CHD3 p.Arg1266=
c.3798G>A · rs200956669 · VCV3035064
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00666%, amr)
Conditions
1
CHD3-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 0.78 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 7.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00666%
Admixed American · 4/60,018 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00031%
5/1,614,166 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00666% | 15,004 |
| African / African-American | 0.00133% | 75,032 |
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.Arg1266=
- Coding
- c.3798G>A
- MANE Select
- NM_001005273
- dbSNP
- rs200956669
- Type
- single nucleotide variant
- Location
- chr17:7903895 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1266
- a UniProt-annotated variant site (in snibcps)
Disease context
CHD3-related disorder
Similar variants
- CHD3 p.Arg1266Gln Uncertain significance ★★ ⚠ same residue
- CHD3 p.Arg1266Trp Uncertain significance ★★ ⚠ same residue
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1342Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg985Gln Pathogenic ★★ same condition
- CHD3 p.Arg1491His Uncertain significance ★★ ⚠ same condition
- CHD3 p.Arg684Ter Pathogenic ★ same condition
- CHD3 p.Glu1653Ter Likely pathogenic ★ 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-arg1266 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown