STS p.Leu522=
c.1566C>T · rs149343264 · VCV772187
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.651%, afr)
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 -3.1 | GERP 0.92 |
| Overall | ||
| CADD | 0.107 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.651%
African / African-American · 374/57,416 alleles
Filtering AF
0.597%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.576%
Overall
0.0363%
440/1,210,584 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.651% | 154 |
| Admixed American | 0.0567% | 1,764 |
| Remaining individualsnot grpmax-eligible | 0.042% | 2,381 |
| Middle Eastern | 0.023% | 4,356 |
| European (non-Finnish) | 0.00212% | 47,121 |
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.Leu522=
- Coding
- c.1566C>T
- MANE Select
- NM_001320752
- dbSNP
- rs149343264
- Type
- single nucleotide variant
- Location
- chrX:7350090 (GRCh38)
- Structure
- AlphaFold pLDDT 94.31 · 2 PDB
- Residue 522
- 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-leu522 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown