CHST8 p.Pro139=
c.417C>A · rs768636087 · VCV3046750
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0709%, afr)
Conditions
1
CHST8-related disorder
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 -2.5 | GERP -3.3 |
| Overall | ||
| CADD | 0.678 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0709%
African / African-American · 53/74,706 alleles
Filtering AF
0.0557%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0503%
Overall
0.00458%
73/1,594,182 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0709% | 1,410 |
| Admixed American | 0.00692% | 14,453 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,905 |
| East Asian | 0.00226% | 44,216 |
| European (non-Finnish) | 0.00111% | 90,288 |
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
- CHST8
- Protein
- p.Pro139=
- Coding
- c.417C>A
- MANE Select
- NM_001127895
- dbSNP
- rs768636087
- Type
- single nucleotide variant
- Location
- chr19:33772205 (GRCh38)
- Gene constraint
- LOEUF 1.001 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.90
Disease context
CHST8-related disorder
Similar variants
- CHST8 p.Pro139Ser Uncertain significance ★ ⚠ same residue
- CHST8 p.Arg77= Likely benign same condition
- CHST8 p.Lys234= Benign same condition
- CHST8 p.Pro126Arg Likely benign same condition
- CHST8 p.Val186Ala Uncertain significance ★★ ⚠ same type
- CHST8 c.168+64G>A Benign ★★ same type
- CHST8 c.-86-36C>T Benign ★★ same type
- CHST8 p.Arg9= Benign ★★ 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/chst8-p-pro139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown