MSH6 c.3787C>T, p.(Arg1263Cys)

Reasoning

The variant is a missense substitution, so the governing MSH6 missense BP4 rule applies. The exact MSH6 HCI prior entry for c.3787C>T/p.R1263C reports a pathogenicity probability of 0.0236, below the VCEP BP4 supporting threshold of <0.11; this pre-assigned gene-specific result governs over generic predictor thresholds. REVEL is 0.594 and does not independently meet the generic BP4 supporting threshold <=0.29 from Pejaver et al. 2022 (PMID:36413997). BayesDel is 0.306998 and is not interpretable for ACMG strength because no generic BayesDel calibration is established and no MSH6 cutoff is specified. SpliceAI is not evaluated for BP4 because this is not a splice-region or intronic variant.

Rule

MSH6 VCEP: missense HCI prior probability <0.11 = BP4_Supporting. The exact gene-specific HCI assignment governs.

Evidence considered

• The governing MSH6 CSPEC specifies BP4 supporting for a missense variant with HCI prior probability <0.11.
• The exact HCI lookup entry for c.3787C>T / p.R1263C reports pathogenicity probability 0.0236, which meets the governing MSH6 BP4 supporting rule.
• REVEL score 0.594 does not meet the generic BP4 supporting cutoff <=0.29; that calibration is from Pejaver et al. 2022 (PMID:36413997).
• BayesDel score 0.306998 is not independently actionable because no generic ACMG strength calibration exists and the governing MSH6 specification provides no BayesDel cutoff.
• The variant is missense; SpliceAI is therefore outside the BP4 splice-impact path scope for this variant.

Sources

Reasoning

The governing MSH6 VCEP defines PS1 as a missense substitution producing the same amino-acid change through a different nucleotide change, with the comparator previously established by the VCEP as Pathogenic and not attributable to aberrant splicing. The available evidence identifies NM_000179.3:c.3787C>T as p.Arg1263Cys, but provides no qualifying alternate-nucleotide p.Arg1263Cys comparator established as Pathogenic by this VCEP. The exact-variant literature record reports p.R1263C as a somatic gastric-cancer mutation without a VCEP pathogenic classification or criterion-bearing functional evidence. Therefore PS1 is not met.

Rule

MSH6 VCEP PS1: a predicted missense substitution encoding the same amino-acid change with a different nucleotide change previously established by this VCEP as Pathogenic, and not a predicted or confirmed splice defect.

Evidence considered

• The MSH6 VCEP PS1 rule requires the same amino-acid change from a different nucleotide change and prior VCEP establishment of the comparator as Pathogenic, excluding splice defects.
• The case variant is NM_000179.3:c.3787C>T, p.Arg1263Cys; no qualifying alternate-nucleotide p.Arg1263Cys comparator is present in the reviewed evidence.
• PMID:25583476 reports MSH6 p.R1263C as a somatic mutation in a gastric-cancer case but does not provide a VCEP pathogenic classification or qualifying functional evidence.

Sources

Reasoning

The governing MSH6 InSiGHT VCEP specifies PM2 Supporting for an allele frequency below 0.00002 (<1 in 50,000 alleles) in gnomAD v4. The default all-comers gnomAD v4.1 dataset is applicable because the VCEP does not specify a non-cancer or exome-only subset for PM2. The observed total allele frequency is 38/1,613,930 = 2.3545e-05, which is above 0.00002; the highest subpopulation AF is 4.00545e-05. Although the joint grpmax FAF is 1.994e-05, the VCEP PM2 rule says allele frequency rather than grpmax FAF, so PM2 is not met on the reported total AF.

Rule

Absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 dataset.

Evidence considered

• The MSH6 InSiGHT VCEP v2.0 PM2 Supporting rule requires allele frequency <0.00002 (<1 in 50,000 alleles) in the gnomAD v4 dataset.
• The VCEP PM2 rule does not specify a non-cancer or exome-only subset, so the all-comers gnomAD v4.1 entry is used rather than GNOMAD_V2_1_NON_CANCER.
• gnomAD v4.1 reports 38/1,613,930 alleles, total AF 2.3545e-05, highest subpopulation AF 4.00545e-05, and joint grpmax FAF 1.994e-05.
• Because the VCEP PM2 wording specifies allele frequency without a grpmax qualifier, the total AF is the decisive metric and exceeds 0.00002.

Sources

Reasoning

The governing MSH6 VCEP requires a different missense change at the same amino-acid residue that is classified by the VCEP as Pathogenic or Likely Pathogenic at the protein level and not because of aberrant splicing; it further requires PP3 Supporting for the current missense variant. The reviewed PM5 comparator search found zero same-residue candidates at Arg1263, and no qualifying VCEP Pathogenic or Likely Pathogenic comparator is otherwise documented. The available HCI prior for the current variant is 0.0236, below the VCEP PP3 Supporting threshold of >0.68, so the prerequisite PP3 Supporting evidence is not met. Therefore PM5 is not met.

Rule

MSH6 VCEP PM5: same-residue different missense change classified by this VCEP as Pathogenic or Likely Pathogenic at the protein level, not due to aberrant splicing; use only when PP3 Supporting is met.

Evidence considered

• The MSH6 VCEP PM5 rule requires a different missense change at the same residue classified by the VCEP as Pathogenic or Likely Pathogenic at the protein level, not due to aberrant splicing, and requires PP3 Supporting for the current variant.
• The PM5 comparator collection reports zero same-residue candidates, zero expert-panel Pathogenic/Likely Pathogenic candidates, and no useful comparator.
• The MSH6 HCI prior for c.3787C>T/p.R1263C is 0.0236; the VCEP PP3 Supporting threshold is >0.68, so the PM5 prerequisite is absent.

Sources

Reasoning

The variant is a missense substitution, so the MSH6 missense computational path applies. The governing MSH6 HCI prior entry for c.3787C>T/p.R1263C is 0.0236, which is below the VCEP PP3 thresholds (>0.68 for supporting and >0.81 for moderate). REVEL is 0.594, below the ClinGen SVI supporting threshold of 0.644 from Pejaver et al. 2022 (PMID:36413997). BayesDel is 0.306998, but no generic ACMG strength calibration is established for BayesDel and the MSH6 VCEP does not specify a BayesDel cutoff. SpliceAI is not evaluated for PP3 because this is not a splice-region or intronic variant.

Rule

MSH6 VCEP: missense HCI prior >0.81 = PP3_Moderate; >0.68 and <=0.81 = PP3_Supporting. Generic REVEL supporting threshold >=0.644 per ClinGen SVI calibration.

Evidence considered

• The governing MSH6 CSPEC specifies PP3 moderate for an HCI prior probability >0.81 and PP3 supporting for >0.68 and <=0.81.
• The exact HCI lookup entry for c.3787C>T / p.R1263C reports pathogenicity probability 0.0236, so it does not meet the MSH6 PP3 threshold.
• REVEL score 0.594 does not meet the ClinGen SVI supporting cutoff >=0.644; the cutoff is from Pejaver et al. 2022 (PMID:36413997).
• BayesDel score 0.306998 is not actionable because no generic ACMG strength calibration exists and the governing MSH6 specification provides no BayesDel cutoff.
• The variant is missense; SpliceAI is therefore outside the PP3 path scope for this variant.

Sources

Reasoning

The governing MSH6 InSiGHT VCEP specifies BA1 when the gnomAD v4 grpmax filtering allele frequency is at least 0.0022 (0.22%) and the variant is not a founder pathogenic variant. In gnomAD v4.1, the all-comers joint grpmax FAF is 0.00001994 (1.994e-05; 0.001994%), far below 0.0022; therefore BA1 is not met. The highest subpopulation AF is 0.0000400545 (4.00545e-05), also far below the threshold. No founder-pathogenic designation is documented, but the frequency requirement independently fails.

Rule

GnomAD v4 Grpmax filtering allele frequency ≥ 0.0022 (0.22%) and variant is excluded as founder pathogenic variant.

Evidence considered

• The MSH6 InSiGHT VCEP v2.0 rule requires gnomAD v4 grpmax filtering allele frequency ≥0.0022 (0.22%) and exclusion of a founder pathogenic variant.
• gnomAD v4.1 reports all-comers joint grpmax FAF 1.994e-05, total AF 2.3545e-05, and highest subpopulation AF 4.00545e-05; all are below the BA1 threshold.
• No founder-pathogenic designation is documented for this variant; this does not alter the independent failure of the frequency threshold.

Sources

Reasoning

The governing MSH6 InSiGHT VCEP specifies BS1 Strong when the gnomAD v4 grpmax filtering allele frequency is at least 0.00022 and below 0.0022 (0.022–0.22%), with the variant excluded as a founder pathogenic variant. gnomAD v4.1 reports a joint grpmax FAF of 0.00001994 (1.994e-05; 0.001994%), below the lower bound. The highest subpopulation AF is 0.0000400545 (4.00545e-05), also below 0.00022; therefore BS1 is not met.

Rule

GnomAD v4 Grpmax filtering allele frequency ≥ 0.00022 and < 0.0022 (0.022-0.22%) and variant is excluded as founder pathogenic variant.

Evidence considered

• The MSH6 InSiGHT VCEP v2.0 rule requires gnomAD v4 grpmax filtering allele frequency ≥0.00022 and <0.0022 (0.022–0.22%) and exclusion of a founder pathogenic variant.
• gnomAD v4.1 reports all-comers joint grpmax FAF 1.994e-05 and highest subpopulation AF 4.00545e-05, both below 0.00022.

Sources

Reasoning

The MSH6 InSiGHT VCEP requires a documented proband-level de novo observation, with point assignment based on confirmed maternity and paternity and the presence or absence of MMR-deficient Lynch syndrome-spectrum tumor data: 2 points when both parents are confirmed and tumor findings are consistent, 1 point when both parents are confirmed without tumor data, or 0.5 points when de novo status is assumed with one or both parents unconfirmed. The available case evidence does not document a proband, parental testing, maternity or paternity confirmation, de novo testing, or qualifying tumor MSI/IHC/methylation results for NM_000179.3:c.3787C>T; therefore no PS2 points or strength can be assigned.

Rule

MSH6 VCEP PS2: >=4 de novo points = Very Strong; 2-3.5 points = Strong; 1-1.5 points = Moderate; 0.5 points = Supporting.

Evidence considered

• The MSH6 InSiGHT VCEP PS2 specification assigns 2 points for confirmed maternity and paternity with an MMR-deficient Lynch syndrome-spectrum tumor, 1 point for confirmed maternity and paternity without tumor data, and 0.5 points for assumed de novo status with maternity and/or paternity unconfirmed.
• The available case records contain no documented proband-level de novo observation, parental testing, parental confirmation, or qualifying tumor MSI/IHC/methylation result for NM_000179.3:c.3787C>T.

Still missing

• Proband identity and phenotype are not documented.
• Maternity and paternity confirmation are not documented.
• Parental genotypes and de novo testing results are not documented.
• No qualifying tumor MSI, IHC, or methylation results are documented.

Sources

Reasoning

The applicable ClinGen InSiGHT MSH6 VCEP requires calibrated functional odds greater than 2.08 for PS3_Supporting, greater than 4.3 and up to 18.7 for PS3_Moderate, or greater than 18.7 for PS3_Strong; alternatively, PS3_Moderate can be supported by an MMR function defect following the VCEP functional-assay flowchart. The available evidence contains no variant-specific calibrated functional odds, MMR functional assay result, or monoallelic-expression result for NM_000179.3:c.3787C>T (p.Arg1263Cys). The cited report of p.R1263C in a gastric-cancer tumor is a sequencing observation and explicitly provides no functional assay result, so PS3 cannot be assigned.

Rule

Calibrated functional assays with functional odds for pathogenicity > 18.7; PS3_Moderate at >4.3 and <=18.7 or an MMR function defect following the functional assay flowchart; PS3_Supporting at >2.08 and <=4.3.

Evidence considered

• The MSH6 VCEP PS3 thresholds are functional odds for pathogenicity >2.08 and <=4.3 for Supporting, >4.3 and <=18.7 for Moderate, and >18.7 for Strong.
• The MSH6 VCEP also permits PS3_Moderate for an MMR function defect following its functional-assay flowchart or for complete loss of variant-allele expression (<10% of wild-type in cDNA without puromycin) with full-length transcript analysis with and without NMD block.
• The available variant-specific publication extraction reports p.R1263C in a gastric-cancer tumor but states that no functional assay results were provided.

Still missing

• Variant-specific calibrated MMR functional assay with functional odds or a validated quantitative multifactorial functional likelihood ratio.
• Alternatively, two concordant MMR assays interpreted through the MSH6 VCEP functional-assay flowchart, or qualifying monoallelic-expression evidence.

Sources

Reasoning

The MSH6 InSiGHT VCEP specifies PM3 for co-occurrence of a known pathogenic or likely pathogenic variant in the same gene with clinical features consistent with constitutional mismatch repair deficiency: a confirmed pathogenic/likely pathogenic variant in trans contributes 1.0 point, whereas phase-unknown co-occurrence contributes 0.5 points; the total determines strength (supporting at 0.5, moderate at 1–1.5, strong at 2–3.5, and very strong at ≥4 points). This case provides no documented affected proband with CMMRD features, second pathogenic/likely pathogenic MSH6 variant, or phase information, so no PM3 points can be assigned.

Rule

MSH6 InSiGHT VCEP PM3: co-occurrence with a known pathogenic/likely pathogenic sequence variant in the same gene in a patient with clinical features consistent with CMMRD; pathogenic/likely pathogenic in trans = 1.0 point, phase unknown = 0.5 points; supporting = 0.5 points, moderate = 1–1.5 points, strong = 2–3.5 points, very strong = ≥4 points.

Evidence considered

• The MSH6 InSiGHT VCEP PM3 rule requires co-occurrence with a known pathogenic/likely pathogenic variant in the same gene in a patient with CMMRD-consistent clinical features; confirmed trans phase earns 1.0 point and unknown phase earns 0.5 points.
• No affected-proband CMMRD phenotype, second pathogenic/likely pathogenic MSH6 variant, or phase result is documented for NM_000179.3:c.3787C>T (p.Arg1263Cys).

Still missing

• Affected-proband clinical features consistent with CMMRD are not documented.
• A second pathogenic or likely pathogenic MSH6 variant is not documented.
• Parental, offspring, or other testing establishing trans phase is not documented.

Sources

Reasoning

The MSH6 InSiGHT VCEP requires co-segregation in one or more pedigrees quantified with a combined Bayes likelihood ratio, using multiplication across multiple pedigrees: supporting requires a ratio >2.08 and <=4.3, moderate requires >4.3 and <=18.7, and strong requires >18.7 in at least two families. No pedigree, affected-relative genotype, unaffected-relative genotype, meiosis count, segregation likelihood ratio, or COOL analysis result is documented for this variant, so PP1 cannot be assessed.

Rule

MSH6 VCEP PP1: supporting if combined Bayes likelihood ratio >2.08 and <=4.3; moderate if >4.3 and <=18.7; strong if >18.7 in at least 2 families.

Evidence considered

• The MSH6 InSiGHT VCEP PP1 thresholds are combined Bayes likelihood ratio >2.08 to <=4.3 for supporting, >4.3 to <=18.7 for moderate, and >18.7 in at least two families for strong evidence.
• The available case records do not document a pedigree, informative meioses, relative genotypes, or a Bayes likelihood ratio for NM_000179.3:c.3787C>T.

Still missing

• No family pedigree or number of informative meioses is documented.
• No affected or unaffected relative genotypes are documented.
• No combined Bayes likelihood ratio or segregation analysis output is documented.

Sources

Reasoning

The governing MSH6 specification allows PP4 when one or more CRC or endometrial tumors are MSI-H by a standard marker panel or tumor genome and/or show MSH6-consistent loss of MMR protein expression; higher strengths require two or three independent tumors, or at least three tumors in at least two families. The available case evidence does not document any tumor MSI result, tumor-genome result, or MMR IHC result for this variant, so PP4 cannot be assessed.

Rule

Supporting: 1 CRC/endometrial MSI-H tumor by a standard 5-10 marker panel or tumor genome and/or MSH6-consistent MMR protein loss; Moderate: 2 independent qualifying tumors; Strong: at least 3 independent qualifying tumors in at least 2 families. MSI-H with inconsistent protein expression does not meet PP4 at the applicable strength.

Evidence considered

• The governing MSH6 Version 2.0 PP4 Supporting rule requires 1 CRC or endometrial MSI-H tumor using a standard 5-10 marker panel or tumor genome and/or MMR protein loss consistent with MSH6.
• The governing MSH6 Version 2.0 PP4 Moderate rule requires 2 independent CRC or endometrial MSI-H tumors or qualifying consistent MMR protein-loss evidence.
• The governing MSH6 Version 2.0 PP4 Strong rule requires at least 3 independent CRC or endometrial MSI-H tumors in at least 2 families or qualifying consistent MMR protein-loss evidence.
• No case-specific tumor MSI, tumor-genome, or MMR immunohistochemistry result is documented in the reviewed evidence.

Still missing

• Tumor-level MSI result or tumor-genome result is needed.
• Tumor MMR immunohistochemistry, including whether MSH6 loss is present and consistent with the variant location, is needed.
• If multiple tumors exist, the number of independent tumors and families must be documented for strength assignment.

Sources

Reasoning

The governing MSH6 InSiGHT VCEP limits BS2 Strong to documented co-occurrence in trans with a known pathogenic sequence variant in the same gene, in a patient with colorectal cancer after age 45 or another Lynch-spectrum cancer above its median Lynch-syndrome onset age, without clinical CMMRD manifestations; phase must be confirmed through parents or offspring. The available case evidence documents no such co-occurrence, phenotype, age, CMMRD assessment, or phase confirmation. gnomAD reports zero homozygotes but that population observation does not satisfy this VCEP-specific BS2 rule, so the criterion cannot be assessed.

Rule

Co-occurrence in trans with a known pathogenic sequence variant in the same gene in a patient with colorectal cancer after age 45 (or another Lynch-spectrum cancer above the median age of onset), without CMMRD manifestations; phase requires parental or offspring testing.

Evidence considered

• The MSH6 InSiGHT VCEP v2.0 BS2 Strong rule requires qualifying patient-level in-trans co-occurrence, specified Lynch-spectrum cancer timing, no CMMRD manifestations, and phase confirmation through parents or offspring.
• gnomAD v4.1 reports zero homozygotes, but homozygote absence is not the VCEP's specified BS2 evidence and cannot substitute for documented patient-level co-occurrence and phase data.

Still missing

• A qualifying patient-level in-trans co-occurrence with a known pathogenic MSH6 variant is not documented.
• Required cancer type and age, absence of CMMRD manifestations, and parental or offspring phase confirmation are unavailable.

Sources

Reasoning

The applicable ClinGen InSiGHT MSH6 VCEP requires calibrated functional odds for pathogenicity <=0.05 for BS3_Strong or >0.05 and <=0.48 for BS3_Supporting, or qualifying variant-specific proficient function in protein and mRNA-based assays under the MMR functional-assay flowchart. No such functional odds, proficient protein assay, proficient mRNA assay, or qualifying NMD-controlled RNA result is available for NM_000179.3:c.3787C>T (p.Arg1263Cys). The available report of p.R1263C is a tumor sequencing observation without functional testing, so BS3 cannot be assigned.

Rule

Calibrated functional assays with functional odds for pathogenicity <=0.05 for Strong or >0.05 and <=0.48 for Supporting; alternatively, variant-specific proficient function in protein and mRNA-based assays under the MMR functional-assay flowchart.

Evidence considered

• The MSH6 VCEP BS3 thresholds are functional odds for pathogenicity <=0.05 for Strong and >0.05 and <=0.48 for Supporting.
• The MSH6 VCEP also permits BS3_Supporting for variant-specific proficient function in protein and mRNA-based laboratory assays following the MMR functional-assay flowchart, and BS3_Strong for qualifying absence of mRNA aberration in synonymous or intronic variants with NMD inhibition; this missense variant has no such result.
• The available variant-specific publication extraction reports p.R1263C in a gastric-cancer tumor but states that no functional assay results were provided.

Still missing

• Variant-specific calibrated functional assay with pathogenicity odds <=0.48, including the VCEP thresholds for BS3 strength.
• Alternatively, qualifying proficient protein and mRNA-based assays or an NMD-controlled RNA assay showing no aberrant transcript.

Sources

Reasoning

The MSH6 InSiGHT VCEP requires documented lack of co-segregation in a pedigree quantified with a combined Bayes likelihood ratio, with strong BS4 for a ratio <0.05 and supporting BS4 for a ratio >0.05 and <=0.48. No non-segregating affected relatives, pedigree genotypes, informative meioses, phenocopy assessment, or Bayes likelihood ratio is documented for this variant; therefore BS4 cannot be assigned.

Rule

MSH6 VCEP BS4: strong if combined Bayes likelihood ratio <0.05; supporting if >0.05 and <=0.48.

Evidence considered

• The MSH6 InSiGHT VCEP BS4 thresholds are a combined Bayes likelihood ratio <0.05 for strong evidence and >0.05 to <=0.48 for supporting evidence.
• The available case records do not document non-segregating relatives, informative meioses, pedigree genotypes, or a Bayes likelihood ratio for NM_000179.3:c.3787C>T.

Still missing

• No pedigree with affected non-carriers or other non-segregating relatives is documented.
• No informative meioses or relative genotypes are documented.
• No combined Bayes likelihood ratio is documented.
• Potential phenocopy or an alternative pathogenic variant has not been evaluated from the available records.

Sources

Reasoning

BP5 is applicable under the MSH6 specification, but no case-specific tumor findings establish its alternate-molecular-basis rule. The specification requires either at least 2 tumors for Supporting or at least 4 tumors for Strong with MSS and/or no MMR-protein loss, or the specified BRAF V600E/MLH1-methylation evidence; none is documented.

Rule

Supporting: 2 or 3 qualifying tumors, or 1 specified BRAF V600E/MLH1-methylation result; Strong: at least 4 qualifying tumors, or at least 2 specified BRAF V600E/MLH1-methylation results. Qualifying tumors have MSS and/or no MMR-protein loss, or inconsistent MMR loss in an LS-spectrum tumor.

Evidence considered

• The governing MSH6 Version 2.0 BP5 Supporting rule requires 2 or 3 tumors with MSS and/or no MMR-protein loss, or 1 qualifying BRAF V600E or MLH1-methylation result with MSI-H/MLH1 loss.
• The governing MSH6 Version 2.0 BP5 Strong rule requires at least 4 qualifying tumors, or at least 2 qualifying BRAF V600E or MLH1-methylation results with MSI-H/MLH1 loss.
• No case-specific MSS, MMR immunohistochemistry, BRAF V600E, MLH1 methylation, or qualifying tumor-count evidence is documented.

Still missing

• Tumor count and tumor types must be documented.
• For each tumor, MSS status and MMR protein-expression findings are needed.
• If using the alternative rule, BRAF V600E or MLH1 methylation results with MSI-H/MLH1 loss must be documented.

Sources