CHD3 p.Pro1939=
c.5817C>T · VCV4281203
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0624%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.035 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 14.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0624%
East Asian · 28/44,882 alleles
Filtering AF
0.0443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0382%
Overall
0.00409%
66/1,613,534 alleles · ultra-rare
exomes 60/1,461,288 · genomes 6/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0624% | 1,603 |
| Middle Eastern | 0.0164% | 6,082 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,819 |
| Finnishnot grpmax-eligible | 0.00469% | 21,341 |
| African / African-American | 0.00267% | 37,437 |
| European (non-Finnish) | 0.0022% | 45,379 |
| South Asian | 0.0022% | 45,530 |
| Admixed American | 0.00167% | 59,796 |
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.Pro1939=
- Coding
- c.5817C>T
- MANE Select
- NM_001005273
- Type
- single nucleotide variant
- Location
- chr17:7910909 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1939
- the 'required for interaction with pcnt' region; a UniProt-annotated variant site (in snibcps)
Similar variants
- CHD3 p.Pro1939Ala Uncertain significance ★ ⚠ same residue
- CHD3 p.Pro1939Ser Likely benign ★ same residue
- 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
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-pro1939 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown