PMS2 c.1501G>A, p.(Val501Met)

Reasoning

NM_000535.7:c.1501G>A is a missense variant encoding p.Val501Met. The exact c.1501G>A entry in the governing HCI-PRIORS-PMS2 table assigns pathogenicity probability 0.002. The PMS2 VCEP specifies BP4 Supporting for a missense variant with MAPP/PP2 Prior P <0.11, so BP4_Supporting is met. SpliceAI is not used because the variant is missense; the REVEL score of 0.07 is concordantly below the generic BP4 supporting threshold of <=0.29 from Pejaver et al. 2022 (PMID:36413997), but the VCEP pre-assigned HCI result governs.

Rule

PMS2 VCEP HCI prior: BP4 Supporting if the missense MAPP/PP2 Prior P score is <0.11.

Evidence considered

• The PMS2 VCEP index declares HCI-PRIORS-PMS2.txt governing for PP3 and BP4 in missense variants.
• The exact HCI table entry for c.1501G>A / p.V501M assigns pathogenicity probability 0.002.
• The PMS2 VCEP specification assigns BP4 Supporting to a missense variant with MAPP/PP2 Prior P <0.11; 0.002 satisfies this rule.
• The case REVEL score is 0.07, below the published generic BP4 Supporting threshold of <=0.29 from ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
• SpliceAI is not used for this missense BP4 assessment.

Sources

Reasoning

The governing InSiGHT PMS2 VCEP specifies PS1 for a missense substitution encoding the same amino-acid change as a different-nucleotide variant established by the VCEP as Pathogenic, or for a specified non-canonical splice-nucleotide scenario. This variant is a missense change, but the available case evidence identifies no alternate-nucleotide PMS2 variant encoding p.Val501Met that was established by the VCEP as Pathogenic, and the variant is not a non-canonical splice-site change. Therefore PS1 is not met.

Rule

A predicted missense substitution encoding the same amino-acid change with a different underlying nucleotide change, previously established by this VCEP as Pathogenic and not due to aberrant splicing.

Evidence considered

• The PMS2 VCEP PS1 rule requires the same amino-acid change from a different nucleotide and prior VCEP establishment as Pathogenic.
• The case variant is NM_000535.7:c.1501G>A, NP_000526.2:p.(Val501Met), a missense variant rather than a non-canonical splice-nucleotide variant.
• No qualifying alternate-nucleotide p.Val501Met comparator is present in the collected case evidence.

Still missing

• No VCEP-established Pathogenic alternate-nucleotide variant encoding p.Val501Met was identified.

Sources

Reasoning

The governing PMS2 InSiGHT VCEP specifies PM2 Supporting for an absent or extremely rare allele frequency below 0.00002 (less than 1 in 50,000 alleles) in gnomAD v4. The applicable all-comers GNOMAD_V4_1 record reports this variant at 91/1,614,098 alleles, total allele frequency 5.6378237256969525e-05 and grpmax filtering allele frequency 5.628e-05, with zero homozygotes. Both reported frequencies exceed the VCEP PM2 threshold, so PM2 is not met.

Rule

PMS2 InSiGHT VCEP PM2 Supporting: absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4.

Evidence considered

• The PMS2 InSiGHT VCEP Version 2.0 specifies PM2 Supporting for an absent or extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4.
• GNOMAD_V4_1 reports 91 variant alleles among 1,614,098 total alleles, total allele frequency 5.6378237256969525e-05 and grpmax filtering allele frequency 5.628e-05, with zero homozygotes; the allele frequency exceeds 0.00002.
• The VCEP does not specify a non-cancer or exome-only population subset for PM2, so the all-comers gnomAD v4.1 value was used.

Sources

Reasoning

The governing InSiGHT PMS2 VCEP permits PM5 when a different missense change at the same amino-acid residue is established as Pathogenic or Likely Pathogenic at the protein level and is not due to aberrant splicing; PM5 also requires PP3 supporting for the assessed missense variant. The collected PM5 search found zero same-residue candidates at Val501, and the variant's HCI prior probability is 0.002, which does not satisfy the VCEP PP3 supporting interval (>0.68 to <=0.81). Thus PM5 is not met.

Rule

Use PM5 Moderate for a different missense change at the same residue classified by this VCEP as Pathogenic at the protein level, or PM5 Supporting when classified as Likely Pathogenic; only use PM5 when PP3 is supporting for the assessed missense change.

Evidence considered

• The PMS2 VCEP PM5 rule requires a different missense change at the same residue classified as Pathogenic or Likely Pathogenic at the protein level, not due to aberrant splicing, and requires PP3 supporting for the assessed missense variant.
• The PM5 candidate record reports zero same-residue candidates, zero expert-panel Pathogenic/Likely Pathogenic candidates, and zero non-expert-majority Pathogenic/Likely Pathogenic candidates for Val501.
• The PMS2 HCI prior probability for c.1501G>A/p.V501M is 0.002; the VCEP PP3-supporting interval is greater than 0.68 through 0.81, so the required PP3 supporting condition is absent.

Still missing

• The PM5 candidate collection reported no same-residue Val501 missense comparators; an independently identified qualifying comparator could change the assessment.

Sources

Reasoning

NM_000535.7:c.1501G>A is a missense variant encoding p.Val501Met, so the applicable computational path is the VCEP-governed HCI prior lookup rather than SpliceAI. The exact c.1501G>A entry in HCI-PRIORS-PMS2 assigns pathogenicity probability 0.002, which is below the VCEP PP3 supporting threshold of >0.68 and the moderate threshold of >0.81; therefore PP3 is not met. The REVEL score is 0.07, also below the published PP3 supporting threshold of >=0.644 from Pejaver et al. 2022 (PMID:36413997), but the governing VCEP lookup is decisive. BayesDel has no applicable VCEP calibration for PP3.

Rule

PMS2 VCEP HCI prior: PP3 Moderate if pathogenicity probability >0.81; PP3 Supporting if >0.68 and <=0.81.

Evidence considered

• The PMS2 VCEP index declares HCI-PRIORS-PMS2.txt governing for PP3 and BP4 in missense variants.
• The exact HCI table entry for c.1501G>A / p.V501M assigns pathogenicity probability 0.002, with MAPP score 3.75 and custom PP2 score 0.001.
• The PMS2 VCEP specification assigns PP3 Supporting when the MAPP/PP2 Prior P score is >0.68 and <=0.81, and PP3 Moderate when it is >0.81; 0.002 meets neither threshold.
• The case REVEL score is 0.07, below the published PP3 Supporting threshold of >=0.644 from ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
• SpliceAI is not used for this missense PP3 assessment, and no generic BayesDel strength calibration is available.

Sources

Reasoning

The governing PMS2 InSiGHT VCEP specifies BA1 when gnomAD v4 grpmax filtering allele frequency is at least 0.0028 (0.28%) and the variant is excluded as a founder pathogenic variant. The all-comers GNOMAD_V4_1 record is the applicable source because the specification does not require a non-cancer or exome-only subset. This variant has a gnomAD v4.1 grpmax filtering allele frequency of 5.628e-05 (0.005628%), with 91/1,614,098 total alleles and zero homozygotes, which is below 0.0028; therefore BA1 is not met.

Rule

PMS2 InSiGHT VCEP BA1: gnomAD v4 grpmax filtering allele frequency >=0.0028 (0.28%) and exclusion as a founder pathogenic variant.

Evidence considered

• The PMS2 InSiGHT VCEP Version 2.0 specifies BA1 at gnomAD v4 grpmax filtering allele frequency >=0.0028 (0.28%), provided the variant is not a founder pathogenic variant.
• GNOMAD_V4_1 reports grpmax filtering allele frequency 5.628e-05 (0.005628%), total allele frequency 5.6378237256969525e-05 from 91/1,614,098 alleles, and zero homozygotes; this is below the VCEP BA1 threshold.
• The VCEP does not specify a non-cancer or exome-only population subset for BA1, so the all-comers gnomAD v4.1 value was used.

Sources

Reasoning

The governing PMS2 InSiGHT VCEP specifies BS1 Strong when gnomAD v4 grpmax filtering allele frequency is at least 0.00028 and below 0.0028 (0.028%-0.28%), with the variant excluded as a founder pathogenic variant. The applicable all-comers GNOMAD_V4_1 record reports a grpmax filtering allele frequency of 5.628e-05 (0.005628%), which is below 0.00028; therefore BS1 is not met.

Rule

PMS2 InSiGHT VCEP BS1 Strong: gnomAD v4 grpmax filtering allele frequency >=0.00028 and <0.0028 (0.028%-0.28%) and exclusion as a founder pathogenic variant.

Evidence considered

• The PMS2 InSiGHT VCEP Version 2.0 specifies BS1 Strong at gnomAD v4 grpmax filtering allele frequency >=0.00028 and <0.0028 (0.028%-0.28%), provided the variant is not a founder pathogenic variant.
• GNOMAD_V4_1 reports grpmax filtering allele frequency 5.628e-05 (0.005628%), below the VCEP BS1 range; therefore the frequency does not support BS1.
• The VCEP does not specify a non-cancer or exome-only population subset for BS1, so the all-comers gnomAD v4.1 value was used.

Sources

Reasoning

The PMS2 VCEP permits PS2 when a proband with an LS-spectrum tumor has a de novo variant, with strength determined by de novo points: 2 points when maternity and paternity are confirmed and tumor MSI/IHC/methylation data are consistent with PMS2, 1 point when both parents are confirmed but tumor data are unavailable, or 0.5 points when de novo status is assumed and one or both parents are unconfirmed. The available case evidence contains no proband-specific de novo observation, parental testing results, maternity or paternity confirmation, tumor phenotype, or de novo point calculation; therefore PS2 cannot be assigned.

Rule

PMS2 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 governing PMS2 VCEP PS2 rule assigns 2 points per proband when both maternity and paternity are confirmed and an LS-spectrum tumor has MMR-deficient evidence consistent with the affected gene; it assigns 1 point when both parents are confirmed but tumor MSI/IHC/methylation data are unavailable, and 0.5 points when de novo status is assumed with maternity and/or paternity unconfirmed.
• The case-specific materials provide no proband-level parental testing, de novo assertion, parentage confirmation, LS-spectrum tumor phenotype, tumor MSI/IHC/methylation results, or de novo point total.

Still missing

• Documented proband-level identification of NM_000535.7:c.1501G>A.
• Maternal and paternal testing results and confirmation of maternity and paternity.
• LS-spectrum tumor diagnosis and, if available, MSI, PMS2/IHC, and MLH1 methylation results.
• A de novo point calculation under the PMS2 VCEP PS2 rule.

Sources

Reasoning

The PMS2-specific InSiGHT VCEP requires calibrated functional odds >18.7 for PS3_Strong, >4.3 and <=18.7 or a qualifying MMR function defect by the assay flowchart for PS3_Moderate, and calibrated functional odds >2.08 and <=4.3 for PS3_Supporting. The available evidence documents the approved assay framework, controls, and thresholds but contains no result for PMS2 c.1501G>A (p.Val501Met), no functional odds, and no variant-specific protein, MMR activity, localization, or RNA assay result. The reviewed variant-focused literature extracts likewise do not mention this variant or provide functional data. Therefore PS3 cannot be assigned without direct variant-specific assay results.

Rule

Calibrated functional assays with functional odds for Pathogenicity > 18.7; OR calibrated functional odds for pathogenicity >4.3 and <=18.7 or MMR function defect following the functional assay flowchart; OR calibrated functional odds for pathogenicity >2.08 and <=4.3.

Evidence considered

• The PMS2 Version 2.0 VCEP specifies PS3_Strong for calibrated functional odds for pathogenicity >18.7, PS3_Moderate for odds >4.3 and <=18.7 or a qualifying MMR function defect, and PS3_Supporting for odds >2.08 and <=4.3.
• The VCEP functional-assay documentation describes approved MMR assays with wild-type and known-defective controls and validated control sets, but it does not report a result for PMS2 c.1501G>A (p.Val501Met).
• The VCEP functional assay flowchart requires calibrated quantitative evidence or concordant assay evidence for missense variants; no such variant-specific result is available here.
• PMID:26467025 describes a general variant-scoring system and does not report this PMS2 variant or a variant-specific assay result.
• PMID:28492532 describes a general variant-classification framework and does not report this PMS2 variant or a variant-specific assay result.

Still missing

• Variant-specific calibrated functional assay result or quantitative functional odds are unavailable.
• Independent assay results with appropriate wild-type and known-defective controls are unavailable.
• No variant-specific MMR activity, protein expression/localization, or RNA assay result is available.

Sources

Reasoning

The applicable InSiGHT PMS2 VCEP permits PM3 for a pathogenic or likely pathogenic variant in trans with the case variant in a patient with clinical features consistent with constitutional mismatch repair deficiency: 1.0 point when phase is established and 0.5 points when phase is unknown, with strength determined by the summed points (Supporting at 0.5, Moderate at 1-1.5, Strong at 2-3.5, and Very Strong at >=4). The available case evidence contains no affected-proband observation documenting a second pathogenic or likely pathogenic PMS2 variant, no cis/trans phase result, and no CMMRD phenotype assessment that could contribute PM3 points. PM3 therefore cannot be assessed.

Rule

InSiGHT PMS2 VCEP PM3: pathogenic/likely pathogenic variant in trans contributes 1.0 point; phase unknown contributes 0.5 points; Supporting = 0.5 points, Moderate = 1-1.5 points, Strong = 2-3.5 points, Very Strong >=4 points.

Evidence considered

• The InSiGHT PMS2 VCEP PM3 rule requires co-occurrence with a known pathogenic or likely pathogenic variant in the same gene in a patient with clinical features consistent with CMMRD.
• Under the VCEP rule, a pathogenic or likely pathogenic variant in trans contributes 1.0 point, whereas phase-unknown evidence contributes 0.5 points; summed points determine PM3 strength.
• No case-level affected-proband observation, second PMS2 pathogenic/likely pathogenic variant, phase result, or CMMRD feature assessment was identified for this variant.

Still missing

• Affected-proband case data with a second PMS2 pathogenic or likely pathogenic variant is not available.
• Parental, offspring, or other laboratory phase testing establishing cis/trans status is not available.
• Clinical features sufficient to evaluate the VCEP CMMRD requirement are not documented.

Sources

Reasoning

The PMS2 VCEP requires co-segregation with disease in pedigrees and assigns PP1 strength using a combined Bayes likelihood ratio: Supporting for >2.08 to <=4.3, Moderate for >4.3 to <=18.7, and Strong for >18.7 in at least two families. The case evidence contains no affected or unaffected relatives with variant testing, pedigree, meiosis count, segregation likelihood ratio, or COOL analysis, so PP1 cannot be assigned.

Rule

PMS2 VCEP PP1: combined Bayes likelihood ratio >18.7 in >=2 families = Strong; >4.3 and <=18.7 = Moderate; >2.08 and <=4.3 = Supporting.

Evidence considered

• The governing PMS2 VCEP PP1 rule uses a 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.
• No case-specific pedigree, tested-relative genotype, phenotype, meiosis count, segregation result, or Bayes likelihood ratio is available in the reviewed materials.

Still missing

• Pedigree identifying affected and unaffected relatives relevant to PMS2-related disease.
• Variant testing results for informative relatives.
• Phenotype and age information for each tested relative.
• Meiosis-level segregation data and a combined Bayes likelihood ratio, preferably from COOL.

Sources

Reasoning

The InSiGHT PMS2 VCEP permits PP4 for CRC or endometrial MSI-H tumors assessed with a standard marker panel or tumor genome and/or PMS2-consistent loss of MMR protein expression: one tumor supports PP4, two independent tumors support PP4_Moderate, and at least three independent tumors from at least two families support PP4_Strong. The available case evidence contains no variant-specific tumor MSI, IHC, or tumor-genome result, so PP4 cannot be assessed.

Rule

PP4 Supporting: 1 CRC/endometrial MSI-H tumor using a standard 5-10 marker panel or tumor genome and/or MMR protein loss consistent with the variant location; PP4 Moderate requires 2 independent tumors; PP4 Strong requires at least 3 independent tumors in at least 2 families.

Evidence considered

• The VCEP PP4 supporting rule requires 1 CRC or endometrial MSI-H tumor using a standard marker panel or tumor genome and/or loss of MMR protein expression consistent with the variant location.
• The VCEP specifies that PMS2 loss is consistent with a PMS2 pathogenic variant, while inconsistent protein expression does not meet PP4.

Still missing

• Variant-specific tumor MSI result using the VCEP standard marker panel or tumor-genome assessment
• Variant-specific MMR IHC result documenting loss consistent with PMS2

Sources

Reasoning

The governing PMS2 InSiGHT VCEP defines BS2 Strong as confirmed in-trans co-occurrence with a known pathogenic variant in PMS2 in a patient with a sufficiently late Lynch-spectrum cancer and no clinical manifestations of constitutional mismatch repair deficiency, with phase confirmed through parental or offspring testing. The available population data show zero homozygotes in gnomAD v4.1 but do not establish the VCEP-required in-trans clinical co-occurrence, cancer-age, CMMRD-exclusion, or phase evidence; BS2 cannot be assessed from the available evidence.

Rule

PMS2 InSiGHT VCEP BS2 Strong: confirmed in-trans co-occurrence with a known pathogenic variant in the same gene in an appropriately late-onset Lynch-spectrum cancer patient without CMMRD manifestations, with phase confirmed by parents or offspring.

Evidence considered

• The PMS2 InSiGHT VCEP Version 2.0 requires in-trans co-occurrence with a known pathogenic PMS2 variant in a patient with colorectal cancer after age 45 or another Lynch-syndrome cancer above the median age of onset, no evidence of constitutional mismatch repair deficiency, and phase confirmation through parents or offspring.
• GNOMAD_V4_1 reports zero observed homozygotes for this variant, but absence of homozygotes in a population database is not the VCEP-defined BS2 evidence.

Still missing

• Documented in-trans co-occurrence with a known pathogenic PMS2 variant is unavailable.
• The required cancer diagnosis and age criterion are unavailable.
• Evidence excluding clinical manifestations of constitutional mismatch repair deficiency is unavailable.
• Parental or offspring testing confirming phase is unavailable.

Sources

Reasoning

The PMS2-specific InSiGHT VCEP requires calibrated functional odds <=0.05 for BS3_Strong or odds >0.05 and <=0.48 for BS3_Supporting; alternatively, it requires qualifying variant-specific proficient protein and mRNA assay results. The available evidence documents the approved assay framework, controls, and thresholds but contains no result for PMS2 c.1501G>A (p.Val501Met), no functional odds, and no variant-specific proficient protein, MMR activity, localization, or RNA assay result. The reviewed variant-focused literature extracts do not provide benign functional evidence for this variant. Therefore BS3 cannot be assigned without direct variant-specific assay results.

Rule

Calibrated functional assays with functional odds for Pathogenicity <=0.05; OR calibrated functional odds for pathogenicity >0.05 and <=0.48; OR variant-specific proficient function in protein and mRNA-based laboratory assays as per the MMR functional assay flowchart.

Evidence considered

• The PMS2 Version 2.0 VCEP specifies BS3_Strong for calibrated functional odds for pathogenicity <=0.05 and BS3_Supporting for odds >0.05 and <=0.48.
• The VCEP also permits BS3_Supporting for variant-specific proficient function in protein and mRNA-based assays performed according to the MMR functional assay flowchart, but no such result is reported for this variant.
• The VCEP functional-assay documentation describes approved MMR assays with wild-type and known-defective controls and validated control sets, but it does not report a benign or proficient result for PMS2 c.1501G>A (p.Val501Met).
• PMID:26467025 describes a general variant-scoring system and does not report this PMS2 variant or a variant-specific benign functional result.
• PMID:28492532 describes a general variant-classification framework and does not report this PMS2 variant or a variant-specific benign functional result.

Still missing

• Variant-specific calibrated functional assay result or quantitative benign functional odds are unavailable.
• Independent assay results demonstrating proficient function with appropriate controls are unavailable.
• No variant-specific proficient protein and mRNA assay result is available.

Sources

Reasoning

The PMS2 VCEP requires lack of co-segregation with disease and a combined Bayes likelihood ratio to assign BS4: Strong for a ratio <0.05 or Supporting for >0.05 to <=0.48. The case evidence contains no pedigree, tested relatives, non-segregating affected individuals, phenotype and age assessment, or Bayes likelihood ratio; therefore BS4 cannot be assigned. Absence of reported segregation data is not itself evidence of non-segregation.

Rule

PMS2 VCEP BS4: combined Bayes likelihood ratio <0.05 = Strong; >0.05 and <=0.48 = Supporting.

Evidence considered

• The governing PMS2 VCEP BS4 rule assigns Strong evidence for a combined Bayes likelihood ratio <0.05 and Supporting evidence for a ratio >0.05 to <=0.48.
• The reviewed case materials do not document affected relatives who lack the variant, any tested family members, a pedigree, or a Bayes likelihood ratio; missing segregation information cannot be treated as non-segregation.

Still missing

• Pedigree with clinically informative affected and unaffected relatives.
• Variant testing results for affected relatives and relevant unaffected relatives.
• Phenotype, age, and alternative explanations for affected relatives.
• A combined Bayes likelihood ratio demonstrating <0.05 for Strong or >0.05 to <=0.48 for Supporting BS4.

Sources

Reasoning

The InSiGHT PMS2 VCEP defines BP5 from alternate molecular explanations in tumors: two or three qualifying tumors support BP5, while at least four qualify for BP5_Strong, with specified MSS/no MMR-protein-loss or inconsistent MMR-loss patterns, or BRAF V600E/MLH1 methylation findings. No variant-specific tumor phenotype, BRAF V600E result, or MLH1 methylation result is available, so BP5 cannot be assessed. No numeric threshold is applicable to the available evidence.

Rule

BP5 Supporting: 2 or 3 qualifying tumors, or 1 qualifying BRAF V600E/MLH1 methylation result; BP5 Strong: at least 4 qualifying tumors, or at least 2 qualifying BRAF V600E/MLH1 methylation results.

Evidence considered

• The VCEP BP5 supporting rule requires 2 or 3 tumors with MSS and/or no MMR-protein loss inconsistent with PMS2 variation, or 1 BRAF V600E/MLH1 methylation finding with MSI-H/MLH1 loss; the strong rule requires at least 4 tumors or at least 2 such BRAF/methylation findings.

Still missing

• Variant-specific tumor MSI/MSS and MMR IHC results
• Variant-specific BRAF V600E or MLH1 methylation result where relevant

Sources