CHD8 p.Ser113=
c.339G>A · rs1166832405 · VCV2151215
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00945%, eas)
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 -0.77 | GERP -5.8, phastCons 0.001 |
| Overall | ||
| CADD | 5.863 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00945%
East Asian · 4/42,310 alleles
Filtering AF
0.0032%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00188%
Overall
0.00103%
16/1,556,318 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00945% | 10,577 |
| South Asian | 0.00233% | 42,894 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 60,798 |
| European (non-Finnish) | 0.000777% | 128,662 |
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
- CHD8
- Protein
- p.Ser113=
- Coding
- c.339G>A
- MANE Select
- NM_001170629
- dbSNP
- rs1166832405
- Type
- single nucleotide variant
- Location
- chr14:21431305 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.17 · 2 PDB
- Residue 113
- the 'disordered' region
Similar variants
- CHD8 p.Ser113Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- CHD8 p.Ser113Trp Uncertain significance ★ ⚠ same residue
- CHD8 p.Ser113fs Pathogenic ★ same residue
- CHD8 c.3882+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD8 p.Arg1188Ter Pathogenic ★★ same type
- CHD8 p.Arg1242Gln Likely pathogenic ★★ same type
- CHD8 p.Arg1242Ter Pathogenic ★★ same type
- CHD8 p.Arg1245Ter Pathogenic ★★ same type
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-ser113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown