CHST14 p.Pro272=
c.816T>C · VCV3492691
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | GERP -3.8 |
| Overall | ||
| CADD | 4.788 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,870 alleles
Overall
6.2e-05%
1/1,614,192 alleles · very rare
exomes 1/1,461,878 · genomes 0/152,314 · 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
- CHST14
- Protein
- p.Pro272=
- Coding
- c.816T>C
- MANE Select
- NM_130468
- Type
- single nucleotide variant
- Location
- chr15:40472029 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17
Similar variants
- CHST14 p.Arg320Ter Likely pathogenic ★★ same condition
- CHST14 p.Ala100Thr Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala15Pro Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala346Pro Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala373Ser Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala373Val Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala52Val Uncertain significance ★★ ⚠ same condition
- CHST14 p.Arg109Trp 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-pro272 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown