CHD4 p.Pro967=
c.2901C>T · rs2136214353 · VCV1664640
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 -4.7 | GERP -3.7 |
| Overall | ||
| CADD | 2.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,960 alleles
Overall
0.000124%
2/1,608,236 alleles · very rare
exomes 2/1,455,858 · genomes 0/152,378 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,960 |
| European (non-Finnish) | 8.51e-05% | 1,175,236 |
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.Pro967=
- Coding
- c.2901C>T
- MANE Select
- NM_001273
- dbSNP
- rs2136214353
- Type
- single nucleotide variant
- Location
- chr12:6592440 (GRCh38)
- Gene constraint
- LOEUF 0.192 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.41 · 12 PDB
Similar variants
- CHD4 p.Pro967Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro967 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown