NM_000249.3:c.1177C>A (p.Leu393Ile) in MLH1 is a missense substitution absent from gnomAD population databases (PM2_Supporting met) but with a low HCI prior probability of pathogenicity of 0.0225 (BP4_Supporting met).1 The variant is absent from ClinVar and has not been observed in any publication. No variant-specific functional data, tumor phenotype data, segregation data, or de novo observations are available.2 Multiple in silico predictors are indeterminate or benign: SpliceAI max delta 0.02 (no splicing impact), REVEL 0.415, BayesDel -0.07.3 Under the InSiGHT MLH1 VCEP v2.0 framework, the evidence profile (PM2_Supporting + BP4_Supporting) is insufficient to reach a Likely Pathogenic or Likely Benign classification. The variant remains a Variant of Uncertain Significance.4
MLH1
Final classification
Uncertain Significance - Conflicting Evidence
MLH1 c.1177C>A · p.Leu393Ile
MLH1
NM_000249.3:c.1177C>A (p.Leu393Ile) in MLH1 is a missense substitution absent from gnomAD population databases (PM2_Supporting met) but with a low HCI prior probability of pathogenicity of 0.0225 (BP4_Supporting met).
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: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2
BP4
Uncertain Significance - Conflicting Evidence
MLH1 c.1177C>A
PM2 + BP4
→
Uncertain Significance - Conflicting Evidence
Gene diagram
· NM_000249.3 · variants mapped to exon structure
MLH1
NM_000249.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 13 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
NM_000249.3:c.1177C>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0, meeting the InSiGHT VCEP PM2_Supporting threshold of allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4.
Absent from gnomAD v2.1 (0 alleles).Absent from gnomAD v4.1 (0 alleles).Absent from gnomAD-Canada v1.0 (0 alleles).
✓
BP4
supporting
Benign
HCI prior probability for pathogenicity is 0.0225, meeting the InSiGHT VCEP BP4_Supporting threshold of <0.11. Multiple in silico predictors also suggest a benign or indeterminate effect: SpliceAI max delta 0.02 (no splicing impact), REVEL 0.415 (indeterminate), BayesDel -0.07 (indeterminate).
HCI prior probability 0.0225 (<0.11 threshold for BP4_Supporting).SpliceAI max delta 0.02 (no predicted splice impact).REVEL 0.415
Assessed · not applied
Pathogenic
PS1
No different nucleotide change encoding the same amino acid substitution (p.Leu393Ile) has been established as pathogenic by this VCEP.
PS2
No de novo observations have been reported for NM_000249.3:c.1177C>A in the available literature or databases.
PS3
No variant-specific functional data are available for c.1177C>A (p.Leu393Ile).
PM5
No missense change at amino acid residue 393 has been classified as pathogenic or likely pathogenic by this VCEP.
PP1
No co-segregation data are available for this variant in any pedigree.
PP3
HCI prior probability for pathogenicity is 0.0225, well below the InSiGHT VCEP PP3 thresholds (>0.81 for moderate, >0.68 for supporting).
PP4
No tumor data (MSI-H status, MMR protein expression, or MLH1 promoter methylation) are available for carriers of this variant.
Benign
BA1
The variant is absent from gnomAD v4.1, not meeting the BA1 threshold of gnomAD v4 Grpmax filtering allele frequency >= 0.001 (0.1%).
BS1
The variant is absent from gnomAD v4.1, not meeting the BS1 threshold of gnomAD v4 Grpmax filtering allele frequency >= 0.0001 and < 0.001 (0.01-0.1%).
BS2
No observation of this variant in trans with a known pathogenic MLH1 variant in a patient without CMMRD features has been reported.
BS3
No functional data demonstrating a benign effect for c.1177C>A (p.Leu393Ile) are available.
BS4
No lack-of-segregation data are available for this variant.
BP5
No tumor data demonstrating MSS status, retained MMR protein expression, or BRAF V600E/MLH1 methylation in carriers of this variant are available.
N/A · 10
PVS1 · PS4 · PM1 · PM6 · PP2 · PP5 · BP1 · BP2 · 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 = 0.02). REVEL score = 0.415. BayesDel score = -0.0696399. HCI prior probability for pathogenicity = 0.0225. MAPP score = 5.83. Custom PP2 score = 0.335.
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. MLH1, a DNA mismatch repair protein, is recurrently altered by deletion and mutation in various cancer types.
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