USP9X p.Ser38=
c.114T>G · rs762490407 · VCV2174659
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00655%, 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 1.3 | GERP -2.3, phastCons 1 |
| Overall | ||
| CADD | 8.173 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00655%
Admixed American · 3/45,791 alleles
Filtering AF
0.00174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000882%
Overall
0.00033%
4/1,210,718 alleles · very rare
exomes 4/1,096,859 · genomes 0/113,859 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00655% | 15,264 |
| European (non-Finnish) | 0.000112% | 895,031 |
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
- USP9X
- Protein
- p.Ser38=
- Coding
- c.114T>G
- MANE Select
- NM_001039591
- dbSNP
- rs762490407
- Type
- single nucleotide variant
- Location
- chrX:41129017 (GRCh38)
- Structure
- AlphaFold pLDDT 80.06 · 4 PDB
- Residue 38
- the 'disordered' region
Similar variants
- USP9X c.323-1G>A Pathogenic/Likely pathogenic ★★ same type
- USP9X p.Arg2085His Pathogenic/Likely pathogenic ★★ same type
- USP9X p.Arg2366Ter Pathogenic/Likely pathogenic ★★ same type
- USP9X p.Arg592Ter Pathogenic ★★ same type
- USP9X p.Arg916Ter Pathogenic ★★ same type
- USP9X c.6086-7T>G Uncertain significance ★★ same type
- USP9X p.Ala1059Gly Uncertain significance ★★ ⚠ same type
- USP9X p.Ala1059Thr 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/usp9x-p-ser38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown