CHD3 p.Lys128=
c.384G>A · rs778494683 · VCV2232083
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00753%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.229 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.7 | GERP -0.068, phastCons 1 |
| Overall | ||
| CADD | 33.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00753%
Admixed American · 4/53,092 alleles
Filtering AF
0.00256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00148%
Overall
0.000817%
13/1,590,506 alleles · very rare
exomes 12/1,438,926 · genomes 1/151,580 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00753% | 13,273 |
| Remaining individualsnot grpmax-eligible | 0.00326% | 30,675 |
| East Asian | 0.00226% | 44,330 |
| African / African-American | 0.00137% | 72,936 |
| European (non-Finnish) | 0.000427% | 234,176 |
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.Lys128=
- Coding
- c.384G>A
- MANE Select
- NM_001005273
- dbSNP
- rs778494683
- Type
- single nucleotide variant
- Location
- chr17:7890741 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 128
- 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-lys128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown