Is MSH3 p.Ala52= (c.156A>G) pathogenic?

MSH3 p.Ala52= (c.156A>G) is classified Likely benign in MSH3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-12-09). Very rare (popmax 0.00273%, eas); Associated with hereditary neoplastic syndrome.

What condition is associated with MSH3 p.Ala52= (c.156A>G)?

MSH3 p.Ala52= (c.156A>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is MSH3 p.Ala52= (c.156A>G) in the general population?

MSH3 p.Ala52= (c.156A>G) is very rare (popmax 0.00273%, eas) (gnomAD).

MSH3 p.Ala52=

c.156A>G · rs761607646 · VCV1534113

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00273%, eas)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.037	GERP -1.5
Overall
CADD	8.791	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00273% East Asian · 1/36,600 alleles

Overall 0.00026% 2/768,034 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00273%	36,600
European (non-Finnish)	0.000163%	615,381

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MSH3
Protein: p.Ala52=
Coding: c.156A>G
MANE Select: NM_000791 · reported on NM_002439
dbSNP: rs761607646
Type: single nucleotide variant
Location: chr5:80654883 (GRCh38)

Full MSH3 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

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/msh3-p-ala52 (accessed [today's date]).

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