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MLH1
Final classification
VUS
MLH1 c.551C>G · p.Ser184Ter
MLH1

NM_000249.3:c.551C>G (p.Ser184Ter) is a nonsense variant that introduces a premature termination codon at codon 184 of MLH1, well before the VCEP threshold of codon 753, meeting PVS1_VeryStrong.

Gene
MLH1
Transcript
NM_000249.3
HGVS · transcript:coding
NM_000249.3:c.551C>G
Consequence
N/A
GRCh38
chr3:37011825 C>G
GRCh37
chr3:37053316 C>G
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 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 MLH1 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
MLH1 c.551C>G

NM_000249.3:c.551C>G (p.Ser184Ter) is a nonsense variant that introduces a premature termination codon at codon 184 of MLH1, well before the VCEP threshold of codon 753, meeting PVS1_VeryStrong.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, meeting PM2_Supporting under the InSiGHT VCEP threshold of <0.00002 allele frequency.2 ClinVar reports this variant as Pathogenic with 3 clinical laboratory submissions, classified as criteria provided, single submitter. However, under the InSiGHT VCEP, PP5 and BP6 are not applicable, and ClinVar classification alone does not independently satisfy other criteria.3 No variant-specific functional studies, patient phenotype data, co-segregation data, or de novo observations were identified in the available literature or case materials.

PVS1 + PM2 VUS
Gene diagram · NM_000249.3 · variants mapped to exon structure
MLH1 NM_000249.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 10 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_000249.3:c.551C>G is a nonsense variant that introduces a premature termination codon at codon 184 (p.Ser184Ter), well before codon 753 of MLH1. Under the InSiGHT VCEP v2.0 PVS1 rules, nonsense variants introducing a PTC at or before codon 753 qualify for PVS1_VeryStrong. Loss of function is an established disease mechanism for MLH1 in Lynch syndrome.
Nonsense variant (C>G) at codon 184 creates p.(Ser184Ter)PTC located at codon 184well before the VCEP threshold of codon 753
PM2 supporting Pathogenic
NM_000249.3:c.551C>G is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases. Under the InSiGHT VCEP v2.0, PM2_Supporting is met when the variant allele frequency is <0.00002 (<1 in 50,000 alleles) in gnomAD v4, which is satisfied by complete absence.
Absent from gnomAD v2.1Absent from gnomAD v4.1Absent from gnomAD-Canada v1.0
Assessed · not applied
Pathogenic
PS2 No de novo observations have been reported for this variant in the available evidence.
PS3 No variant-specific functional assay data is available for NM_000249.3:c.551C>G in the calibrated MMR functional assay documentation or the literature.
PP1 No co-segregation data is available for this variant in the case materials.
PP4 No patient-specific phenotype data (MSI status, IHC, tumor type) is available for this variant in the case materials.
Benign
BA1 BA1 under the InSiGHT VCEP v2.0 requires a gnomAD v4 Grpmax filtering allele frequency ≥ 0.001 (0.1%).
BS1 BS1 under the InSiGHT VCEP v2.0 requires a gnomAD v4 Grpmax filtering allele frequency ≥ 0.0001 and < 0.001 (0.01-0.1%) with exclusion of founder pathogenic variants.
BS2 BS2 under the InSiGHT VCEP v2.0 requires co-occurrence in trans with a known pathogenic variant in a patient with colorectal cancer after age 45 without CMMRD features.
BS3 No variant-specific functional data demonstrating a benign or normal functional effect is available.
BS4 No co-segregation or lack-of-segregation data is available for this variant.
BP5 No tumor data demonstrating MSS status, retained MMR protein expression, or an alternate molecular basis for disease is available for this variant.
N/A · 13 PS1 · PS4 · PM1 · PM5 · PM6 · PP2 · PP3 · PP5 · BP1 · BP2 · 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 (3 clinical laboratories). (ClinVarID = 455446)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.112. BayesDel score = 0.66.
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 · 8 PMIDs not cited in assessment
15713769 ↗ Conversion analysis for mutation detection in MLH1 and MSH2 in patients with colorectal cancer. ONCOKB
10359802 ↗ Different mutator phenotypes in Mlh1- versus Pms2-deficient mice. ONCOKB
11781295 ↗ Functional analysis of hMLH1 variants and HNPCC-related mutations using a human expression system. ONCOKB
12697830 ↗ Dimerization of MLH1 and PMS2 limits nuclear localization of MutLalpha. ONCOKB
16216036 ↗ Tumours from MSH2 mutation carriers show loss of MSH2 expression but many tumours from MLH1 mutation carriers exhibit weak positive MLH1 staining. ONCOKB
24362816 ↗ Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. 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
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR