CHST14 p.Val189=
c.567G>A · rs758319940 · VCV713138
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.14%, eas)
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 2.1 | GERP -0.44, phastCons 1 |
| Overall | ||
| CADD | 11.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.14%
East Asian · 63/44,896 alleles
Filtering AF
0.112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.102%
Overall
0.00403%
65/1,613,648 alleles · rare
exomes 56/1,461,418 · genomes 9/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.14% | 713 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
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.Val189=
- Coding
- c.567G>A
- MANE Select
- NM_130468
- dbSNP
- rs758319940
- Type
- single nucleotide variant
- Location
- chr15:40471780 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17
Similar variants
- 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
- CHST14 p.Ala11Val Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala15Pro 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-val189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown