CHST9 p.Pro393=
c.1179C>G · rs80190384 · VCV788912
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.22%, 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 -2.2 | GERP -5.3 |
| Overall | ||
| CADD | 1.603 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.22%
African / African-American · 3,162/74,970 alleles
Filtering AF
4.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.05%
Overall
0.216%
3,489/1,613,690 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.22% | 24 |
| Remaining individualsnot grpmax-eligible | 0.266% | 376 |
| Middle Eastern | 0.247% | 404 |
| Admixed American | 0.185% | 540 |
| South Asian | 0.00879% | 11,383 |
| European (non-Finnish) | 0.00229% | 43,693 |
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
- CHST9
- Protein
- p.Pro393=
- Coding
- c.1179C>G
- MANE Select
- NM_031422
- dbSNP
- rs80190384
- Type
- single nucleotide variant
- Location
- chr18:26916412 (GRCh38)
- Gene constraint
- LOEUF 1.422 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.39
Similar variants
- CHST9 p.Arg62Trp Uncertain significance ★ ⚠ same type
- CHST9 p.Asn9Asp Uncertain significance ★ ⚠ same type
- CHST9 p.Gly41Glu Uncertain significance ★ ⚠ same type
- CHST9 p.Ile35Met Uncertain significance ★ ⚠ same type
- CHST9 p.Lys72Arg Uncertain significance ★ ⚠ same type
- CHST9 p.Met8Val Uncertain significance ★ ⚠ same type
- CHST9 p.Pro57Leu Uncertain significance ★ ⚠ same type
- CHST9 p.Ser53Leu 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/chst9-p-pro393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown