STS p.Ala403=
c.1209C>A · VCV4948683
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000165%)
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 0.62 | GERP 5.5 |
| Overall | ||
| CADD | 1.077 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000165%
Overall
0.000165%
2/1,211,247 alleles · very rare
exomes 2/1,097,945 · genomes 0/113,302 · 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
- STS
- Protein
- p.Ala403=
- Coding
- c.1209C>A
- MANE Select
- NM_001320752
- Type
- single nucleotide variant
- Location
- chrX:7325466 (GRCh38)
- Structure
- AlphaFold pLDDT 94.31 · 2 PDB
- Residue 403
- an α-helix
Similar variants
- STS p.Gly354Arg Likely pathogenic ★★ same type
- STS p.Arg381Ser Uncertain significance ★★ ⚠ same type
- STS p.Asp397Asn Uncertain significance ★★ ⚠ same type
- STS c.1082-55C>T Likely benign ★★ same type
- STS c.1082-76G>A Benign ★★ same type
- STS c.1241+15G>C Benign ★★ same type
- STS c.138-9T>G Likely benign ★★ same type
- STS c.383-16C>T Benign/Likely benign ★★ 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/sts-p-ala403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown