Is MSH2 p.Ala45= (c.135G>A) pathogenic?

MSH2 p.Ala45= (c.135G>A) is classified Benign/Likely benign in MSH2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-12-03). No allele count reported in gnomAD v4.1 (AN 1,606,070); Associated with Hereditary nonpolyposis colorectal neoplasms.

What condition is associated with MSH2 p.Ala45= (c.135G>A)?

MSH2 p.Ala45= (c.135G>A) is associated with Hereditary nonpolyposis colorectal neoplasms, Lynch syndrome 1, hereditary neoplastic syndrome (ClinVar).

How common is MSH2 p.Ala45= (c.135G>A) in the general population?

MSH2 p.Ala45= (c.135G>A) is no allele count reported in gnomAD v4.1 (AN 1,606,070) (gnomAD).

MSH2 p.Ala45=

c.135G>A · rs890172773 · VCV415003

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,606,070)

Conditions

Hereditary nonpolyposis colorectal neoplasms

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 0.13	GERP -3.8, phastCons 0.58
Overall
CADD	11.12	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,606,070). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MSH2
Protein: p.Ala45=
Coding: c.135G>A
MANE Select: NM_000251
dbSNP: rs890172773
Type: single nucleotide variant
Location: chr2:47403326 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.60 · 30 PDB
Residue 45: a β-strand; a UniProt-annotated variant site (in lynch1; uncertain significance; no decrease in mismatch repair activity)

Full MSH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Hereditary nonpolyposis colorectal neoplasms — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Lynch syndrome 1 hereditary neoplastic syndrome

Similar variants

MSH2 p.Ala45Glu Uncertain significance ★★ ⚠ same residue
MSH2 p.Ala45Val Benign/Likely benign ★★ same residue
MSH2 p.Ala45Thr Uncertain significance ★ ⚠ same residue
MSH2 c.1076+1G>A Pathogenic ★★★ same condition
MSH2 c.1076+1G>T Likely pathogenic ★★★ same condition
MSH2 c.1077-1G>C Likely pathogenic ★★★ same condition
MSH2 c.1077-1G>T Likely pathogenic ★★★ same condition
MSH2 c.1077-2A>C 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/msh2-p-ala45 (accessed [today's date]).

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