NM_000249.4:c.549T>A is a nonsense variant predicted to introduce a premature termination codon at codon 183 (p.Tyr183Ter) in MLH1, a gene in which loss of function is an established cause of Lynch syndrome.1 Per the InSiGHT MLH1 VCEP, a nonsense/frameshift variant introducing a premature termination codon at or before codon 753 meets PVS1 at very strong strength.2 This variant has not been observed in gnomAD v2.1 or v4.1, meeting the InSiGHT MLH1 VCEP PM2_Supporting criterion.3 No ClinVar expert-panel classification exists for this variant; the only retrieved ClinVar record was a mismatched c.1272T>A entry and therefore carries no weight for PP5/BP6 (which are not applicable in this VCEP).4 PVS1 at very strong strength is independently sufficient for a Pathogenic classification under the InSiGHT MLH1 VCEP combination rules (Rule 1: one very strong pathogenic criterion).5
MLH1
Final classification
VUS
PVS1PM2
MLH1
c.549T>A
p.Tyr183Ter
stop gained
This variant
NM_000249.4:c.549T>A is a nonsense variant predicted to introduce a premature termination codon at codon 183 (p.Tyr183Ter) in MLH1, a gene in which loss of function is an established cause of Lynch syndrome.
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.549T>A
stop gained
PVS1 + PM2
→
VUS
Gene diagram
· NM_000249.4 · variants mapped to exon structure
MLH1
NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 10 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PVS1
very strong
Pathogenic
NM_000249.4:c.549T>A is a nonsense variant that introduces a premature termination codon at codon 183 (p.Tyr183Ter), well before the MLH1 cutoff of codon 753, and loss of function is an established disease mechanism for MLH1 in Lynch syndrome; this satisfies PVS1 at very strong strength per the InSiGHT MLH1 VCEP.
Nonsense (stop-gain) variant p.Tyr183Ter in exon 7Premature termination codon at codon 183before the codon 753 threshold
✓
PM2
supporting
Pathogenic
The variant is absent from gnomAD v2.1 and v4.1, meeting the InSiGHT MLH1 VCEP PM2_Supporting threshold of an allele frequency below 0.00002 (fewer than 1 in 50,000 alleles).
Absent from gnomAD v2.1 (exome)Absent from gnomAD v4.1 (exome)
Assessed · not applied
· 10 not met · 0 not assessed
Pathogenic
PS2
No de novo occurrence of this variant with confirmed maternity and paternity has been reported in the available evidence.
PS3
No calibrated functional assay or variant-specific functional study of p.Tyr183Ter was identified; the reviewed publications describe MLH1 function at the gene or domain level only.
PP1
No co-segregation data are available for this variant.
PP4
No tumor microsatellite instability (MSI) or MMR protein immunohistochemistry data are available for this variant to support PP4.
Benign
BA1
The variant is absent from gnomAD, so it does not meet the BA1 allele frequency threshold (>= 0.001 in gnomAD v4).
BS1
The variant is absent from gnomAD, so it does not meet the BS1 allele frequency threshold (>= 0.0001 and < 0.001 in gnomAD v4).
BS2
No observation of this variant in trans with a known pathogenic MLH1 variant in a patient without CMMRD has been reported.
BS3
No functional assay demonstrating normal (proficient) protein function for p.Tyr183Ter was identified; the reviewed publications are gene-level studies only.
BS4
No segregation data demonstrating lack of co-segregation with disease are available.
BP5
No tumor data (MSS tumors, no loss of MMR protein expression, BRAF V600E, or MLH1 promoter methylation) are available to support BP5.
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
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
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.273. BayesDel score = 0.66.
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.
COSMIC
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
Triaged references · 6 PMIDs not cited in assessment
11781295 ↗
Functional analysis of hMLH1 variants and HNPCC-related mutations using a human expression system.
ONCOKB
15713769 ↗
Conversion analysis for mutation detection in MLH1 and MSH2 in patients with colorectal cancer.
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
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