CHD3 p.Arg1442=
c.4326G>A · VCV3341662
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.66 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.8 | GERP -0.21, phastCons 1 |
| Overall | ||
| CADD | 7.211 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.00582%
94/1,614,164 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| European (non-Finnish) | 0.00678% | 14,750 |
| Admixed American | 0.005% | 20,007 |
| Finnishnot grpmax-eligible | 0.00312% | 32,015 |
| African / African-American | 0.00133% | 75,046 |
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.Arg1442=
- Coding
- c.4326G>A
- MANE Select
- NM_001005273
- Type
- single nucleotide variant
- Location
- chr17:7905957 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1442
- a UniProt-annotated variant site (in snibcps)
Similar variants
- CHD3 p.Arg1442Gln Uncertain significance ★★ ⚠ same residue
- 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
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-arg1442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown