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PMS2
Final classification
VUS
PMS2 c.1321G>T · p.Glu441Ter
PMS2

NM_000535.6:c.1321G>T (p.Glu441Ter) is a nonsense variant in PMS2 exon 11 introducing a premature termination codon at position 441, which is well before the VCEP-defined PVS1 boundary at codon 798.

Gene
PMS2
Transcript
NM_000535.6
HGVS · transcript:coding
NM_000535.6:c.1321G>T
Consequence
N/A
GRCh38
chr7:5987444 C>A
GRCh37
chr7:6027075 C>A
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PMS2 Version 2.0 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: PVS1 very strong, PM2 supporting; 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 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: PVS1 very strong, PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PVS1PM2 VUS
PMS2 c.1321G>T

NM_000535.6:c.1321G>T (p.Glu441Ter) is a nonsense variant in PMS2 exon 11 introducing a premature termination codon at position 441, which is well before the VCEP-defined PVS1 boundary at codon 798.1 This variant meets PVS1 at Very Strong strength under the InSiGHT PMS2 VCEP v2.0 criteria for nonsense variants introducing a PTC ≤ codon 798.2 The variant is absent from gnomAD v2.1 and v4.1 population databases (0 alleles), meeting PM2 at Supporting strength under VCEP criteria (<0.00002 allele frequency threshold).3 No variant-specific functional data, de novo observations, cosegregation data, or tumor phenotype data were identified in the case materials or reviewed literature. SpliceAI predicts no significant splice impact (max delta 0.03), confirming that the primary molecular consequence is protein truncation rather than aberrant splicing.4 Under the InSiGHT PMS2 VCEP v2.0 combination rules, 1 Very Strong criterion (PVS1) plus 1 Supporting criterion (PM2) is sufficient for a Pathogenic classification (Rule 1 or Rule 4).5

PVS1 + PM2 VUS
Gene diagram · NM_000535.6 · variants mapped to exon structure
PMS2 NM_000535.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 10 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
Nonsense variant NM_000535.6:c.1321G>T introduces a premature termination codon at position 441 (p.Glu441Ter), which is ≤ codon 798. Per InSiGHT PMS2 VCEP v2.0, nonsense/frameshift variants introducing a PTC ≤ codon 798 meet PVS1 at Very Strong strength.
VCEP PVS1 rule: nonsense/frameshift PTC ≤ codon 798 in PMS2 → PVS1_VeryStrongMutalyzer confirms c.1321G>T produces p.(Glu441Ter) with premature termination at codon 441 of 863SpliceAI max delta 0.03 — no cryptic splice rescue concern
PM2 supporting Pathogenic
NM_000535.6:c.1321G>T is absent from gnomAD v2.1 and v4.1 (0 alleles). Per PMS2 VCEP v2.0, absence or extremely rare allele frequency (<0.00002, <1 in 50,000 alleles) in gnomAD v4 meets PM2 at Supporting strength.
Absent from gnomAD v2.1 (0 alleles)Absent from gnomAD v4.1 (0 alleles)Absent from gnomAD-Canada v1.0 (0 alleles)
Assessed · not applied
Pathogenic
PS2 No de novo occurrence data for NM_000535.6:c.1321G>T is present in the case materials or literature reviewed.
PS3 No variant-specific functional data exists for NM_000535.6:c.1321G>T (p.Glu441Ter).
PP1 No cosegregation data is available for NM_000535.6:c.1321G>T.
PP4 No tumor-specific MSI or IHC data is available for NM_000535.6:c.1321G>T carriers in the case materials.
Benign
BA1 NM_000535.6:c.1321G>T is absent from gnomAD v4.1 (Grpmax filtering allele frequency = 0).
BS1 NM_000535.6:c.1321G>T is absent from gnomAD v4.1.
BS2 No evidence of co-occurrence in trans with a known pathogenic PMS2 variant in a patient with CRC after age 45 and no CMMRD features.
BS3 No variant-specific functional data demonstrating proficient MMR function for NM_000535.6:c.1321G>T.
BS4 No lack-of-cosegregation data is available.
BP5 No tumor data showing MSS and/or retained PMS2 protein expression in variant carriers is available.
N/A · 16 PS1 · PS4 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BP1 · BP2 · BP3 · BP4 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory). (ClinVarID = 1769925)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). BayesDel score = 0.297099.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
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 · 6 PMIDs not cited in assessment
10439048 ↗ Mice defective in the DNA mismatch gene PMS2 are hypersensitive to MNU induced thymic lymphoma and are partially protected by transgenic expression of human MGMT. ONCOKB
10874005 ↗ Mutagenesis in PMS2- and MSH2-deficient mice indicates differential protection from transversions and frameshifts. ONCOKB
12697830 ↗ Dimerization of MLH1 and PMS2 limits nuclear localization of MutLalpha. ONCOKB
16144131 ↗ Two PMS2 mutations in a Turcot syndrome family with small bowel cancers. ONCOKB
20487569 ↗ MSH6 and PMS2 mutation positive Australian Lynch syndrome families: novel mutations, cancer risk and age of diagnosis of colorectal cancer. ONCOKB
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