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NM_000249.4:c.1759A>G
p.Met587Val · MLH1
0%
complete
Final classification
VUS
PM2
MLH1
c.1759A>G
p.Met587Val
missense · exon 16

MLH1 encodes a DNA mismatch repair protein that, together with partners such as PMS2, corrects errors that arise during DNA replication. Loss of this repair function leads to the accumulation of mutations, particularly in repetitive microsatellite sequences, and tumors with defective MLH1 typically show high microsatellite instability. Germline mutations in MLH1 cause Lynch syndrome (hereditary non-polyposis colorectal cancer), which strongly predisposes to colorectal, endometrial, ovarian, and other cancers, while biallelic mutations cause constitutional mismatch repair deficiency (CMMRD). Because it normally protects against cancer by maintaining genomic stability, MLH1 acts as a tumor suppressor, and mismatch-repair-deficient tumors often respond well to immunotherapy.

This variant

MLH1 encodes a DNA mismatch repair protein whose loss of function causes genomic instability and predisposes to Lynch syndrome and constitutional mismatch repair deficiency.

Transcript
NM_000249.4
HGVS · transcript:coding
NM_000249.4:c.1759A>G
GRCh38
chr3:37047546 A>G
GRCh37
chr3:37089037 A>G
VUS: PM2 (supporting) is met, but the MLH1 VCEP's criteria-combination rules do not establish a pathogenic or benign classification.
Classification rationale
PM2 VUS
MLH1 c.1759A>G missense · exon 16

PM2 Supporting: the variant is absent from gnomAD v4.1, meeting the VCEP rarity threshold.

PM2 → VUS
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_000249.4 · variants mapped to exon structure
MLH1 NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 15 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 · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met, Supporting: the variant is absent from gnomAD v4.1, satisfying the VCEP PM2 threshold of <0.00002.
gnomAD v4.1: variant absent, corresponding to an allele frequency below 0.00002 for application of the VCEP PM2 rule.VCEP-pilot-variants---MMR.xlsx was searched for c.1759A>G, p.Met587Val, and p.M587V; no matching row was found.
Assessed · not applied · 6 not met · 9 not assessed
Pathogenic
PS1 Not met: no different nucleotide change encoding p.Met587Val was established as Pathogenic by the MLH1 VCEP in the searched governing materials.
PS2 Not assessed: no documented de novo result, parental confirmation, qualifying LS-spectrum tumor, or VCEP de novo-point assignment is available.
PS3 Not assessed: no variant-specific calibrated functional odds or flowchart-qualified MMR function-defect result is available.
PM3 Not assessed: PM2_Supporting is met because the variant is absent from gnomAD v4.1, but no second MLH1 variant or phase/CMMRD evidence is available.
PM5 Not met: the target HCI prior is 0.5956, below the VCEP PP3-supporting threshold of >0.68 required before PM5 can be used.
PP1 Not assessed: no informative pedigree observations or combined Bayes likelihood ratio is available to compare with the VCEP PP1 thresholds.
PP3 Not met: HCI prior probability 0.5956 is below the VCEP PP3 Supporting threshold of >0.68 for missense variants.
PP4 Not assessed: no qualifying CRC/endometrial MSI-H or consistent MMR-protein-loss evidence with excluded MLH1 methylation is documented.
Benign
BA1 Not met: the variant is absent from gnomAD v4.1, below the VCEP's BA1 threshold of >=0.001 (0.1%).
BS1 Not met: the variant is absent from gnomAD v4.1, below the VCEP's BS1 frequency interval of 0.0001 to <0.001.
BS2 Not assessed: no documented qualifying trans co-occurrence, clinical eligibility, CMMRD assessment, or parental/offspring phase confirmation is available.
BS3 Not assessed: no variant-specific calibrated functional odds or flowchart-qualified proficient protein or mRNA assay result is available.
BS4 Not assessed: no non-segregation observation or combined Bayes likelihood ratio is available to compare with the VCEP BS4 thresholds.
BP4 Not met: HCI prior probability 0.5956 is not below the VCEP BP4 threshold of <0.11 for missense variants.
BP5 Not assessed: no qualifying MSS, MMR-protein, BRAF V600E, or MLH1-methylation tumor evidence is documented for this patient.
N/A · 12 PVS1 · PS4 · PM1 · PM4 · 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
Absent from gnomAD v4.1.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.97978e-06; MAF= 0.00040%, 1/251270 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26627e-05; MAF= 0.00327%, 1/30616 alleles, homozygotes = 0).
🇨🇦 CA
Not available in 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
0.0004% · 1 / 251,270
0 hom
South Asian
1 / 30,616
0.0033%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-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 (5 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 629891)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.648. BayesDel score = 0.232938. HCI prior probability for pathogenicity = 0.5956. MAPP score = 27.32. Custom PP2 score = 0.488.
Functional / OncoKB screenshot
Functional Inconclusive
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Inconclusive; curated oncogenicity label: Inconclusive.
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 previously been reported in somatic cancers (COSMIC; COSV51618651, n = 2 times).
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
18206535 ↗ Somatic mutations in mismatch repair genes in sporadic gastric carcinomas are no ONCOKB
20301390 ↗ Lynch Syndrome. CLINVAR
22167527 ↗ Identification of individuals at risk for Lynch syndrome using targeted evaluati CLINVAR
23408351 ↗ Revised guidelines for the clinical management of Lynch syndrome (HNPCC): recomm CLINVAR
24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint co CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification crite CLINVAR
31302137 ↗ Lynch Syndrome in Urologic Malignancies - What Does the Urologist Need to Know? CLINVAR