Developmental and epileptic encephalopathy 107

disease

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Also known as DEE107

Summary

Developmental and epileptic encephalopathy 107 (MONDO:0031055) is a disease caused by NAPB (GenCC Definitive), with 2 cohort genes.

At a glance

Causal gene: NAPB (GenCC Definitive)
Cohort genes: 2
ClinVar variants: 5

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	developmental and epileptic encephalopathy 107
Mondo ID	MONDO:0031055
OMIM	620033
DOID	DOID:0070393
UMLS	C5774215
MedGen	1823988
GARD	0025687
Is cancer (heuristic)	no

Also known as: DEE107 · developmental and epileptic encephalopathy 107

Data availability: 5 ClinVar variants · 3 GenCC gene-disease records · 3 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 107

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

5 retrieved; paginated sample, class counts are floors:

3 pathogenic, 1 uncertain significance, 1 conflicting classifications of pathogenicity

ClinVar	Variant (HGVS)	Gene	Classification	Review
234936	NM_022080.3(NAPB):c.479C>A (p.Ser160Ter)	NAPB	Pathogenic	no assertion criteria provided
2572575	NM_022080.3(NAPB):c.333C>A (p.Tyr111Ter)	NAPB	Pathogenic	criteria provided, single submitter
984717	NM_022080.3(NAPB):c.173G>A (p.Trp58Ter)	NAPB	Pathogenic	criteria provided, single submitter
978476	NM_022080.3(NAPB):c.421-1G>A	NAPB	Conflicting classifications of pathogenicity	no assertion criteria provided
2663807	NM_022080.3(NAPB):c.2T>G (p.Met1Arg)	LOC130065540	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 0 · 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
NAPB	Definitive	Autosomal recessive	developmental and epileptic encephalopathy 107	3
NAPSB	Definitive	Autosomal recessive	developmental and epileptic encephalopathy 107	3

Cohort genes → proteins

2 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
NAPSB	HGNC:13396	ENSG00000131401		napsin B aspartic peptidase (pseudogene)	gencc,clinvar
NAPB	HGNC:15751	ENSG00000125814	Q9H115	Beta-soluble NSF attachment protein	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
NAPB	Beta-soluble NSF attachment protein	Required for vesicular transport between the endoplasmic reticulum and the Golgi apparatus.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 2 · 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	2	1.8×	0.312

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
NAPSB	Other/Unknown	no
NAPB	Other/Unknown	no		NSF_attach, TPR-like_helical_dom_sf

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
granulocyte	1
spleen	1
vermiform appendix	1
Brodmann (1909) area 23	1
endothelial cell	1
middle temporal gyrus	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
NAPSB	192	broad	marker	granulocyte, spleen, vermiform appendix
NAPB	245	ubiquitous	marker	middle temporal gyrus, Brodmann (1909) area 23, endothelial cell

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
NAPB	1,344
NAPSB	0

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
NAPB	Q9H115	89.55

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 14. Enrichment computed across 2 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
Intra-Golgi traffic	1	259.6×	0.015	NAPB
Retrograde transport at the Trans-Golgi-Network	1	219.6×	0.015	NAPB
COPII-mediated vesicle transport	1	163.1×	0.015	NAPB
ER to Golgi Anterograde Transport	1	132.8×	0.015	NAPB
Golgi-to-ER retrograde transport	1	132.8×	0.015	NAPB
COPI-dependent Golgi-to-ER retrograde traffic	1	110.9×	0.015	NAPB
COPI-mediated anterograde transport	1	109.8×	0.015	NAPB
Intra-Golgi and retrograde Golgi-to-ER traffic	1	104.8×	0.015	NAPB
Transport to the Golgi and subsequent modification	1	102.9×	0.015	NAPB
Asparagine N-linked glycosylation	1	60.1×	0.023	NAPB
Membrane Trafficking	1	37.1×	0.034	NAPB
Vesicle-mediated transport	1	34.8×	0.034	NAPB
Post-translational protein modification	1	19.2×	0.056	NAPB
Metabolism of proteins	1	12.4×	0.081	NAPB

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
SNARE complex disassembly	1	5617.3×	7e-04	NAPB
regulation of synaptic vesicle priming	1	1685.2×	0.001	NAPB
synaptic transmission, glutamatergic	1	358.6×	0.004	NAPB
intracellular protein transport	1	64.8×	0.015	NAPB

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 0 of 2 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
NAPSB	0	0
NAPB	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

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	2	NAPSB, NAPB

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
NAPSB	0	—
NAPB	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: NAPB