CHD3 p.Pro42=
c.126G>T · VCV3345186
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,613,294)
Conditions
1
CHD3-related disorder
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 1.6 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 13.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,613,294). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CHD3
- Protein
- p.Pro42=
- Coding
- c.126G>T
- MANE Select
- NM_001005273
- Type
- single nucleotide variant
- Location
- chr17:7889689 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 42
- the 'disordered' region
Disease context
CHD3-related disorder
Similar variants
- CHD3 p.Pro42Ser Uncertain significance ★ ⚠ same residue
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1342Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg985Gln Pathogenic ★★ same condition
- CHD3 p.Arg1491His Uncertain significance ★★ ⚠ same condition
- CHD3 p.Arg684Ter Pathogenic ★ same condition
- CHD3 p.Glu1653Ter Likely pathogenic ★ same condition
- CHD3 p.Met1085Ile 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-pro42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown