CHD2 p.Glu339=
c.1017G>A · rs141957556 · VCV382915
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.433%, eas)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 9.299 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.433%
East Asian · 194/44,852 alleles
Filtering AF
0.383%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.364%
Overall
0.0156%
251/1,613,796 alleles · rare
exomes 211/1,461,584 · genomes 40/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.433% | 231 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,786 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.0133% | 7,501 |
| Admixed American | 0.0117% | 8,571 |
| South Asian | 0.0022% | 45,535 |
| European (non-Finnish) | 0.00017% | 589,915 |
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
- CHD2
- Protein
- p.Glu339=
- Coding
- c.1017G>A
- MANE Select
- NM_001271
- dbSNP
- rs141957556
- Type
- single nucleotide variant
- Location
- chr15:92943033 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
- Residue 339
- the chromo 1 domain; a UniProt-annotated variant site (in dee94); a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy; uncertain significance)
Similar variants
- CHD2 p.Glu339Lys Uncertain significance ★★ ⚠ same residue
- CHD2 c.1153+1G>C Pathogenic ★★ same condition
- CHD2 c.1809+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD2 c.294+1G>T Likely pathogenic ★★ same condition
- CHD2 c.443+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD2 c.693-1G>A Likely pathogenic ★★ same condition
- CHD2 p.Ala879Val Pathogenic/Likely pathogenic ★★ same condition
- CHD2 p.Arg1072Ter 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/chd2-p-glu339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown