Is MSH3 p.Ser33= (c.99C>T) pathogenic?

MSH3 p.Ser33= (c.99C>T) is classified Likely benign in MSH3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-19). No allele count reported in gnomAD v4.1 (AN 1,606,628); Associated with hereditary neoplastic syndrome.

What condition is associated with MSH3 p.Ser33= (c.99C>T)?

MSH3 p.Ser33= (c.99C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is MSH3 p.Ser33= (c.99C>T) in the general population?

MSH3 p.Ser33= (c.99C>T) is no allele count reported in gnomAD v4.1 (AN 1,606,628) (gnomAD).

MSH3 p.Ser33=

c.99C>T · rs2546710001 · VCV2991562

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,606,628)

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 1.5	GERP -3.7, phastCons 1
Overall
CADD	13.34	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,606,628). 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.Ser33=
Coding: c.99C>T
MANE Select: NM_002439
dbSNP: rs2546710001
Type: single nucleotide variant
Location: chr5:80654826 (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-ser33 (accessed [today's date]).

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