CHDH p.Ser85=
c.255G>T · rs72982050 · VCV719637
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.537%, 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 -2.4 | GERP -5 |
| Overall | ||
| CADD | 0.423 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.537%
African / African-American · 395/73,530 alleles
Filtering AF
0.493%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.476%
Overall
0.0333%
519/1,558,264 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.537% | 186 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,078 |
| Middle Eastern | 0.0894% | 1,119 |
| Admixed American | 0.0574% | 1,742 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0105% | 9,562 |
| European (non-Finnish) | 0.00243% | 41,162 |
| South Asian | 0.00236% | 42,427 |
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
- CHDH
- Protein
- p.Ser85=
- Coding
- c.255G>T
- MANE Select
- NM_018397
- dbSNP
- rs72982050
- Type
- single nucleotide variant
- Location
- chr3:53823754 (GRCh38)
- Gene constraint
- LOEUF 1.092 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.84
Similar variants
- CHDH p.Ser85Leu Likely benign ★ ⚠ same residue
- CHDH p.Pro396Leu Uncertain significance ★★ ⚠ same type
- CHDH c.704-3C>T Benign ★★ same type
- CHDH p.Gly235= Benign ★★ same type
- CHDH p.Val45= Benign ★★ same type
- CHDH p.Ala13Val Uncertain significance ★ ⚠ same type
- CHDH p.Ala170Thr Uncertain significance ★ ⚠ same type
- CHDH p.Ala177Thr 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/chdh-p-ser85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown