Is MSH3 p.Arg4Trp (c.10C>T) pathogenic?

MSH3 p.Arg4Trp (c.10C>T) is classified Uncertain significance in MSH3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-18). AlphaMissense: ambiguous (0.5581); Very rare (popmax 0.00034%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with MSH3 p.Arg4Trp (c.10C>T)?

MSH3 p.Arg4Trp (c.10C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is MSH3 p.Arg4Trp (c.10C>T) in the general population?

MSH3 p.Arg4Trp (c.10C>T) is very rare (popmax 0.00034%, nfe) (gnomAD).

What do computational predictors say about MSH3 p.Arg4Trp (c.10C>T)?

AlphaMissense predicts ambiguous (score 0.5581) — an in-silico prediction, not a clinical call.

MSH3 p.Arg4Trp

c.10C>T · rs761912573 · VCV970069

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.5581 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00034%, nfe)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.5581	ambiguous
REVEL	0.398	indeterminate
SaProt	LLR -11.80	damaging
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.4	GERP -0.073, phastCons 0.65
Regional constraint	o/e 1.08	unconstrained · MANE · 221 kb · p 0.0024 · regional, not allelic
Overall
CADD	25.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00034% European (non-Finnish) · 4/1,175,564 alleles

Filtering AF 8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000276% 4/1,448,928 alleles · very rare

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.Arg4Trp
Coding: c.10C>T
MANE Select: NM_000791 · reported on NM_002439
dbSNP: rs761912573
Type: single nucleotide variant
Location: chr5:80654737 (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-arg4trp (accessed [today's date]).

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