STS p.His205=
c.615C>T · VCV4809351
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0568%, 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 -9.8 | GERP -7.3 |
| Overall | ||
| CADD | 0.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0568%
Admixed American · 26/45,757 alleles
Filtering AF
0.0398%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0341%
Overall
0.00355%
43/1,209,617 alleles · ultra-rare
exomes 39/1,098,100 · genomes 4/111,517 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0568% | 1,760 |
| African / African-American | 0.0105% | 9,521 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,792 |
| East Asian | 0.00297% | 33,716 |
| South Asian | 0.00176% | 56,747 |
| European (non-Finnish) | 0.000782% | 127,868 |
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.His205=
- Coding
- c.615C>T
- MANE Select
- NM_001320752
- Type
- single nucleotide variant
- Location
- chrX:7259581 (GRCh38)
- Structure
- AlphaFold pLDDT 94.31 · 2 PDB
- Residue 205
- an α-helix
Similar variants
- STS p.His205Arg Uncertain significance ★ ⚠ same residue
- 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
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-his205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown