Is CHD2 p.Pro155fs (c.462_470delinsGATGAACAGG) pathogenic?

CHD2 p.Pro155fs (c.462470delinsGATGAACAGG) is classified Pathogenic in CHD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-14). No gnomAD frequency available for this variant; Associated with developmental and epileptic encephalopathy 94.

What condition is associated with CHD2 p.Pro155fs (c.462_470delinsGATGAACAGG)?

CHD2 p.Pro155fs (c.462_470delinsGATGAACAGG) is associated with developmental and epileptic encephalopathy 94 (ClinVar).

How common is CHD2 p.Pro155fs (c.462_470delinsGATGAACAGG) in the general population?

CHD2 p.Pro155fs (c.462_470delinsGATGAACAGG) is no gnomAD frequency available for this variant (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.Pro155fs

c.462_470delinsGATGAACAGG · rs2505426416 · VCV1709021

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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 6 of 39
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.5	GERP -5.9, phastCons 0.003

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: CHD2
Protein: p.Pro155fs
Coding: c.462_470delinsGATGAACAGG
MANE Select: NM_001271
dbSNP: rs2505426416
Type: Indel
Location: chr15:92937536 (GRCh38)
Gene constraint: LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 60.81
Residue 155: a UniProt-annotated variant site (in dee94); 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.Pro155Thr Uncertain significance ★ ⚠ same residue
CHD2 p.Pro155= Likely benign ★ same residue
CHD2 p.Glu412Thr Uncertain significance ★★ same condition
CHD2 c.4138-19_4138-18delinsTA Likely benign ★★ same condition
CHD2 c.1720-155_1727delinsT Likely pathogenic ★ same condition
CHD2 p.Ala869Phe Likely pathogenic ★ same condition
CHD2 p.Ala929_Val934delinsTer Pathogenic ★ same condition
CHD2 p.Leu461delinsGlnValTer 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-pro155fs (accessed [today's date]).

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