HS6ST2 p.Ala79=
c.237G>A · rs1384043599 · VCV2661457
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000112%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.21 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 0.39, phastCons 1 |
| Overall | ||
| CADD | 21.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000112%
European (non-Finnish) · 1/893,374 alleles
Overall
8.34e-05%
1/1,199,071 alleles · very rare
exomes 1/1,085,031 · genomes 0/114,040 · 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
- HS6ST2
- Protein
- p.Ala79=
- Coding
- c.237G>A
- MANE Select
- NM_001394073
- dbSNP
- rs1384043599
- Type
- single nucleotide variant
- Location
- chrX:132958366 (GRCh38)
- Structure
- AlphaFold pLDDT 74.28
Similar variants
- HS6ST2 p.Arg9Trp Uncertain significance ★★ ⚠ same type
- HS6ST2 p.Gly306Ala Uncertain significance ★★ ⚠ same type
- HS6ST2 p.Lys218Gln Uncertain significance ★★ ⚠ same type
- HS6ST2 p.Pro581Leu Uncertain significance ★★ ⚠ same type
- HS6ST2 p.Ala325= Benign/Likely benign ★★ same type
- HS6ST2 p.Arg51Leu Benign ★★ same type
- HS6ST2 p.Leu107= Benign ★★ same type
- HS6ST2 p.Ala202Ser 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/hs6st2-p-ala79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown