CHD4 p.Leu779=
c.2335C>T · rs530395831 · VCV2902876
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0648%, sas)
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 4 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 10.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0648%
South Asian · 59/91,086 alleles
Filtering AF
0.0515%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0467%
Overall
0.00403%
65/1,614,156 alleles · ultra-rare
exomes 61/1,461,892 · genomes 4/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0648% | 1,544 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| East Asian | 0.00223% | 44,876 |
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
- CHD4
- Protein
- p.Leu779=
- Coding
- c.2335C>T
- MANE Select
- NM_001273
- dbSNP
- rs530395831
- Type
- single nucleotide variant
- Location
- chr12:6593595 (GRCh38)
- Gene constraint
- LOEUF 0.192 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.41 · 12 PDB
- Residue 779
- a β-strand; the helicase atp-binding domain
Similar variants
- CHD4 p.Arg1068His Pathogenic/Likely pathogenic ★★ same type
- CHD4 p.Arg1173Gln Pathogenic/Likely pathogenic ★★ same type
- CHD4 p.Arg1173Trp Pathogenic/Likely pathogenic ★★ same type
- CHD4 p.Arg1177Cys Pathogenic/Likely pathogenic ★★ same type
- CHD4 p.Arg1177His Pathogenic/Likely pathogenic ★★ same type
- CHD4 p.Arg1183Cys Pathogenic/Likely pathogenic ★★ same type
- CHD4 p.Arg1183His Pathogenic/Likely pathogenic ★★ same type
- CHD4 p.Arg1340Cys 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/chd4-p-leu779 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown