CHD3 p.Ser1058=
c.3174G>A · rs144911273 · VCV2277898
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.113%, afr)
Conditions
1
Inborn genetic diseases
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 -5.9 | GERP -3.8 |
| Overall | ||
| CADD | 1.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.113%
African / African-American · 85/75,010 alleles
Filtering AF
0.0938%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0867%
Overall
0.0221%
356/1,613,834 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.113% | 882 |
| Admixed American | 0.025% | 3,997 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,166 |
| European (non-Finnish) | 0.0192% | 5,221 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0121% | 8,278 |
| East Asian | 0.00669% | 14,957 |
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.Ser1058=
- Coding
- c.3174G>A
- MANE Select
- NM_001005273
- dbSNP
- rs144911273
- Type
- single nucleotide variant
- Location
- chr17:7901297 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1058
- a UniProt-annotated variant site (in snibcps)
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-ser1058 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown