CHD2 p.Ser1099fs
c.3294del · VCV4293367
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
developmental and epileptic encephalopathy 94
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 26 of 39 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CHD2
- Protein
- p.Ser1099fs
- Coding
- c.3294del
- MANE Select
- NM_001271
- Type
- Deletion
- Location
- chr15:92985553 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
- Residue 1099
- a UniProt-annotated variant site (in dee94); a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy; uncertain significance); the 'disordered' region
Disease context
developmental and epileptic encephalopathy 94 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Lennox-Gastaut syndrome (Orphanet):
- Inheritance
- Autosomal dominant, Multigenic/multifactorial, Not applicable
- Onset
- Childhood, Infancy
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- CHD2 p.Glu1412fs Pathogenic ★★ same condition
- CHD2 p.Lys1393fs Pathogenic ★★ same condition
- CHD2 p.Lys174_Val175insTer Pathogenic/Likely pathogenic ★★ same condition
- CHD2 p.Pro399fs Pathogenic ★★ same condition
- CHD2 c.1199-12del Benign/Likely benign ★★ same condition
- CHD2 c.381+12del Likely benign ★★ same condition
- CHD2 p.Lys1411del Benign/Likely benign ★★ same condition
- CHD2 c.1151_1153+4del 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/chd2-p-ser1099fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown