Developmental and epileptic encephalopathy, 90

disease

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Also known as DEE90developmental and epileptic encephalopathy 90developmental and epileptic encephalopathy 90, X-linked recessive, X-linked dominant

Summary

Developmental and epileptic encephalopathy, 90 (MONDO:0025353) is a disease caused by FGF13 (GenCC Strong), with 1 cohort gene.

At a glance

Causal gene: FGF13 (GenCC Strong)
Cohort genes: 1
ClinVar variants: 15

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	developmental and epileptic encephalopathy, 90
Mondo ID	MONDO:0025353
OMIM	301058
DOID	DOID:0070381
UMLS	C5542345
MedGen	1786502
GARD	0015286
Is cancer (heuristic)	no

Also known as: DEE90 · developmental and epileptic encephalopathy 90 · developmental and epileptic encephalopathy 90, X-linked recessive, X-linked dominant

Data availability: 15 ClinVar variants · 4 GenCC gene-disease records.

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, 90

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

15 retrieved; paginated sample, class counts are floors:

9 uncertain significance, 4 pathogenic, 2 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1708476	NM_004114.5(FGF13):c.23C>A (p.Ser8Ter)	FGF13	Pathogenic	criteria provided, single submitter
997407	NM_004114.5(FGF13):c.31C>T (p.Arg11Cys)	FGF13	Pathogenic	criteria provided, single submitter
997408	NM_004114.5(FGF13):c.41G>C (p.Arg14Thr)	FGF13	Pathogenic	criteria provided, single submitter
997409	NM_004114.5(FGF13):c.32G>C (p.Arg11Pro)	FGF13	Pathogenic	no assertion criteria provided
1184442	NM_004114.5(FGF13):c.14T>G (p.Ile5Ser)	FGF13	Likely pathogenic	criteria provided, single submitter
1809807	NM_004114.5(FGF13):c.5C>G (p.Ala2Gly)	FGF13	Likely pathogenic	no assertion criteria provided
2441792	NM_001139500.2(FGF13):c.137C>T (p.Ser46Phe)	FGF13	Uncertain significance	criteria provided, single submitter
2442774	NM_004114.5(FGF13):c.289A>G (p.Ser97Gly)	FGF13	Uncertain significance	criteria provided, multiple submitters, no conflicts
2664209	NM_004114.5(FGF13):c.127T>G (p.Leu43Val)	FGF13	Uncertain significance	criteria provided, single submitter
3341477	NM_004114.5(FGF13):c.589A>G (p.Lys197Glu)	FGF13	Uncertain significance	criteria provided, single submitter
3383366	NM_004114.5(FGF13):c.482G>A (p.Arg161His)	FGF13	Uncertain significance	criteria provided, single submitter
3598105	NM_001139500.2(FGF13):c.116C>T (p.Ala39Val)	FGF13	Uncertain significance	criteria provided, single submitter
4277630	NM_001139500.2(FGF13):c.212C>A (p.Pro71Gln)	FGF13	Uncertain significance	criteria provided, single submitter
4277649	NM_004114.5(FGF13):c.403-1G>A	FGF13	Uncertain significance	criteria provided, single submitter
4293743	NM_001139501.2(FGF13):c.7C>T (p.Arg3Ter)	FGF13	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 1 · 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
FGF13	Strong	X-linked	developmental and epileptic encephalopathy, 90	6

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
FGF13	Orphanet:36387	Genetic epilepsy with febrile seizure plus

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
FGF13	HGNC:3670	ENSG00000129682	Q92913	Fibroblast growth factor 13	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
FGF13	Fibroblast growth factor 13	Microtubule-binding protein which directly binds tubulin and is involved in both polymerization and stabilization of microtubules.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.0

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
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
FGF13	Other/Unknown	no		Fibroblast_GF_fam, IL1/FGF

Expression context

Cohort genes with no expression data: 0.

1 cohort gene 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)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
cortical plate	1
dorsal root ganglion	1
endothelial cell	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
FGF13	268	ubiquitous	marker	endothelial cell, dorsal root ganglion, cortical plate

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
FGF13	3,763

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
FGF13	Q92913	3

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 1. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Phase 0 - rapid depolarisation	1	346.1×	0.003	FGF13

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
positive regulation of voltage-gated sodium channel activity	1	5617.3×	0.002	FGF13
establishment of neuroblast polarity	1	4213.0×	0.002	FGF13
branching morphogenesis of a nerve	1	2407.4×	0.002	FGF13
regulation of cardiac muscle cell action potential involved in regulation of contraction	1	1872.4×	0.002	FGF13
cerebral cortex cell migration	1	1532.0×	0.002	FGF13
negative regulation of collateral sprouting	1	1532.0×	0.002	FGF13
microtubule polymerization	1	887.0×	0.003	FGF13
inhibitory synapse assembly	1	624.1×	0.004	FGF13
negative regulation of microtubule depolymerization	1	495.6×	0.004	FGF13
learning	1	280.9×	0.007	FGF13
sodium ion transport	1	271.8×	0.007	FGF13
hippocampus development	1	230.8×	0.007	FGF13
neurogenesis	1	208.1×	0.007	FGF13
memory	1	183.2×	0.008	FGF13
MAPK cascade	1	153.2×	0.009	FGF13
neuron migration	1	133.8×	0.009	FGF13
protein localization to plasma membrane	1	108.7×	0.011	FGF13
cell-cell signaling	1	69.6×	0.016	FGF13
nervous system development	1	45.9×	0.023	FGF13
signal transduction	1	16.1×	0.062	FGF13

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
FGF13	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
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	FGF13

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)
FGF13	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: FGF13