CHST14 p.Ser43=
c.129C>T · VCV4683962
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000174%, nfe)
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 2.6 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 13.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000174%
European (non-Finnish) · 2/1,151,586 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000129%
2/1,547,986 alleles · very rare
exomes 2/1,395,718 · genomes 0/152,268 · 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.Ser43=
- Coding
- c.129C>T
- MANE Select
- NM_130468
- Type
- single nucleotide variant
- Location
- chr15:40471342 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17
Similar variants
- CHST14 p.Ser43Phe Uncertain significance ★ ⚠ same residue
- CHST14 p.Ser43Pro Uncertain significance ★ ⚠ same residue
- CHST14 p.Arg213Pro Likely pathogenic ★★ same type
- CHST14 p.Arg320Ter Likely pathogenic ★★ same type
- CHST14 p.Gln204Ter Pathogenic/Likely pathogenic ★★ same type
- CHST14 p.Glu262Lys Pathogenic/Likely pathogenic ★★ same type
- CHST14 p.Tyr293Cys Pathogenic/Likely pathogenic ★★ same type
- CHST14 p.Ala100Thr Uncertain significance ★★ ⚠ same type
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-ser43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown