CHST14 p.Ala331=
c.993C>A · rs138273557 · VCV1622615
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0932%, afr)
Conditions
2
Cardiovascular phenotype
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 1.5 | GERP -0.64, phastCons 1 |
| Overall | ||
| CADD | 9.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0932%
African / African-American · 70/75,070 alleles
Filtering AF
0.0756%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0692%
Overall
0.00452%
73/1,614,162 alleles · ultra-rare
exomes 37/1,461,812 · genomes 36/152,350 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0932% | 1,072 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
| Admixed American | 0.00167% | 60,030 |
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
- CHST14
- Protein
- p.Ala331=
- Coding
- c.993C>A
- MANE Select
- NM_130468
- dbSNP
- rs138273557
- Type
- single nucleotide variant
- Location
- chr15:40472206 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17
Similar variants
- CHST14 p.Ala331Gly Uncertain significance ★ ⚠ same residue
- CHST14 p.Ala331Pro Uncertain significance ★ ⚠ same residue
- CHST14 p.Arg213Pro Likely pathogenic ★★ same condition
- CHST14 p.Arg320Ter Likely pathogenic ★★ same condition
- CHST14 p.Gln204Ter Pathogenic/Likely pathogenic ★★ same condition
- CHST14 p.Glu262Lys Pathogenic/Likely pathogenic ★★ same condition
- CHST14 p.Tyr293Cys Pathogenic/Likely pathogenic ★★ same condition
- CHST14 p.Ala100Thr Uncertain significance ★★ ⚠ 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/chst14-p-ala331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown