CHST14 p.Pro281=
c.843C>T · rs778120798 · VCV1106308
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -4.3 | GERP -3.8 |
| Overall | ||
| CADD | 6.651 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00206%
Overall
0.000372%
6/1,614,074 alleles · ultra-rare
exomes 5/1,461,880 · genomes 1/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Admixed American | 0.00833% | 12,003 |
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.Pro281=
- Coding
- c.843C>T
- MANE Select
- NM_130468
- dbSNP
- rs778120798
- Type
- single nucleotide variant
- Location
- chr15:40472056 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17
- Residue 281
- a UniProt-annotated variant site (in edsmc1; loss of activity)
Similar variants
- CHST14 p.Pro281Leu Pathogenic ★ 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
- CHST14 p.Ala11Val 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-pro281 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown