposis gene.
• PMID:20233475 states that one M1413V carrier also had a separate mutation causing a premature termination codon, but the reported gene context is APC; this is not an alternate-gene basis for BP5.

Still missing

• No independent molecular result for another adenomatous polyposis gene is available in the reviewed evidence.

Sources

Reasoning

The APC VCEP requires at least 1 de novo score for PS2 at Moderate strength, 2–3.5 scores for Strong, or ≥4 scores for Very Strong. The available case evidence does not document the proband's phenotype together with confirmed maternity and paternity, nor does it provide a validated de novo observation for this variant. Therefore PS2 cannot be applied.

Rule

APC VCEP Version 2.1: PS2 Moderate requires 1–1.5 de novo scores; Strong requires 2–3.5; Very Strong requires ≥4, with de novo scores curated using Tables 1 and 2.

Evidence considered

• The APC VCEP PS2 rule assigns Moderate strength at 1–1.5 de novo scores, Strong at 2–3.5 de novo scores, and Very Strong at ≥4 de novo scores.
• No source in the reviewed case evidence documents confirmed maternity and paternity for this proband or a validated de novo event for APC c.4237A>G (p.Met1413Val).

Still missing

• Proband-level report documenting the phenotype and the variant result.
• Variant testing results for both biological parents, with maternity and paternity confirmation.
• Evidence excluding parental mosaicism or other alternative inheritance explanations if de novo status is claimed.

Sources

Reasoning

The APC InSiGHT VCEP specifies PS3 for variant-level functional evidence: RNA assays demonstrating a premature stop codon or relevant exon skipping with transcript loss, or protein assays showing increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding for variants in codons 959-2129. This missense variant encodes p.(Met1413Val), within that domain, but the reviewed literature provides no variant-specific functional assay result. PMID:20233475 reports M1413V in patients and unaffected relatives and states that the missense changes, including M1413V, could not be unequivocally associated with altered APC protein function; PMID:18199528 reports M1413V in a patient and healthy controls without a functional assay; PMID:21859464 is a review stating that most APC missense mutations remain functionally uncharacterized; and PMID:23085758 does not mention M1413V and provides no variant-specific functional data. Therefore, the evidence is insufficient to apply PS3 at any strength.

Rule

APC VCEP PS3: damaging RNA assay findings or, for variants in codons 959-2129, increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding by protein assay; strength depends on the specified RNA result.

Evidence considered

• The APC InSiGHT VCEP PS3 rule requires specified damaging RNA findings or, for variants in codons 959-2129, increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding by protein assay.
• PMID:20233475 reports APC M1413V in two patients, including one with a separate premature-termination mutation, and in unaffected relatives; the authors state that the missense changes could not be unequivocally associated with altered APC protein function or polyposis risk.
• PMID:18199528 reports M1413V in one non-FAP/non-MUTYH-associated polyposis patient and three healthy controls, without a variant-specific functional assay result.
• PMID:21859464 states that most APC missense mutations remain functionally uncharacterized and that their molecular consequences remain unresolved; it does not report this variant-specific assay.
• PMID:23085758 does not explicitly mention M1413V and provides no variant-specific functional evidence.

Still missing

• A validated, variant-specific RNA or protein functional assay result is unavailable.
• No assay result establishes altered beta-catenin-regulated transcription or beta-catenin binding for p.(Met1413Val).

Sources

Reasoning

The APC VCEP PM5 rule requires a different missense change at the same residue that is established as pathogenic or likely pathogenic under APC-specific modifications, with the assessed substitution meeting or exceeding the comparator's Grantham distance. The reviewed evidence identifies p.Met1413Val but no qualifying alternate missense variant at residue 1413. The same-residue candidate retrieval also ended with an HTTP 429 rate-limit error, so the absence of a comparator cannot be treated as a complete negative search.

Rule

For PM5 Moderate or Supporting, a different missense variant at the same residue must be established as Pathogenic or Likely Pathogenic according to APC-specific modifications; the assessed variant's Grantham distance must be equal to or higher than the reported comparator's.

Evidence considered

• The APC VCEP PM5 rule requires a different missense variant at the same amino-acid position that is pathogenic or likely pathogenic under APC-specific modifications, and requires the assessed variant's Grantham distance to be at least as high as the comparator's.
• The collected PM5 candidate artifact contains zero same-residue candidates and records an HTTP 429 rate-limit error, so it does not establish that no comparator exists.
• The reviewed papers document M1413V but do not identify a qualifying alternate missense comparator at residue 1413.

Still missing

• A complete same-residue search for APC missense variants at codon 1413, including pathogenic or likely pathogenic classifications and Grantham distances, is still required.

Sources

Reasoning

The APC VCEP permits PM6 at Supporting strength for 0.5 de novo score, Moderate strength for 1–1.5 scores, and Strong strength for 2–3.5 scores when de novo status is assumed without confirmed paternity and maternity. The reviewed evidence does not describe a proband with this variant as apparently de novo or provide parental testing results, so there is no basis to assign a PM6 de novo score.

Rule

APC VCEP Version 2.1: PM6 Supporting requires 0.5 de novo score; Moderate requires 1–1.5; Strong requires 2–3.5, with de novo scores curated using Tables 1 and 2.

Evidence considered

• The APC VCEP PM6 rule assigns Supporting strength at 0.5 de novo score, Moderate strength at 1–1.5 scores, and Strong strength at 2–3.5 scores.
• The reviewed variant-specific reports describe M1413V in patients and controls but do not document an apparently de novo occurrence or parental testing for this variant.

Still missing

• A case report or laboratory record identifying the variant in a proband and describing it as apparently de novo.
• Parental genotype information, even if maternity and paternity are not confirmed.
• Proband phenotype information needed for the APC VCEP de novo scoring tables.

Sources

Reasoning

The APC VCEP requires segregation in 3–4 meioses for PP1 Supporting, 5–6 meioses for Moderate, or ≥7 meioses in ≥2 families for Strong. PMID:20233475 reports M1413V in two patients and identifies the same variant combination in unaffected relatives; PMID:18199528 lists M1413V in one affected individual and three healthy controls, without variant-specific segregation analysis. These reports do not establish qualifying affected meioses in one or more families, so PP1 is not assessed.

Rule

APC VCEP Version 2.1: PP1 Supporting requires segregation in 3–4 meioses in at least 1 family; Moderate requires 5–6 meioses in at least 1 family; Strong requires ≥7 meioses in at least 2 families.

Evidence considered

• The APC VCEP PP1 rule requires 3–4 segregating meioses for Supporting, 5–6 for Moderate, or ≥7 segregating meioses in at least 2 families for Strong.
• PMID:20233475 reports M1413V in two patients and states that the same M1413V/D1822V combination was found in unaffected relatives; it does not provide a qualifying count of segregating affected meioses.
• PMID:18199528 lists M1413V in one non-FAP, non-MUTYH-associated polyposis patient and three healthy controls and reports no variant-specific segregation analysis.

Still missing

• Pedigree-level genotype and phenotype data for affected relatives.
• A countable number of informative affected meioses involving APC c.4237A>G.
• Family identifiers and phenotype details sufficient to determine whether the observations represent segregation or non-segregation.

Sources

Reasoning

The APC InSiGHT VCEP specifies BS3 Supporting when a protein assay shows retention of beta-catenin-regulated transcription activity comparable to wild type for a variant within the beta-catenin binding domain, and BS3 Strong for qualifying RNA evidence with biallelic expression and/or nonsense-mediated decay inhibition. This missense variant encodes p.(Met1413Val), within the specified codon 959-2129 domain, but no reviewed source reports a variant-specific assay showing retained wild-type activity, normal splicing, biallelic expression, or NMD inhibition. PMID:20233475 explicitly states that M1413V could not be unequivocally associated with altered APC protein function, while PMID:18199528 reports the variant without a functional assay. Thus, the available evidence cannot establish BS3 at Supporting or Strong strength.

Rule

APC VCEP BS3: Strong requires a qualifying RNA assay with no mRNA aberration plus biallelic expression and/or NMD inhibition; Supporting requires such RNA evidence without those controls or a protein assay showing beta-catenin-regulated transcription comparable to wild type for codons 959-2129.

Evidence considered

• The APC InSiGHT VCEP BS3 rule allows Supporting evidence from a protein assay showing beta-catenin-regulated transcription comparable to wild type for variants in codons 959-2129, or Strong evidence from qualifying RNA assays with biallelic expression and/or NMD inhibition.
• PMID:20233475 reports M1413V in patients and unaffected relatives but states that the missense changes could not be unequivocally associated with altered APC protein function; it does not provide a qualifying benign functional assay.
• PMID:18199528 reports M1413V in a patient and healthy controls without a variant-specific functional assay result.
• PMID:21859464 provides general discussion that most APC missense mutations remain functionally uncharacterized and does not establish normal function for M1413V.
• PMID:23085758 does not explicitly mention M1413V and provides no variant-specific benign functional assay evidence.

Still missing

• A variant-specific protein assay demonstrating beta-catenin-regulated transcription comparable to wild type is unavailable.
• No qualifying RNA assay demonstrates normal mRNA processing with the VCEP-required controls.

Sources

Reasoning

The APC VCEP requires an affected member without the variant who scores at least 1 phenotype point for BS4 Strong, or one affected noncarrier scoring at least 0.5 points for BS4 Supporting; alternatively, two affected noncarriers must each score at least 0.5 points for Strong. The available reports describe M1413V in unaffected relatives and healthy controls, but do not document an affected noncarrier with the required APC phenotype score. Therefore the VCEP BS4 threshold is not established.

Rule

APC VCEP Version 2.1: BS4 Strong requires an affected member without the variant scoring at least 1 phenotype point or two affected members without the variant each scoring at least 0.5 points; Supporting requires one affected member without the variant scoring at least 0.5 points.

Evidence considered

• The APC VCEP BS4 rule requires one affected member without the variant scoring at least 1 phenotype point, or one affected noncarrier scoring at least 0.5 points for Supporting; two affected noncarriers each scoring at least 0.5 points satisfy Strong.
• PMID:20233475 reports the M1413V/D1822V combination in unaffected relatives, not an affected noncarrier meeting the APC phenotype-point threshold.
• PMID:18199528 reports M1413V in three healthy controls but does not provide affected noncarrier segregation evidence.

Still missing

• Affected relatives' genotype results showing absence of APC c.4237A>G.
• Phenotype details sufficient to assign APC VCEP Table 1 phenotype points to affected noncarriers.
• Family-level information confirming that any noncarrier is an informative affected relative.

Sources

Reasoning

The APC VCEP permits BP2 at Supporting strength when the variant is observed in trans with a (Likely) Pathogenic APC variant, or at least three times with different (Likely) Pathogenic APC variants in unknown phase. PMID:20233475 reports M1413V in one patient who also carried a premature-termination APC mutation, but does not establish phase and provides only one such observation; the available evidence therefore cannot satisfy either APC-specific BP2 route.

Rule

Observed in trans with a (Likely) Pathogenic APC variant OR ≥ 3 times in an unknown phase with different (Likely) Pathogenic APC variants; Supporting.

Evidence considered

• The APC VCEP BP2 rule requires observation in trans with a (Likely) Pathogenic APC variant, or at least three observations in unknown phase with different (Likely) Pathogenic APC variants.
• PMID:20233475 reports: "The second patient found to have the M1413V change was subsequently shown to harbour a mutation, which resulted in a premature termination codon." The report does not establish whether the two variants were in trans or cis, and it describes only one such patient.

Still missing

• Phase between M1413V and the reported premature-termination APC variant is not established.
• Fewer than the three unknown-phase observations required by the APC VCEP are documented.

Sources