CHD3 p.Pro1921=
c.5763G>A · VCV4084741
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00542%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.061 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.23 | GERP -2.3, phastCons 0.26 |
| Overall | ||
| CADD | 12.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00542%
African / African-American · 4/73,820 alleles
Filtering AF
0.00176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00105%
Overall
0.00137%
22/1,601,732 alleles · very rare
exomes 21/1,449,640 · genomes 1/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00542% | 18,455 |
| South Asian | 0.00224% | 44,737 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 61,950 |
| Finnishnot grpmax-eligible | 0.00157% | 63,890 |
| European (non-Finnish) | 0.00119% | 83,993 |
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.Pro1921=
- Coding
- c.5763G>A
- MANE Select
- NM_001005273
- Type
- single nucleotide variant
- Location
- chr17:7910855 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1921
- the 'required for interaction with pcnt' region; a UniProt-annotated variant site (in snibcps)
Similar variants
- 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
- CHD3 p.Arg1172Gln 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/chd3-p-pro1921 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown