Developmental and epileptic encephalopathy 97

disease

On this page

Also known as DEE97

Summary

Developmental and epileptic encephalopathy 97 (MONDO:0030453) is a disease caused by CELF2 (GenCC Strong), with 2 cohort genes.

At a glance

Causal gene: CELF2 (GenCC Strong)
Cohort genes: 2
ClinVar variants: 19

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	developmental and epileptic encephalopathy 97
Mondo ID	MONDO:0030453
OMIM	619561
DOID	DOID:0070383
UMLS	C5561999
MedGen	1794209
GARD	0025564
Is cancer (heuristic)	no

Also known as: DEE97

Data availability: 19 ClinVar variants · 3 GenCC gene-disease records · 2 cell lines.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › hereditary neurological disease › Mendelian neurodevelopmental disorder › genetic developmental and epileptic encephalopathy › developmental and epileptic encephalopathy 97

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

19 retrieved; paginated sample, class counts are floors:

9 uncertain significance, 6 pathogenic, 3 likely pathogenic, 1 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1175765	NM_001326342.2(CELF2):c.709C>T (p.Gln237Ter)	CELF2	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1299463	NM_001326342.2(CELF2):c.1558C>T (p.Pro520Ser)	CELF2	Pathogenic	no assertion criteria provided
1299464	NM_001326342.2(CELF2):c.1516C>G (p.Arg506Gly)	CELF2	Pathogenic	no assertion criteria provided
1299465	NM_001326342.2(CELF2):c.1562dup (p.Tyr521Ter)	CELF2	Pathogenic	criteria provided, single submitter
1334733	NM_001326342.2(CELF2):c.1517G>A (p.Arg506His)	CELF2	Pathogenic	criteria provided, single submitter
1685612	NM_001326342.2(CELF2):c.1353del (p.Asp451fs)	CELF2	Pathogenic	criteria provided, single submitter
3359034	NM_001326342.2(CELF2):c.883del (p.Ala295fs)	CELF2	Pathogenic	criteria provided, single submitter
3338598	NM_001326342.2(CELF2):c.938_939del (p.Ser313fs)	CELF2	Likely pathogenic	criteria provided, single submitter
3375484	NM_001326342.2(CELF2):c.241_262dup (p.Gln88fs)	CELF2	Likely pathogenic	criteria provided, single submitter
4526633	NM_001326342.2(CELF2):c.1412_1415del (p.Lys471fs)	CELF2	Likely pathogenic	criteria provided, single submitter
2498378	NM_001326342.2(CELF2):c.1559C>T (p.Pro520Leu)	CELF2	Uncertain significance	no assertion criteria provided
2505351	NM_001326342.2(CELF2):c.746G>T (p.Gly249Val)	CELF2	Uncertain significance	criteria provided, single submitter
2570693	NM_001326342.2(CELF2):c.289T>G (p.Phe97Val)	CELF2	Uncertain significance	criteria provided, single submitter
2576986	NM_001326342.2(CELF2):c.1507G>A (p.Gly503Ser)	CELF2	Uncertain significance	criteria provided, single submitter
3392520	NM_001326342.2(CELF2):c.589A>C (p.Lys197Gln)	CELF2	Uncertain significance	no assertion criteria provided
4081890	NM_001326342.2(CELF2):c.173G>A (p.Trp58Ter)	CELF2	Uncertain significance	no assertion criteria provided
4686044	NM_001326342.2(CELF2):c.74+5189A>C	CELF2	Uncertain significance	criteria provided, single submitter
4813605	NM_001326342.2(CELF2):c.1090del (p.Ala363_Leu364insTer)	CELF2	Uncertain significance	criteria provided, single submitter
1367124	NM_020822.3(KCNT1):c.256G>A (p.Val86Ile)	KCNT1	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
CELF2	Strong	Autosomal dominant	developmental and epileptic encephalopathy 97	5

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
CELF2	Orphanet:442835	Non-specific early-onset epileptic encephalopathy
KCNT1	Orphanet:293181	Epilepsy of infancy with migrating focal seizures
KCNT1	Orphanet:98784	Sleep-related hypermotor epilepsy

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
CELF2	HGNC:2550	ENSG00000048740	O95319	CUGBP Elav-like family member 2	gencc,clinvar
KCNT1	HGNC:18865	ENSG00000107147	Q5JUK3	Potassium channel subfamily T member 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CELF2	CUGBP Elav-like family member 2	RNA-binding protein implicated in the regulation of several post-transcriptional events.
KCNT1	Potassium channel subfamily T member 1	Sodium-activated K(+) channel.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.5

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Ion channel	1	55.8×	0.036
Other/Unknown	1	0.9×	0.805

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CELF2	Other/Unknown	no		RRM_dom, Hud_Sxl_RNA, Nucleotide-bd_a/b_plait_sf
KCNT1	Ion channel	yes		RCK_N, K_chnl_BK_asu, K_chnl_dom

Expression context

Cohort genes with no expression data: 0.

2 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
CA1 field of hippocampus	1
entorhinal cortex	1
orbitofrontal cortex	1
cerebellar cortex	1
cerebellar hemisphere	1
right hemisphere of cerebellum	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CELF2	289	ubiquitous	marker	CA1 field of hippocampus, orbitofrontal cortex, entorhinal cortex
KCNT1	153	tissue_specific	marker	right hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
KCNT1	1,562
CELF2	1,428

Structural data

PDB: 2 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
CELF2	O95319	7
KCNT1	Q5JUK3	6

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 2 evidence-associated genes (0 with Reactome annotation).

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
mRNA splice site recognition	1	401.2×	0.011	CELF2
regulation of heart contraction	1	247.8×	0.011	CELF2
regulation of alternative mRNA splicing, via spliceosome	1	122.1×	0.011	CELF2
protein homotetramerization	1	118.7×	0.011	KCNT1
RNA processing	1	109.4×	0.011	CELF2
potassium ion transmembrane transport	1	68.0×	0.015	KCNT1

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 1

Druggability breadth: 2 of 2 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

Symbol	Example approved molecule
KCNT1	BEPRIDIL

Top cohort targets by molecule count

Symbol	Molecules	Max phase
KCNT1	2	4
CELF2	0	0

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
BEPRIDIL	4	KCNT1
QUINIDINE	4	KCNT1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
KCNT1	24	Binding:24
CELF2	1	Binding:1

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

2 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Compound	Max phase	Cohort target (bioactivity)
BEPRIDIL	4	KCNT1
QUINIDINE	4	KCNT1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	KCNT1
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	CELF2

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
CELF2	1	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: CELF2, KCNT1