Is CHD2 p.Glu11del (c.30GGA[1]) pathogenic?

CHD2 p.Glu11del (c.30GGA[1]) is classified Uncertain significance in CHD2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-01). Very rare (popmax 0.00501%, amr); Associated with developmental and epileptic encephalopathy 94.

What condition is associated with CHD2 p.Glu11del (c.30GGA[1])?

CHD2 p.Glu11del (c.30GGA[1]) is associated with developmental and epileptic encephalopathy 94 (ClinVar).

How common is CHD2 p.Glu11del (c.30GGA[1]) in the general population?

CHD2 p.Glu11del (c.30GGA[1]) is very rare (popmax 0.00501%, amr) (gnomAD).

How is Lennox-Gastaut syndrome inherited?

Typically Autosomal dominant, Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

CHD2 p.Glu11del

c.30GGA[1] · rs772244385 · VCV2053767

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00501%, amr)

Conditions

developmental and epileptic encephalopathy 94

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.1	GERP 2.5, phastCons 1
Overall
CADD	20.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00501% Admixed American · 3/59,908 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.00056% 9/1,606,488 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00501%	19,969
South Asian	0.0022%	45,362
Remaining individualsnot grpmax-eligible	0.00161%	62,192
European (non-Finnish)	0.000256%	391,218

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.Glu11del
Coding: c.30GGA[1]
MANE Select: NM_001271
dbSNP: rs772244385
Type: Microsatellite
Location: chr15:92901265 (GRCh38)
Gene constraint: LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 60.81
Residue 11: the 'disordered' region

Full CHD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy 94 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 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.Glu11Gly Uncertain significance ★ ⚠ same residue
CHD2 p.Asp1107_Ser1108insTer Pathogenic ★★ same condition
CHD2 p.Glu1006_Asn1007insTer Pathogenic/Likely pathogenic ★★ same condition
CHD2 p.Glu551fs Pathogenic ★★ same condition
CHD2 p.Glu924del Likely pathogenic ★★ same condition
CHD2 p.Leu1591fs Pathogenic ★★ same condition
CHD2 p.Leu633fs Pathogenic ★★ same condition
CHD2 p.Val605fs Pathogenic/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-glu11del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown