CHDH p.Pro512=
c.1536C>G · rs34336629 · VCV777801
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.219%, nfe)
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 -1.7 | GERP -3.8 |
| Overall | ||
| CADD | 5.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.219%
European (non-Finnish) · 2,580/1,180,046 alleles
Filtering AF
0.212%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.209%
Overall
0.178%
2,867/1,614,238 alleles · rare
exomes 2,630/1,461,852 · genomes 237/152,386 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.219% | 457 |
| Admixed American | 0.213% | 469 |
| Remaining individualsnot grpmax-eligible | 0.149% | 672 |
| Middle Eastern | 0.099% | 1,010 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0844% | 1,184 |
| African / African-American | 0.0333% | 3,003 |
| Finnishnot grpmax-eligible | 0.0156% | 6,401 |
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.Pro512=
- Coding
- c.1536C>G
- MANE Select
- NM_018397
- dbSNP
- rs34336629
- Type
- single nucleotide variant
- Location
- chr3:53818026 (GRCh38)
- Gene constraint
- LOEUF 1.092 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.84
Similar variants
- 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
- CHDH p.Ala240Val 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-pro512 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown