CHST3 p.Val397=
c.1191G>A · rs886042739 · VCV283922
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,558,484)
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 3 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 7.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,558,484). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CHST3
- Protein
- p.Val397=
- Coding
- c.1191G>A
- MANE Select
- NM_004273
- dbSNP
- rs886042739
- Type
- single nucleotide variant
- Location
- chr10:72008222 (GRCh38)
- Gene constraint
- LOEUF 1.119 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.58
Similar variants
- CHST3 p.Val397Ala Uncertain significance ★ ⚠ same residue
- CHST3 p.Arg221Cys Pathogenic/Likely pathogenic ★★ same type
- CHST3 p.Glu230Ter Pathogenic/Likely pathogenic ★★ same type
- CHST3 p.Phe159Ile Pathogenic/Likely pathogenic ★★ same type
- CHST3 c.*57G>T Uncertain significance ★★ same type
- CHST3 c.*66G>T Uncertain significance ★★ same type
- CHST3 p.Ala106Thr Uncertain significance ★★ ⚠ same type
- CHST3 p.Ala129Glu 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/chst3-p-val397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown