USP10 p.Ser203=
c.609A>C · VCV4821635
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00834%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -3.9 |
| Overall | ||
| CADD | 0.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00834%
Admixed American · 5/59,988 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00031%
5/1,613,608 alleles · very rare
exomes 5/1,461,318 · genomes 0/152,290 · joint denominator
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
- USP10
- Protein
- p.Ser203=
- Coding
- c.609A>C
- MANE Select
- NM_005153
- Type
- single nucleotide variant
- Location
- chr16:84745090 (GRCh38)
- Gene constraint
- LOEUF 0.404 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.19 · 2 PDB
- Residue 203
- a UniProt-annotated variant site (in); the 'disordered' region
Similar variants
- USP10 p.Ala108Gly Uncertain significance ★ ⚠ same type
- USP10 p.Ala123Thr Uncertain significance ★ ⚠ same type
- USP10 p.Ala132Ser Uncertain significance ★ ⚠ same type
- USP10 p.Ala239Ser Uncertain significance ★ ⚠ same type
- USP10 p.Ala259Gly Uncertain significance ★ ⚠ same type
- USP10 p.Ala270Thr Uncertain significance ★ ⚠ same type
- USP10 p.Ala298Pro Uncertain significance ★ ⚠ same type
- USP10 p.Ala320Val Uncertain significance ★ ⚠ same type
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/usp10-p-ser203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown