MSH3 p.Pro923fs
c.2768del · VCV3904729
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
familial adenomatous polyposis 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 20 of 24 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -3.9, phastCons 0.001 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- MSH3
- Protein
- p.Pro923fs
- Coding
- c.2768del
- MANE Select
- NM_002439
- Type
- Deletion
- Location
- chr5:80813695 (GRCh38)
- Gene constraint
- LOEUF 1.027 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.48 · 25 PDB
- Residue 923
- a β-strand
Disease context
familial adenomatous polyposis 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor MSH3-related polyposis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Neonatal
Similar variants
- MSH3 c.1564_1568+18del Pathogenic/Likely pathogenic ★★ same condition
- MSH3 c.2814delG Pathogenic ★★ same condition
- MSH3 p.Ala283fs Pathogenic ★★ same condition
- MSH3 p.Arg85fs Pathogenic ★★ same condition
- MSH3 p.Asn591fs Pathogenic ★★ same condition
- MSH3 p.Asn880fs Pathogenic ★★ same condition
- MSH3 p.Asp1051fs Pathogenic ★★ same condition
- MSH3 p.Asp199fs 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/msh3-p-pro923fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown