CHD3 p.Pro82del
c.222GCC[6] · rs759738955 · VCV2343495
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.206%, sas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 0.3, phastCons 1 |
| Overall | ||
| CADD | 16.07 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (CCG)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.206%
South Asian · 50/24,260 alleles
Filtering AF
0.161%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.144%
Overall
0.0825%
949/1,150,156 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.206% | 485 |
| Admixed American | 0.197% | 507 |
| East Asian | 0.159% | 628 |
| Middle Eastern | 0.14% | 714 |
| Ashkenazi Jewishnot grpmax-eligible | 0.12% | 832 |
| Finnishnot grpmax-eligible | 0.105% | 950 |
| Remaining individualsnot grpmax-eligible | 0.0915% | 1,093 |
| African / African-American | 0.0859% | 1,164 |
| European (non-Finnish) | 0.0725% | 1,379 |
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.Pro82del
- Coding
- c.222GCC[6]
- MANE Select
- NM_001005273 · reported on NM_001005271
- dbSNP
- rs759738955
- Type
- Microsatellite
- Location
- chr17:7885026 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 82
- the 'disordered' region
Similar variants
- CHD3 p.Pro82_Leu83insProProPro Likely benign ★ same residue
- CHD3 p.Pro82_Leu83insPro Benign/Likely benign ★★ same residue
- CHD3 p.Pro82_Leu83insProPro Uncertain significance ★ same residue
- CHD3 p.Glu89fs Pathogenic ★ same condition
- CHD3 p.Arg103Ter Pathogenic ★★ same condition
- CHD3 p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg540fs Pathogenic ★★ same condition
- CHD3 p.Arg966Trp Pathogenic ★★ 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-pro82del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown