PMS2 c.682G>A, p.(Gly228Ser)

Reasoning

This is a missense variant, so BP4 is applicable. The governing PMS2 VCEP HCI prior table contains the exact c.682G>A / p.G228S entry with MAPP/PP2 Prior P = 0.0077. The VCEP assigns BP4 Supporting when the missense MAPP/PP2 Prior P is <0.11; 0.0077 satisfies that rule. This governing pre-assigned result is used directly, without substituting the SpliceAI score.

Rule

PMS2 VCEP BP4: missense variant with MAPP/PP2 Prior P <0.11 = Supporting.

Evidence considered

• The PMS2 HCI prior table was searched for c.682G>A, p.Gly228Ser, and p.G228S; the exact c.682G>A / p.G228S entry was found.
• The exact HCI entry reports MAPP/PP2 Prior P = 0.0077.
• The governing PMS2 VCEP specifies BP4 Supporting for a missense variant with MAPP/PP2 Prior P <0.11; the observed 0.0077 satisfies this threshold.
• Because the variant is missense, the missense computational path is used and SpliceAI is not used as BP4 evidence.

Sources

Reasoning

PVS1 is not met. The applicable ClinGen InSiGHT PMS2 Version 2.0 specification applies PVS1 to nonsense/frameshift variants introducing a premature termination codon at or before codon 798, qualifying large genomic alterations, canonical splice variants with qualifying effects, or confirmed aberrant splicing that creates a damaging premature stop or in-frame domain-disrupting deletion. NM_000535.7:c.682G>A is a missense variant encoding NP_000526.2:p.(Gly228Ser) at codon 228, not a null, truncating, canonical splice, or confirmed aberrant-splicing variant; therefore NMD, exon-specific PVS1 downgrades, and protein-length loss do not apply.

Rule

PMS2 VCEP PVS1 rule: qualifying nonsense/frameshift, large genomic alteration, canonical splice alteration, or confirmed damaging aberrant splicing; missense variants do not meet PVS1.

Evidence considered

• The PMS2 Version 2.0 VCEP specification lists full-strength PVS1 for qualifying nonsense/frameshift variants at or before codon 798, qualifying splice alterations, large genomic alterations, or confirmed damaging aberrant splicing.
• The case variant is NM_000535.7:c.682G>A, annotated as the missense substitution NP_000526.2:p.(Gly228Ser) at codon 228; it does not introduce a premature termination codon or protein-length change and is not a canonical splice-site variant.

Sources

Reasoning

The PMS2 VCEP Version 2.0 specifies PS1 only for a missense variant encoding the same amino-acid change as a different nucleotide change previously established by the VCEP as Pathogenic, or for a specified non-canonical splice scenario. NM_000535.7:c.682G>A produces p.Gly228Ser, but the reviewed variant-specific report identifies only this same nucleotide change and does not establish a different-nucleotide p.Gly228Ser comparator as Pathogenic. Therefore PS1 is not met.

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).

Evidence considered

• The PMS2 VCEP Version 2.0 PS1 rule requires the same amino-acid change from a different nucleotide change previously established by the VCEP as Pathogenic, or a specified non-canonical splice comparison.
• PMID:31433215 reports PMS2 c.682G>A, p.Gly228Ser in one proband and classifies it as a class 3 variant of unknown significance; it does not provide a different-nucleotide p.Gly228Ser comparator established as Pathogenic.

Still missing

• No VCEP-established Pathogenic alternate-nucleotide variant encoding p.Gly228Ser was identified.

Sources

Reasoning

The governing PMS2 InSiGHT VCEP specifies PM2 at supporting strength only when the allele frequency is less than 0.00002 (<1 in 50,000 alleles) in gnomAD v4. gnomAD v4.1 reports total AF 0.0000501871 (81/1,613,962 alleles) and grpmax FAF 0.00006237, both above the VCEP threshold. The older gnomAD v2.1 non-cancer exome-only subset also has AF 0.0000379827 (9/236,950 alleles), and gnomAD v3.1 non-cancer genomes have AF 0.0000473543 (7/147,822 alleles); neither rescues the VCEP PM2 requirement. Therefore PM2 is not met.

Rule

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

Evidence considered

• The PMS2 Version 2.0 VCEP defines PM2_supporting as an absent or extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4.
• gnomAD v4.1 reports 81/1,613,962 alleles, total AF 5.0187055e-05, grpmax FAF 6.237e-05, and zero homozygotes; these frequencies exceed 0.00002.
• The non-cancer subsets do not meet the VCEP threshold either: gnomAD v2.1 non-cancer exomes show 9/236,950 alleles (AF 3.7982697e-05), and gnomAD v3.1 non-cancer genomes show 7/147,822 alleles (AF 4.7354250e-05).
• PMID:31433215 reports this exact variant in one Danish proband and gives an ExAC frequency of <0.01, but that coarse historical value is not sufficient to establish the VCEP's <0.00002 PM2 threshold.

Sources

Reasoning

The PMS2 VCEP Version 2.0 PM5 rule requires a different missense change at the same amino-acid residue classified by the VCEP as Pathogenic or Likely Pathogenic at the protein level and not due to aberrant splicing; the rule also requires PP3 supporting for the current missense variant. The available same-residue search identified zero candidates at residue 228, so no qualifying comparator exists and PM5 is not met.

Rule

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

Evidence considered

• The PMS2 VCEP Version 2.0 PM5 rule requires a different missense change at the same amino-acid residue classified by this VCEP as Pathogenic or Likely Pathogenic at the protein level and not due to aberrant splicing; PM5 additionally requires PP3 supporting for the current missense change.
• The case-specific PM5 candidate record reports 0 same-residue candidates, 0 expert-panel Pathogenic/Likely Pathogenic candidates, and 0 non-expert-majority Pathogenic/Likely Pathogenic candidates.

Still missing

• No qualifying alternate missense change at PMS2 residue 228 classified by the VCEP as Pathogenic or Likely Pathogenic was identified.

Sources

Reasoning

This is a missense variant, so PP3 is applicable. The governing PMS2 VCEP HCI prior table contains the exact c.682G>A / p.G228S entry with MAPP/PP2 Prior P = 0.0077. The VCEP assigns PP3 Moderate only when this prior is >0.81 and PP3 Supporting when it is >0.68 and <=0.81; 0.0077 meets neither pathogenic threshold. The governing lookup therefore controls the adjudication; no splice prediction is used for missense PP3.

Rule

PMS2 VCEP PP3: missense variant with MAPP/PP2 Prior P >0.81 = Moderate; >0.68 and <=0.81 = Supporting.

Evidence considered

• The PMS2 HCI prior table was searched for c.682G>A, p.Gly228Ser, and p.G228S; the exact c.682G>A / p.G228S entry was found.
• The exact HCI entry reports MAPP/PP2 Prior P = 0.0077.
• The governing PMS2 VCEP specifies PP3 Moderate for MAPP/PP2 Prior P >0.81 and PP3 Supporting for >0.68 and <=0.81; the observed 0.0077 reaches neither threshold.
• The PMS2 VCEP consequence-specific framework identifies this variant as missense and the HCI lookup as the governing PP3/BP4 specification.

Sources

Reasoning

The PMS2 VCEP requires one or more CRC/endometrial MSI-H tumors with standard MSI testing or tumor-genome evidence and/or loss of MMR protein expression consistent with the variant location for PP4 Supporting. PMID:31433215 reports this exact variant in one proband, but Table 1 records both immunohistochemistry and microsatellite-instability results as ND; no qualifying tumor phenotype is documented. The other reviewed exact-variant literature extraction does not provide a qualifying MSI-H or consistent MMR-protein-loss observation.

Rule

PP4 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; MSI-H tumor with inconsistent protein expression does not meet PP4.

Evidence considered

• The PMS2 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; an MSI-H tumor with inconsistent protein expression does not meet PP4.
• PMID:31433215 reports NM_000535.7:c.682G>A (p.Gly228Ser) in one Danish proband, but Table 1 records immunohistochemistry and microsatellite-instability results as ND.
• The exact-variant paper extraction reports no additional variant-specific functional, segregation, or clinical tumor analysis supporting PP4.

Still missing

• A variant-specific CRC or endometrial tumor with documented MSI-H status or MMR-protein loss consistent with PMS2 is not available.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar Expert Panel assertion of Pathogenic or Likely Pathogenic. ClinVar shows no Expert Panel submissions for this exact variant; the available classifications are single-submitter Uncertain significance or Benign laboratory submissions, and the governing PMS2 VCEP marks PP5 Not Applicable. Therefore PP5 is not met.

Rule

PP5: apply only for an exact-variant ClinVar Expert Panel Pathogenic or Likely Pathogenic classification; ordinary laboratory, aggregate, and non-expert assertions do not qualify.

Evidence considered

• The exact-variant ClinVar audit reports expert_panel_submissions: 0 and identifies the available submissions as single-submitter classifications.
• The ClinVar record reports Uncertain significance as the aggregate classification, with 13 clinical laboratories, and one Benign clinical-laboratory submission; neither is an Expert Panel Pathogenic/Likely Pathogenic assertion.
• The PMS2 VCEP specification marks PP5 as Not Applicable.

Still missing

• No exact-variant ClinVar Expert Panel Pathogenic or Likely Pathogenic classification is available.

Sources

Reasoning

The governing PMS2 InSiGHT VCEP specifies BA1 when the gnomAD v4 grpmax filtering allele frequency is at least 0.0028 (0.28%) and the variant is not an excluded founder pathogenic variant. gnomAD v4.1 reports a grpmax filtering allele frequency of 0.00006237 (0.006237%), well below 0.0028; therefore BA1 is not met. The available evidence does not identify this variant as a founder pathogenic variant, but that does not alter the frequency-based failure of the BA1 threshold.

Rule

GnomAD v4 Grpmax filtering allele frequency >= 0.0028 (0.28%) and variant is excluded as founder pathogenic variant.

Evidence considered

• The PMS2 Version 2.0 VCEP defines BA1 as gnomAD v4 grpmax filtering allele frequency >=0.0028 (0.28%), provided the variant is not a founder pathogenic variant.
• gnomAD v4.1 reports 81/1,613,962 total alleles, total AF 5.0187055e-05, no homozygotes, and grpmax FAF 6.237e-05 (0.006237%).
• The observed gnomAD v4.1 grpmax FAF is approximately 45-fold below the VCEP BA1 cutoff.

Sources

Reasoning

The governing PMS2 InSiGHT VCEP specifies BS1 when the gnomAD v4 grpmax filtering allele frequency is at least 0.00028 and less than 0.0028 (0.028%–0.28%), with exclusion of founder pathogenic variants. gnomAD v4.1 reports grpmax FAF 0.00006237 (0.006237%), below the lower VCEP threshold, so BS1 is not met.

Rule

GnomAD v4 Grpmax filtering allele frequency >= 0.00028 and < 0.0028 (0.028-0.28%) and variant is excluded as founder pathogenic variant.

Evidence considered

• The PMS2 Version 2.0 VCEP defines BS1 as 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 FAF 6.237e-05 (0.006237%), with total AF 5.0187055e-05 and 81 observed alleles among 1,613,962 alleles.
• The observed gnomAD v4.1 grpmax FAF is below the VCEP BS1 interval.

Sources

Reasoning

The PMS2 VCEP BP5 rule requires either at least two tumors with MSS and/or no loss of MMR protein expression, or qualifying BRAF V600E/MLH1-methylation findings. The exact-variant report identifies one proband but provides no tumor MSS, MMR-protein, BRAF, or MLH1-methylation result; consequently no BP5 threshold is reached. The VCEP does not provide a numeric BP5 comparator threshold for this rule.

Rule

BP5 Supporting: 2 or 3 tumors with MSS and/or no loss of MMR protein expression and/or LS-spectrum tumors with MMR-protein loss inconsistent with the gene demonstrating genetic variation; OR 1 BRAF V600E (colon only)/MLH1 methylation finding in an LS-spectrum tumor with MSI-H/MLH1 loss. BP5 Strong requires at least 4 tumors or at least 2 BRAF V600E/MLH1-methylation findings.

Evidence considered

• The PMS2 VCEP BP5 Supporting rule requires 2 or 3 tumors with MSS and/or no loss of MMR protein expression and/or an LS-spectrum tumor with MMR-protein loss inconsistent with PMS2, 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/MLH1 findings.
• PMID:31433215 reports one exact-variant proband and records immunohistochemistry and microsatellite-instability results as ND, with no BRAF V600E or MLH1-methylation result.

Still missing

• At least two qualifying tumor observations, or one qualifying BRAF V600E/MLH1-methylation observation, are not available for this variant.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar Expert Panel assertion of Benign or Likely Benign. ClinVar shows zero Expert Panel submissions for this exact variant; the single Benign entry is a laboratory submission, while the aggregate record is conflicting and the remaining assertions are non-expert. The governing PMS2 VCEP also marks BP6 Not Applicable. Therefore BP6 is not met.

Rule

BP6: apply only for an exact-variant ClinVar Expert Panel Benign or Likely Benign classification; ordinary laboratory, aggregate, and non-expert assertions do not qualify.

Evidence considered

• The exact-variant ClinVar audit reports expert_panel_submissions: 0.
• ClinVar contains one Benign laboratory submission but no Benign or Likely Benign Expert Panel assertion; the aggregate classification is conflicting/Uncertain significance.
• The PMS2 VCEP specification marks BP6 as Not Applicable.

Still missing

• No exact-variant ClinVar Expert Panel Benign or Likely Benign classification is available.

Sources

Reasoning

The PMS2 VCEP specifies PS2 strength by de novo points: supporting at 0.5 points, moderate at 1–1.5, strong at 2–3.5, and very strong at ≥4. The exact variant c.682G>A (p.Gly228Ser) was reported in one Danish proband, but the available report documents no parental testing, confirmed de novo status, maternity/paternity confirmation, or de novo point assignment. Therefore, PS2 cannot be assessed from the available evidence.

Rule

PMS2 VCEP PS2: ≥4 de novo points = Very Strong; 2–3.5 = Strong; 1–1.5 = Moderate; 0.5 = Supporting.

Evidence considered

• The PMS2 VCEP PS2 rule assigns supporting strength at 0.5 de novo points, moderate at 1–1.5 points, strong at 2–3.5 points, and very strong at ≥4 points.
• PMID:31433215 reports c.682G>A (p.Gly228Ser) in one Danish proband (proband 28, age 37) but reports no parental testing, confirmed de novo status, or variant-specific de novo analysis.

Still missing

• Parental genotypes and confirmed maternity/paternity are not reported.
• No de novo point assignment or evidence of the variant being absent from both parents is available.

Sources

Reasoning

The applicable InSiGHT PMS2 VCEP requires calibrated functional odds or, for this missense variant, concordant functional testing under the MMR functional-assay flowchart. The reviewed evidence identifies NM_000535.7:c.682G>A (p.Gly228Ser) in one proband but explicitly reports no variant-specific functional assay, and no validated mammalian MMR activity, protein expression/stability, localization, or cellular assay result is available. PS3 therefore cannot be assigned at any strength from the available evidence.

Rule

Calibrated functional assays with functional odds for Pathogenicity >18.7 = Strong; >4.3 and <=18.7, or MMR function defect following the functional assay flowchart = Moderate; >2.08 and <=4.3 = Supporting.

Evidence considered

• The PMS2 VCEP specifies PS3 Strong for calibrated functional odds for pathogenicity >18.7, PS3 Moderate for odds >4.3 and <=18.7 or an MMR function defect following the functional-assay flowchart, and PS3 Supporting for odds >2.08 and <=4.3.
• The MMR functional-assay flowchart directs missense variants without predicted splicing impact to calibrated functional testing or two independent concordant assays, including mammalian MMR activity and follow-up protein or cellular assays when needed.
• PMID:31433215 reports c.682G>A/p.Gly228Ser in one Danish proband and classifies it as C3 (variant of unknown significance), but reports no variant-specific functional assay or functional measurement.

Still missing

• A validated, variant-specific functional assay is needed, preferably calibrated to clinical outcomes or meeting the VCEP MMR functional-assay flowchart requirements.
• No quantitative functional odds or functional likelihood ratio is available.

Sources

Reasoning

The 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 constitutional mismatch repair deficiency, with 1.0 point for a confirmed pathogenic/likely pathogenic variant in trans or 0.5 points when phase is unknown; 0.5, 1.0, 1.5, 2.0-3.5, and >=4 points correspond to Supporting, Moderate, Strong, and Very Strong PM3, respectively. The available case evidence documents NM_000535.7:c.682G>A (p.Gly228Ser) in one Danish proband, but reports no second PMS2 variant, no pathogenic/likely pathogenic classification of a partner allele, no phase information, and no CMMRD phenotype assessment. Therefore no PM3 points can be assigned and the criterion remains not assessed rather than met or not met.

Rule

PMS2 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; total points determine Supporting (0.5), Moderate (1-1.5), Strong (2-3.5), or Very Strong (>=4).

Evidence considered

• The PMS2 VCEP specifies PM3 for co-occurrence with a known pathogenic/likely pathogenic variant in the same gene in a patient with CMMRD-compatible clinical features; a pathogenic/likely pathogenic variant in trans contributes 1.0 point and phase-unknown co-occurrence contributes 0.5 points.
• The variant was reported in one Danish proband (proband 28, age 37 years) as c.682G>A/p.Gly228Ser and classified as a class 3 variant of unknown significance; the report gives no second PMS2 variant, phase, or variant-specific CMMRD assessment.
• Because neither a qualifying partner allele nor phase and CMMRD evidence are available, no PM3 points can be assigned.

Still missing

• A second PMS2 pathogenic or likely pathogenic variant is not documented.
• Trans or cis phase is not documented through parental, offspring, or other phasing studies.
• CMMRD-compatible clinical features for the proband are not documented.

Sources

Reasoning

The PMS2 VCEP requires cosegregation with disease and a combined Bayes likelihood ratio greater than 2.08 and up to 4.3 for supporting, greater than 4.3 and up to 18.7 for moderate, or greater than 18.7 in at least two families for strong. The exact variant is reported in one proband, with no affected or unaffected relatives, meioses, pedigree-level segregation results, or combined Bayes likelihood ratio documented. PP1 therefore cannot be assessed.

Rule

PMS2 VCEP PP1: supporting for combined Bayes likelihood ratio >2.08 and ≤4.3; moderate for >4.3 and ≤18.7; strong for >18.7 in ≥2 families.

Evidence considered

• The PMS2 VCEP PP1 thresholds are supporting for a combined Bayes likelihood ratio >2.08 and ≤4.3, moderate for >4.3 and ≤18.7, and strong for >18.7 in ≥2 families.
• PMID:31433215 reports c.682G>A (p.Gly228Ser) in one Danish proband but provides no variant-specific family segregation, informative meioses, or Bayes likelihood ratio.

Still missing

• No affected or unaffected relatives with variant testing are reported.
• No informative meioses, pedigree-level segregation analysis, or combined Bayes likelihood ratio is available.

Sources

Reasoning

The governing PMS2 InSiGHT VCEP requires BS2 for confirmed in-trans co-occurrence with a known pathogenic variant in the same gene in a patient with colorectal cancer after age 45 or another Lynch-spectrum cancer above its median age of onset, without prior or current CMMRD manifestations; parental or offspring testing must confirm phase. The available evidence contains no qualifying in-trans co-occurrence, phase confirmation, or sufficiently documented clinical/CMMRD assessment. gnomAD v4.1 reports zero homozygotes, but absence of homozygotes in a population database is not the VCEP BS2 rule and cannot establish BS2.

Rule

Co-occurrence in trans with a known pathogenic sequence variant in PMS2 in a patient with colorectal cancer after age 45 or another Lynch-spectrum cancer above the median age of onset, without clinical manifestations of CMMRD; phase requires parental or offspring testing.

Evidence considered

• The PMS2 Version 2.0 VCEP requires confirmed in-trans co-occurrence with a known pathogenic variant, qualifying cancer age/context, no CMMRD manifestations, and phase confirmation for BS2.
• gnomAD v4.1 reports zero homozygotes among 1,613,962 alleles, but this population observation does not satisfy the patient-level VCEP BS2 rule.

Still missing

• No qualifying patient-level in-trans co-occurrence with a known pathogenic PMS2 variant is documented.
• No parental or offspring testing confirms phase.
• No sufficient documentation establishes the required cancer age/context and absence of CMMRD manifestations.

Sources

Reasoning

The applicable InSiGHT PMS2 VCEP requires calibrated functional odds for benignity or variant-specific proficient protein and mRNA-based laboratory results under the MMR functional-assay flowchart. The reviewed evidence identifies NM_000535.7:c.682G>A (p.Gly228Ser) in one proband but explicitly reports no variant-specific functional assay, and no proficient MMR activity, protein, mRNA, or cellular assay result is available. BS3 therefore cannot be assigned at any strength from the available evidence.

Rule

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

Evidence considered

• The PMS2 VCEP specifies BS3 Strong for calibrated functional odds for pathogenicity <=0.05 or qualifying normal mRNA findings, and BS3 Supporting for odds >0.05 and <=0.48 or variant-specific proficient function in protein and mRNA-based assays following the MMR functional-assay flowchart.
• The MMR functional-assay flowchart requires variant-specific assay evidence establishing proficient function; absence of a reported assay does not establish benign function.
• PMID:31433215 reports c.682G>A/p.Gly228Ser in one Danish proband and classifies it as C3 (variant of unknown significance), but reports no variant-specific functional assay or proficient-function result.

Still missing

• A validated, variant-specific benign/proficient functional assay is needed, preferably calibrated to clinical outcomes or meeting the VCEP MMR functional-assay flowchart requirements.
• No quantitative functional odds or functional likelihood ratio is available.
• No variant-specific mRNA or protein-based proficient-function result is available.

Sources

Reasoning

The PMS2 VCEP requires lack of cosegregation with disease and a combined Bayes likelihood ratio below 0.05 for strong BS4 or greater than 0.05 and up to 0.48 for supporting BS4. The available exact-variant report contains no tested relatives, non-segregating observations, pedigree analysis, or combined Bayes likelihood ratio. BS4 cannot therefore be assessed.

Rule

PMS2 VCEP BS4: strong for combined Bayes likelihood ratio <0.05; supporting for >0.05 and ≤0.48.

Evidence considered

• The PMS2 VCEP BS4 thresholds are strong for a combined Bayes likelihood ratio <0.05 and supporting for >0.05 and ≤0.48.
• PMID:31433215 reports the exact variant in one proband but no relatives, non-segregation observations, pedigree analysis, or Bayes likelihood ratio.

Still missing

• No affected or unaffected relatives with variant and phenotype data are reported.
• No non-segregation events, pedigree analysis, or combined Bayes likelihood ratio is available.

Sources