CHST6 p.Ala13=
c.39G>A · rs760232320 · VCV3040696
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0314%, amr)
Conditions
1
CHST6-related disorder
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 -3.6 | GERP -3.7 |
| Overall | ||
| CADD | 3.821 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0314%
Admixed American · 17/54,120 alleles
Filtering AF
0.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0164%
Overall
0.0024%
38/1,582,210 alleles · ultra-rare
exomes 27/1,429,996 · genomes 11/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0314% | 3,184 |
| Remaining individualsnot grpmax-eligible | 0.00326% | 30,700 |
| European (non-Finnish) | 0.00163% | 61,359 |
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
- CHST6
- Protein
- p.Ala13=
- Coding
- c.39G>A
- MANE Select
- NM_021615
- dbSNP
- rs760232320
- Type
- single nucleotide variant
- Location
- chr16:75479790 (GRCh38)
- Gene constraint
- LOEUF 1.71 · pLI 0.26 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 90.66
Disease context
CHST6-related disorder
Similar variants
- CHST6 p.Ala128Thr Likely pathogenic ★★ ⚠ same condition
- CHST6 p.Arg127Cys Pathogenic ★★ same condition
- CHST6 p.Glu274Lys Pathogenic ★★ same condition
- CHST6 p.Leu200Arg Pathogenic ★★ same condition
- CHST6 p.Ala128Val Pathogenic ★ same condition
- CHST6 p.Ser131Leu Pathogenic ★ same condition
- CHST6 p.Ser210Phe Likely pathogenic ★ same condition
- CHST6 p.Val329Leu Pathogenic ★ ⚠ same condition
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/chst6-p-ala13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown