CHD3 p.Pro914=
c.2742A>G · rs144370104 · VCV3051004
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.05%, amr)
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 -1.4 | GERP -2.8 |
| Overall | ||
| CADD | 4.312 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.05%
Admixed American · 30/60,028 alleles
Filtering AF
0.0359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0312%
Overall
0.0163%
263/1,614,202 alleles · ultra-rare
exomes 231/1,461,880 · genomes 32/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.05% | 2,001 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,809 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,934 |
| European (non-Finnish) | 0.0178% | 5,619 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.00267% | 37,518 |
| Finnishnot grpmax-eligible | 0.00156% | 64,038 |
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.Pro914=
- Coding
- c.2742A>G
- MANE Select
- NM_001005273
- dbSNP
- rs144370104
- Type
- single nucleotide variant
- Location
- chr17:7900349 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 914
- the helicase atp-binding domain; a UniProt-annotated variant site (in snibcps)
Similar variants
- CHD3 c.4073-2A>C Likely pathogenic ★★ same type
- CHD3 p.Arg103Ter Pathogenic ★★ same type
- CHD3 p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1121Pro Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1169Gln Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1169Pro Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1169Trp Pathogenic ★★ same type
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ 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/chd3-p-pro914 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown