MSH6 c.187T>C, p.(Ser63Pro)

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 grpmax filtering allele frequency 0.00055895 (0.055895%), within this interval. No founder-pathogenic designation is present in the governing framework or case evidence, so the VCEP BS1 Strong rule is 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 BS1 Strong rule requires gnomAD v4 grpmax filtering allele frequency ≥0.00022 and <0.0022 (0.022–0.22%) and exclusion as a founder pathogenic variant.
• gnomAD v4.1 reports grpmax filtering allele frequency 0.00055895 (0.055895%), which lies within the VCEP BS1 interval; no founder-pathogenic designation is documented.

Sources

Reasoning

The variant is a missense substitution, and the governing MSH6 VCEP HCI lookup applies. The exact HCI row for c.187T>C (p.S63P) assigns an HCI prior probability of pathogenicity of 0.0027, which is below the VCEP BP4 Supporting cutoff of <0.11. BP4 Supporting is therefore met directly by the gene-specific pre-assigned HCI rule. The available REVEL score of 0.276 is not used to replace or weaken this governing VCEP assignment.

Rule

MSH6 VCEP: missense variant with HCI prior probability for pathogenicity <0.11 = BP4 Supporting.

Evidence considered

• The governing MSH6 VCEP specification assigns BP4 Supporting to a missense variant with HCI prior probability <0.11.
• The exact HCI-PRIORS-MSH6 row for c.187T>C / p.S63P reports HCI prior probability 0.0027; the same row's custom PP2 score is 0.015 and is not the HCI prior probability used for this rule.
• The source registry reports a REVEL score of 0.276, but the governing VCEP HCI lookup directly pre-assigns BP4 Supporting and takes precedence over generic predictor thresholds.

Sources

Reasoning

The governing MSH6 InSiGHT VCEP specifies PM2 Supporting for an absent or extremely rare allele frequency below 0.00002 (<1 in 50,000 alleles) in gnomAD v4. gnomAD v4.1 reports the variant in 52 of 1,510,744 alleles, with total allele frequency 0.0000344201267747, which exceeds 0.00002. The gnomAD v4 grpmax frequency is also 0.00055895, so the variant does not satisfy the VCEP PM2 threshold.

Rule

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

Evidence considered

• The MSH6 InSiGHT VCEP PM2 Supporting rule requires allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4.
• gnomAD v4.1 reports 52/1,510,744 alleles and total allele frequency 0.0000344201267747, above the VCEP PM2 cutoff.

Sources

Reasoning

The variant is a missense substitution, so the MSH6-specific HCI prior governs PP3/BP4. The exact HCI row for c.187T>C (p.S63P) assigns an HCI prior probability of pathogenicity of 0.0027, which is below the VCEP PP3 Supporting threshold of >0.68 and therefore does not meet PP3. The VCEP specification takes precedence over generic REVEL thresholds; the available REVEL score of 0.276 is not used to substitute another path or override the pre-assigned HCI rule.

Rule

MSH6 VCEP: missense variant with HCI prior probability for pathogenicity >0.68 = PP3 Supporting; >0.81 = PP3 Moderate.

Evidence considered

• The governing MSH6 VCEP specification assigns PP3 Supporting to a missense variant with HCI prior probability >0.68 and PP3 Moderate to a probability >0.81.
• The exact HCI-PRIORS-MSH6 row for c.187T>C / p.S63P reports HCI prior probability 0.0027; the same row's custom PP2 score is 0.015 and is not the HCI prior probability used for this rule.
• The source registry reports a REVEL score of 0.276, but the governing VCEP HCI lookup is the applicable pre-assigned rule and outranks generic REVEL calibration for this criterion.

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. gnomAD v4.1 reports a grpmax filtering allele frequency of 0.00055895 (0.055895%), which is below 0.0022; therefore BA1 is not met. No VCEP founder-pathogenic designation is present, but the frequency threshold alone is not reached.

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 BA1 rule requires gnomAD v4 grpmax filtering allele frequency ≥0.0022 (0.22%) and exclusion as a founder pathogenic variant.
• gnomAD v4.1 reports grpmax filtering allele frequency 0.00055895 (0.055895%) for NM_000179.3:c.187T>C; this is below the VCEP threshold.

Sources

Reasoning

The MSH6 VCEP PS1 rule requires a different nucleotide change encoding the same amino-acid substitution that was established by the VCEP as Pathogenic or, at moderate strength, Likely Pathogenic with a normal RNA result plus PM2_supporting. The case variant is NM_000179.3:c.187T>C (p.Ser63Pro), but no verified alternate-codon p.Ser63Pro comparator was identified. The PM5 comparator artifact reports zero same-residue candidates and a soft retrieval error (HTTP 429), so the available evidence does not establish that the required comparator search was complete.

Rule

A predicted missense substitution that encodes the same amino acid change with a different underlying nucleotide change previously established by this VCEP as Pathogenic (not a predicted or confirmed splice defect). Moderate: the alternate-nucleotide same-amino-acid change is a previously established Likely Pathogenic missense variant with normal RNA and PM2_supporting.

Evidence considered

• The governing MSH6 VCEP PS1 rule requires a different underlying nucleotide change producing the same amino-acid change, established as Pathogenic or qualifying Likely Pathogenic with normal RNA and PM2_supporting.
• The target variant is NM_000179.3:c.187T>C, p.Ser63Pro.
• The collected PM5 comparator artifact found zero same-residue candidates and recorded HTTP Error 429, leaving comparator ascertainment incomplete.

Still missing

• Verify a complete search for alternate-nucleotide variants encoding p.Ser63Pro and their VCEP classifications and RNA evidence.

Sources

Reasoning

The MSH6-specific VCEP permits PS2 from de novo observations scored as 0.5 points when maternity and/or paternity is unconfirmed, 1 point when both are confirmed without tumor data, or 2 points when both are confirmed and an MMR-deficient Lynch-spectrum tumor is documented; no variant-specific proband, parental testing, maternity/paternity confirmation, tumor MSI/IHC/methylation result, or de novo point is documented in the available case evidence. Therefore PS2 cannot be assessed.

Rule

MSH6 VCEP PS2: 0.5 de novo points supports Supporting; 1-1.5 points supports Moderate; 2-3.5 points supports Strong; at least 4 points supports Very Strong. Points require the specified de novo, parental-confirmation, and tumor evidence.

Evidence considered

• The MSH6 InSiGHT VCEP PS2 rule assigns 0.5 points for assumed de novo status with unconfirmed maternity and/or paternity, 1 point for confirmed maternity and paternity without tumor data, and 2 points when both are confirmed with an MMR-deficient Lynch-spectrum tumor.
• The case-specific evidence contains no variant-specific report of a proband, parental testing, maternity or paternity confirmation, Lynch-spectrum tumor phenotype, or de novo point assignment.
• PMID:26467025 was reviewed in the extracted literature and explicitly reports no MSH6-specific patient observation or segregation result for this variant.
• PMID:27363726 was reviewed in the extracted literature and reports a general Lynch syndrome history-weighting study rather than variant-specific de novo or parental-testing evidence.

Still missing

• Variant-specific proband phenotype and Lynch-spectrum tumor documentation
• Testing confirmation of maternity and paternity
• Tumor MSI, MMR IHC, and MLH1 methylation results when applicable
• A validated de novo evidence point assignment

Sources

Reasoning

The governing InSiGHT MSH6 V2.0 specification requires calibrated functional odds >2.08 for PS3_Supporting, >4.3 and <=18.7 for PS3_Moderate, or >18.7 for PS3_Strong; alternatively, a documented MMR function defect may support PS3_Moderate. The available variant-specific literature records do not report an assay for NM_000179.3:c.187T>C (p.Ser63Pro), and the reviewed papers are general classification or clinical-history studies without a result for this variant. Therefore, no validated assay result, assay control comparison, functional odds, or variant-specific MMR defect is available to apply PS3.

Rule

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

Evidence considered

• The InSiGHT MSH6 V2.0 specification defines PS3_Supporting as calibrated functional odds for pathogenicity >2.08 and <=4.3, PS3_Moderate as >4.3 and <=18.7 or an MMR function defect following the functional assay flowchart, and PS3_Strong as >18.7.
• The extracted record for PMID:26467025 states that the paper provides no MSH6-specific assay or functional result for c.187T>C (p.Ser63Pro).
• The extracted record for PMID:27363726 states that the paper evaluates a clinical history-weighting algorithm and does not report or evaluate MSH6 c.187T>C (p.Ser63Pro).
• The available evidence does not document variant-specific assay controls, quantitative MMR activity, protein expression or stability, localization, or functional odds for this variant.

Still missing

• A validated variant-specific MSH6 functional assay with appropriate wild-type and deficient/pathogenic controls is needed.
• Calibrated functional odds for pathogenicity or a documented MMR function defect are not available.

Sources

Reasoning

The applicable ClinGen InSiGHT MSH6 VCEP specifies PM3 point-based interpretation: 0.5 points for Supporting, 1–1.5 for Moderate, 2–3.5 for Strong, and at least 4 for Very Strong. The available case evidence contains no affected-proband observation documenting this variant with a pathogenic or likely pathogenic MSH6 variant in trans, no confirmed phase, and no qualifying biallelic inheritance observation. Therefore no PM3 points can be assigned; targeted family or proband data establishing the second pathogenic allele and phase would be required.

Rule

MSH6 VCEP PM3 point-based rule: 0.5 points Supporting; 1–1.5 Moderate; 2–3.5 Strong; ≥4 Very Strong.

Evidence considered

• The MSH6 VCEP PM3 rule assigns strength by points: 0.5 Supporting, 1–1.5 Moderate, 2–3.5 Strong, and ≥4 Very Strong.
• No qualifying affected-proband, biallelic, pathogenic-in-trans, or confirmed-phase observation for NM_000179.3:c.187T>C (p.Ser63Pro) is present in the available case evidence.

Still missing

• Affected-proband or affected-family observation with this variant and a pathogenic or likely pathogenic MSH6 variant is not documented.
• The phase of any second MSH6 variant is not established; parental or offspring testing or equivalent phasing is needed.

Sources

Reasoning

The MSH6 VCEP PM5 rule requires a different missense change at the same amino-acid residue classified by the VCEP as Pathogenic or Likely Pathogenic due to a protein-level missense effect, with PM5 use additionally conditioned on PP3_supporting for the target missense variant. The target is p.Ser63Pro, but the collected comparator artifact found zero same-residue candidates and recorded HTTP Error 429. Consequently, a complete verified comparator assessment and the VCEP's PP3 prerequisite cannot be established from the available evidence.

Rule

Moderate: missense change at an amino acid residue where a different missense change was classified by this VCEP as Pathogenic on the protein level and not due to aberrant splicing; use only if PP3 is supporting for the missense change. Supporting: the other variant is Likely Pathogenic; use PM5_supporting only if the other variant is Likely Pathogenic and use PM5 if it is Pathogenic.

Evidence considered

• The governing MSH6 VCEP PM5 rule requires a different missense change at the same residue, classified by the VCEP as Pathogenic or Likely Pathogenic due to a protein-level missense effect, and requires PP3_supporting for the target variant.
• The target variant is p.Ser63Pro.
• The collected PM5 artifact found zero same-residue candidates and recorded HTTP Error 429, so the comparator review is incomplete.

Still missing

• Complete and verify same-residue missense comparator retrieval, VCEP classifications, splice basis, and the target's VCEP PP3_supporting prerequisite.

Sources

Reasoning

The MSH6-specific VCEP requires co-segregation evidence evaluated with a combined Bayes likelihood ratio, with Supporting strength above 2.08 and up to 4.3, Moderate strength above 4.3 and up to 18.7, and Strong strength above 18.7 in at least two families; no variant-specific pedigree, affected or unaffected relative genotypes, meioses, segregation observations, or Bayes likelihood ratio is available. Therefore PP1 cannot be assessed.

Rule

MSH6 VCEP PP1: combined Bayes likelihood ratio >2.08 and <=4.3 supports Supporting; >4.3 and <=18.7 supports Moderate; >18.7 in at least two families supports Strong.

Evidence considered

• The MSH6 InSiGHT VCEP PP1 rule requires a combined Bayes likelihood ratio greater than 2.08 for Supporting, greater than 4.3 through 18.7 for Moderate, and greater than 18.7 in at least two families for Strong.
• The case-specific evidence contains no variant-specific pedigree, segregation table, relative genotype/phenotype data, meiosis count, independent-family count, or Bayes likelihood ratio.
• PMID:26467025 was reviewed in the extracted literature and explicitly reports no MSH6-specific segregation result for this variant.
• PMID:27363726 was reviewed in the extracted literature and concerns a general clinical history-weighting algorithm, not variant-specific co-segregation analysis.

Still missing

• Variant-specific pedigree structure and phenotype assignments
• Genotypes and disease status for informative affected and unaffected relatives
• Number of informative meioses and independent families
• Combined Bayes likelihood ratio

Sources

Reasoning

The governing MSH6 VCEP permits PP4 from one or more CRC/endometrial MSI-H tumors tested with a standard MSI panel or tumor genome and/or MSH6-consistent loss of MMR protein expression; stronger levels require two or three or more independent tumors. The available case evidence identifies only general MSH6/Lynch syndrome context and does not provide a variant-specific patient tumor count, MSI result, tumor-genome result, or MSH6-consistent IHC result for NM_000179.3:c.187T>C (p.Ser63Pro). The criterion therefore cannot be adjudicated.

Rule

Supporting: 1 CRC/Endometrial MSI-H tumor using a standard panel of 5-10 markers or tumor genome and/or loss of MMR protein expression consistent with the variant location. Moderate: 2 independent CRC/Endometrial MSI-H tumors using a standard panel of 5-10 markers or tumor genome and/or loss of MMR protein expression consistent with the variant location. Strong: >=3 independent CRC/Endometrial MSI-H tumors in >=2 families using a standard panel of 5-10 markers or tumor genome and/or loss of MMR protein expression consistent with the variant location.

Evidence considered

• The governing MSH6 VCEP PP4 Supporting rule requires 1 CRC/Endometrial MSI-H tumor using a standard panel of 5-10 markers or tumor genome and/or loss of MMR protein expression consistent with the variant location; MSI-H with inconsistent protein expression does not meet PP4.
• The VCEP PP4 Moderate rule requires 2 independent CRC/Endometrial MSI-H tumors, and the Strong rule requires at least 3 independent CRC/Endometrial MSI-H tumors in at least 2 families, with the specified MSI/IHC consistency.
• The exact-variant literature extraction for the available cited papers does not report this variant's patient-specific tumor MSI or IHC findings; general MSH6/Lynch syndrome phenotype descriptions are insufficient for PP4.

Still missing

• Variant-specific clinical tumor data are needed: number of independent CRC/endometrial tumors, MSI testing method and results, tumor-genome findings if used, and MMR IHC results with consistency to MSH6 loss.

Sources

Reasoning

The governing MSH6 InSiGHT VCEP restricts BS2 Strong to documented co-occurrence in trans with a known pathogenic variant in the same gene in a patient with colorectal cancer after age 45 or another Lynch-syndrome cancer above its median age of onset, without clinical manifestations of constitutional mismatch repair deficiency, with phase confirmed through parental or offspring testing. The available case evidence reports zero gnomAD homozygotes but provides no qualifying patient-level co-occurrence, cancer-age, CMMRD, or phase-confirmation data; therefore BS2 cannot be assessed from population data alone.

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 other LS cancer above the median age of onset for that cancer in LS), and who has no previous or current evidence of clinical manifestations of CMMRD; confirmation of phase requires testing of parents or offspring.

Evidence considered

• The MSH6 InSiGHT VCEP BS2 Strong rule requires qualifying in-trans co-occurrence with a known pathogenic same-gene variant, appropriate Lynch-syndrome cancer age, absence of CMMRD manifestations, and confirmed phase.
• gnomAD v4.1 reports 0 homozygotes for the variant, but this population observation does not establish the VCEP's required patient-level co-occurrence evidence.

Still missing

• Qualifying patient-level co-occurrence in trans with a known pathogenic MSH6 variant.
• Cancer type and age meeting the MSH6 VCEP requirement.
• Evidence excluding current or previous CMMRD manifestations.
• Parental or offspring testing confirming phase.

Sources

Reasoning

The governing InSiGHT MSH6 V2.0 specification requires calibrated functional odds for pathogenicity <=0.05 for BS3_Strong, or variant-specific proficient function in protein and mRNA-based laboratory assays under the MMR functional assay flowchart for BS3_Supporting. The available variant-specific literature records do not report an assay for NM_000179.3:c.187T>C (p.Ser63Pro), and the reviewed papers provide no variant-specific proficient-function result, assay controls, or functional odds. Therefore, BS3 cannot be applied.

Rule

Calibrated functional assays with functional odds for Pathogenicity <= 0.05, or synonymous/intronic variants with no associated mRNA aberration; BS3_Supporting: calibrated functional assays with functional odds for Pathogenicity >0.05 and <=0.48, or variant-specific proficient function in protein and mRNA-based lab assays as per the MMR functional assay flowchart.

Evidence considered

• The InSiGHT MSH6 V2.0 specification defines BS3_Strong as calibrated functional odds for pathogenicity <=0.05, or no mRNA aberration for applicable synonymous or intronic variants, and BS3_Supporting as calibrated functional odds >0.05 and <=0.48 or variant-specific proficient function in protein and mRNA-based assays.
• This is a missense variant, so the MSH6 synonymous/intronic no-mRNA-aberration alternative does not apply.
• The extracted record for PMID:26467025 states that the paper provides no MSH6-specific assay or functional result for c.187T>C (p.Ser63Pro).
• The extracted record for PMID:27363726 states that the paper evaluates a clinical history-weighting algorithm and does not report or evaluate MSH6 c.187T>C (p.Ser63Pro).

Still missing

• A validated variant-specific protein or mRNA functional assay with appropriate controls is needed.
• Calibrated functional odds for pathogenicity <=0.05 or documented proficient function are not available.

Sources

Reasoning

The MSH6-specific VCEP requires lack of co-segregation evaluated with a combined Bayes likelihood ratio, with Supporting strength above 0.05 through 0.48 and Strong strength below 0.05; no variant-specific non-segregation observation, affected-relative mismatch, pedigree, meiosis data, or Bayes likelihood ratio is available. Potential absence of family evidence cannot be treated as evidence of non-segregation, so BS4 cannot be assessed.

Rule

MSH6 VCEP BS4: combined Bayes likelihood ratio <0.05 supports Strong; >0.05 and <=0.48 supports Supporting.

Evidence considered

• The MSH6 InSiGHT VCEP BS4 rule requires a combined Bayes likelihood ratio below 0.05 for Strong or above 0.05 and up to 0.48 for Supporting.
• The case-specific evidence contains no variant-specific affected-relative mismatch, non-segregation observation, pedigree, meiosis data, or Bayes likelihood ratio; missing segregation data are not evidence of lack of segregation.
• PMID:26467025 was reviewed in the extracted literature and explicitly reports no MSH6-specific segregation result for this variant.
• PMID:27363726 was reviewed in the extracted literature and does not provide variant-specific family segregation or non-segregation evidence.

Still missing

• Variant-specific affected-relative non-segregation observations
• Pedigree structure, phenotypes, and relative genotypes
• Assessment of phenocopies or additional pathogenic variants
• Combined Bayes likelihood ratio

Sources

Reasoning

The governing MSH6 VCEP defines BP5 from an alternate molecular or tumor basis: 2 or 3 qualifying tumors for Supporting or at least 4 qualifying tumors for Strong, or specified BRAF V600E/MLH1 methylation findings. The available evidence does not document any variant-specific CRC/endometrial tumor MSS results, preserved MMR protein expression, discordant LS-spectrum tumor IHC, BRAF V600E result, or MLH1 methylation result. BP5 cannot therefore be adjudicated.

Rule

Supporting: 2 or 3 tumors: CRC/Endometrial tumors with MSS and/or no loss of MMR protein expression and/or LS spectrum tumors with loss of MMR protein(s) inconsistent with the gene demonstrating genetic variation; or 1 BRAF V600E (Colon only)/MLH1 methylation finding in the specified context. Strong: >=4 tumors with those findings; or >=2 BRAF V600E/MLH1 methylation findings in the specified context.

Evidence considered

• The governing MSH6 VCEP BP5 Supporting rule requires 2 or 3 tumors with CRC/endometrial MSS and/or no loss of MMR protein expression and/or LS-spectrum tumor MMR-protein loss inconsistent with the gene carrying the variant, or 1 BRAF V600E/MLH1 methylation finding in the specified context.
• The VCEP BP5 Strong rule requires at least 4 qualifying tumors or at least 2 specified BRAF V600E/MLH1 methylation findings.
• No variant-specific alternate molecular-basis tumor results are provided in the available evidence; general Lynch syndrome phenotype descriptions do not satisfy BP5.

Still missing

• Variant-specific alternate-basis tumor data are needed: qualifying tumor count, MSS status, MMR IHC results, and any CRC BRAF V600E or LS-spectrum tumor MLH1 methylation results.

Sources