Is MLH1 p.Val15= (c.45G>A) pathogenic?

MLH1 p.Val15= (c.45G>A) is classified Benign/Likely benign in MLH1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-15). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with MLH1 p.Val15= (c.45G>A)?

MLH1 p.Val15= (c.45G>A) is associated with hereditary neoplastic syndrome, Lynch syndrome 2 (ClinVar).

How common is MLH1 p.Val15= (c.45G>A) in the general population?

MLH1 p.Val15= (c.45G>A) is absent from gnomAD v4.1 (gnomAD).

MLH1 p.Val15=

c.45G>A · rs768409958 · VCV1668903

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.79	phastCons 1
Overall
CADD	12.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MLH1
Protein: p.Val15=
Coding: c.45G>A
MANE Select: NM_000249
dbSNP: rs768409958
Type: single nucleotide variant
Location: chr3:36993592 (GRCh38)
Gene constraint: LOEUF 0.639 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.89 · 13 PDB
Residue 15: an α-helix

Full MLH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Lynch syndrome 2

Similar variants

MLH1 p.Val15Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
MLH1 p.Val15Met Conflicting classifications of pathogenicity ★ ⚠ same residue
MLH1 p.Val15fs Pathogenic ★ same residue
MLH1 p.Val15Gly Uncertain significance ★ ⚠ same residue
MLH1 p.Val15Leu Uncertain significance ★ ⚠ same residue
MLH1 c.1038+1G>C Likely pathogenic ★★★ same condition
MLH1 c.1039-1G>A Pathogenic ★★★ same condition
MLH1 c.1039-2A>G Likely pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mlh1-p-val15 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown