Is MSH3 p.Pro49= (c.147T>C) pathogenic?

MSH3 p.Pro49= (c.147T>C) is classified Likely benign in MSH3 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-02-01). No allele count reported in gnomAD v4.1 (AN 1,538,668); Associated with hereditary neoplastic syndrome.

What condition is associated with MSH3 p.Pro49= (c.147T>C)?

MSH3 p.Pro49= (c.147T>C) is associated with hereditary neoplastic syndrome (ClinVar).

How common is MSH3 p.Pro49= (c.147T>C) in the general population?

MSH3 p.Pro49= (c.147T>C) is no allele count reported in gnomAD v4.1 (AN 1,538,668) (gnomAD).

MSH3 p.Pro49=

c.147T>C · rs1450213881 · VCV1114240

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,538,668)

Conditions

hereditary neoplastic syndrome

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 -2.4	GERP -3.6
Overall
CADD	3.014	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,538,668). 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: MSH3
Protein: p.Pro49=
Coding: c.147T>C
MANE Select: NM_002439
dbSNP: rs1450213881
Type: single nucleotide variant
Location: chr5:80654874 (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-pro49 (accessed [today's date]).

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