CHD3 p.Pro67Ser
c.199C>T · rs935201217 · VCV2266876
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0158%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.187 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 0.3, phastCons 1 |
| Overall | ||
| CADD | 17.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0158%
African / African-American · 10/63,374 alleles
Filtering AF
0.00855%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00649%
Overall
0.00129%
16/1,240,710 alleles · ultra-rare
exomes 8/1,094,096 · genomes 8/146,614 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0158% | 6,337 |
| Remaining individualsnot grpmax-eligible | 0.00437% | 22,866 |
| Admixed American | 0.00405% | 24,710 |
| European (non-Finnish) | 0.000303% | 330,561 |
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
- CHD3
- Protein
- p.Pro67Ser
- Coding
- c.199C>T
- MANE Select
- NM_001005273 · reported on NM_001005271
- dbSNP
- rs935201217
- Type
- single nucleotide variant
- Location
- chr17:7885005 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 67
- the 'disordered' region
Similar variants
- CHD3 p.Arg103Ter Pathogenic ★★ same condition
- CHD3 p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg966Trp Pathogenic ★★ ⚠ same condition
- CHD3 p.Arg985Trp Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Pro1918= Likely pathogenic ★★ same condition
- CHD3 p.Arg1266Trp Uncertain significance ★★ ⚠ same condition
- CHD3 p.Arg1377Cys Uncertain significance ★★ ⚠ same condition
- CHD3 p.Arg1381Leu Uncertain significance ★★ ⚠ same condition
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/chd3-p-pro67ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown