CHD3 p.Pro84Thr
c.250C>A · rs1329540442 · VCV2688772
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000119%, nfe)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.018 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 0.2, phastCons 1 |
| Overall | ||
| CADD | 12.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000119%
European (non-Finnish) · 1/841,922 alleles
Overall
0.000117%
1/855,222 alleles · very rare
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.Pro84Thr
- Coding
- c.250C>A
- MANE Select
- NM_001005273 · reported on NM_001005271
- dbSNP
- rs1329540442
- Type
- single nucleotide variant
- Location
- chr17:7885056 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 84
- the 'disordered' region
Similar variants
- CHD3 p.Pro84Leu Likely benign ★★ same residue
- CHD3 p.Pro84Ser Uncertain significance ★ same residue
- CHD3 c.4073-2A>C Likely pathogenic ★★ same condition
- CHD3 p.Arg103Ter Pathogenic ★★ same condition
- CHD3 p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1121Pro Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1169Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1169Pro Pathogenic/Likely 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-pro84thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown