CHD8 p.Pro563=
c.1689T>A · rs1566441828 · VCV589673
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -4.4, phastCons 1 |
| Overall | ||
| CADD | 6.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CHD8
- Protein
- p.Pro563=
- Coding
- c.1689T>A
- MANE Select
- NM_001170629
- dbSNP
- rs1566441828
- Type
- single nucleotide variant
- Location
- chr14:21426155 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.17 · 2 PDB
- Residue 563
- the 'disordered' region
Similar variants
- CHD8 c.3882+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD8 p.Arg1462Ter Pathogenic ★★ same condition
- CHD8 p.Arg1582Ter Pathogenic/Likely pathogenic ★★ same condition
- CHD8 p.Arg2217Ter Pathogenic ★★ same condition
- CHD8 p.Arg243Ter Pathogenic ★★ same condition
- CHD8 c.4921+4C>T Uncertain significance ★★ same condition
- CHD8 c.-1G>A Uncertain significance ★★ same condition
- CHD8 p.Ala1960Thr Uncertain significance ★★ ⚠ 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/chd8-p-pro563 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown