CHD8 p.Pro2499=
c.7497C>T · rs1396179930 · VCV1759173
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,548,576)
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 4.5 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 7.877 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,548,576). 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
- CHD8
- Protein
- p.Pro2499=
- Coding
- c.7497C>T
- MANE Select
- NM_001170629
- dbSNP
- rs1396179930
- Type
- single nucleotide variant
- Location
- chr14:21385862 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.17 · 2 PDB
- Residue 2499
- the 'disordered' region
Similar variants
- CHD8 p.Pro2499His Uncertain significance ★★ ⚠ same residue
- 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
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-pro2499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown