CHST15 p.Pro371=
c.1113G>A · rs148665029 · VCV789479
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.763%, afr)
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 -7.7 | GERP -3 |
| Overall | ||
| CADD | 0.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.763%
African / African-American · 573/75,060 alleles
Filtering AF
0.712%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.691%
Overall
0.0433%
699/1,614,220 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.763% | 131 |
| Admixed American | 0.1% | 1,000 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.0022% | 45,546 |
| European (non-Finnish) | 0.0011% | 90,772 |
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
- CHST15
- Protein
- p.Pro371=
- Coding
- c.1113G>A
- MANE Select
- NM_001270764
- dbSNP
- rs148665029
- Type
- single nucleotide variant
- Location
- chr10:124038592 (GRCh38)
- Gene constraint
- LOEUF 0.743 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.20
Similar variants
- CHST15 p.Ala16Thr Benign ★★ same type
- CHST15 p.Arg224= Benign ★★ same type
- CHST15 p.Ala241Val Uncertain significance ★ ⚠ same type
- CHST15 p.Ala283Ser Uncertain significance ★ ⚠ same type
- CHST15 p.Ala321Thr Uncertain significance ★ ⚠ same type
- CHST15 p.Ala330Ser Uncertain significance ★ ⚠ same type
- CHST15 p.Ala357Ser Uncertain significance ★ ⚠ same type
- CHST15 p.Ala412Thr 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/chst15-p-pro371 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown