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PMS2
Final classification
VUS
PMS2 c.2380C>T · p.Pro794Ser
PMS2

NM_000535.7:c.2380C>T (p.Pro794Ser) is a missense variant in exon 14 of PMS2.

Gene
PMS2
Transcript
NM_000535.7
HGVS · transcript:coding
NM_000535.7:c.2380C>T
Consequence
N/A
GRCh38
chr7:5977653 G>A
GRCh37
chr7:6017284 G>A
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PMS2 Version 2.0.0 v2.0.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 moderate; no rule matched the adjudicated criteria.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PMS2 Version 2.0.0 v2.0.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 moderate; no rule matched the adjudicated criteria.
Classification rationale
PM2PP3 VUS
PMS2 c.2380C>T

NM_000535.7:c.2380C>T (p.Pro794Ser) is a missense variant in exon 14 of PMS2. This variant is extremely rare in population databases: gnomAD v4.1 grpmax filtering allele frequency is 3.67e-06 (5/1,604,584 alleles), meeting the VCEP PM2_Supporting threshold of <0.00002.1 The HCI prior probability for pathogenicity is 0.8253, exceeding the VCEP PP3_Moderate threshold of >0.81, supporting a deleterious computational prediction.2 No functional studies, segregation data, tumor pathology data, or de novo observations are available for this variant. The variant is absent from COSMIC and OncoKB reports no variant-specific functional evidence.3 In ClinVar, this variant is classified as Uncertain Significance by 12 clinical laboratories and as Benign by 1 laboratory (ClinVar ID 220740), with no expert panel classification.4 Applying the ClinGen InSiGHT PMS2 VCEP v2.0.0 combining criteria: PM2_Supporting (1 point) and PP3_Moderate (2 points) are met. These do not reach any pathogenic classification tier (requires ≥1 Strong or ≥3 Moderate for Likely Pathogenic, or ≥2 Supporting for Likely Benign). The variant remains a Variant of Uncertain Significance.5

PM2 + PP3 VUS
Gene diagram · NM_000535.7 · variants mapped to exon structure
PMS2 NM_000535.7
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 13 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is extremely rare in population databases, meeting the VCEP PM2_Supporting threshold. In gnomAD v4.1, the grpmax filtering allele frequency is 3.67e-06 (5/1,604,584 alleles), well below the VCEP cutoff of <0.00002 (<1 in 50,000 alleles). One homozygote is observed in gnomAD v4.1, which may represent a technical artifact given the PMS2/PMS2CL pseudogene homology, but does not disqualify the allele frequency criterion.
gnomAD v4.1 grpmax FAF = 3.67e-06 (< 0.00002 VCEP PM2_Supporting threshold)gnomAD v2.1 AF = 8.07e-06 (2/247772 alleles
PP3 moderate Pathogenic
The HCI prior probability for pathogenicity (MAPP/PP2 Prior P score) for c.2380C>T (p.Pro794Ser) is 0.8253, exceeding the VCEP PP3_Moderate threshold of >0.81. This in silico predictor, calibrated for PMS2 missense variants, supports a deleterious effect. SpliceAI predicts no splicing impact (max delta = 0.00), so the in silico evidence is limited to the amino acid substitution effect.
HCI prior probability = 0.8253 (> 0.81 PP3_Moderate threshold)MAPP score = 17.5custom PP2 score = 0.999
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change (p.Pro794Ser) from a different underlying nucleotide change previously classified as Pathogenic or Likely Pathogenic by this VCEP.
PS2 PS2 requires de novo occurrence with confirmed maternity and paternity in a patient with MMR-deficient LS-spectrum tumor.
PS3 PS3 requires variant-specific functional evidence from calibrated assays with defined odds of pathogenicity.
PM5 PM5 requires a different missense change at the same amino acid residue (codon 794) previously classified as Pathogenic or Likely Pathogenic by this VCEP, with PP3 also being met.
PP1 PP1 requires co-segregation with disease in pedigrees with a combined Bayes Likelihood Ratio meeting VCEP thresholds.
PP4 PP4 requires MSI-H colorectal/endometrial tumors with loss of MMR protein expression consistent with PMS2.
Benign
BA1 BA1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.0028 (0.28%).
BS1 BS1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.00028 and < 0.0028.
BS2 BS2 requires co-occurrence in trans with a known pathogenic PMS2 variant in a CRC patient after age 45 without CMMRD features.
BS3 BS3 requires calibrated functional assays demonstrating a benign effect (odds of pathogenicity ≤ 0.05 for BS3_Strong, or proficient function per the MMR functional assay flowchart for BS3_Supporting).
BS4 BS4 requires lack of co-segregation with disease in pedigrees meeting Bayes Likelihood Ratio thresholds.
BP4 BP4_Supporting for missense variants requires an HCI prior probability < 0.11.
BP5 BP5 requires MSS colorectal/endometrial tumors and/or loss of MMR protein expression inconsistent with PMS2.
N/A · 11 PVS1 · PS4 · PM1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 3.11607e-06; MAF= 0.00031%, 5/1604584 alleles, homozygotes = 1) and has highest observed frequency in the South Asian population (AF= 2.20955e-05; MAF= 0.00221%, 2/90516 alleles, homozygotes = 0); grpmax FAF= 3.67e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 8.07194e-06; MAF= 0.00081%, 2/247772 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.29012e-05; MAF= 0.00329%, 1/30394 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00031% · 5 / 1,604,584
1 hom · FAF 0.00037%
South Asian
2 / 90,516
0.0022%
European (non-Finnish)
3 / 1,173,772
0.00026%
1 hom
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.00081% · 2 / 247,772
0 hom
South Asian
1 / 30,394
0.0033%
European (non-Finnish)
1 / 111,322
0.0009%
+ 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (12 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 220740)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.543. BayesDel score = 0.0268987. HCI prior probability for pathogenicity = 0.8253. MAPP score = 17.5. Custom PP2 score = 0.999.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PMS2, an endonuclease involved in DNA repair, is altered in various cancers.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 9 PMIDs not cited in assessment
20186688 ↗ Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of Lynch syndrome patients. CLINVAR
23709753 ↗ Refining the role of PMS2 in Lynch syndrome: germline mutational analysis improved by comprehensive assessment of variants. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
20301390 ↗ Lynch Syndrome. CLINVAR
22167527 ↗ Identification of individuals at risk for Lynch syndrome using targeted evaluations and genetic testing: National Society of Genetic Counselors and the Collaborative Group of the Americas on Inherited Colorectal Cancer joint practice guideline. CLINVAR
23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR