Developmental and epileptic encephalopathy 102

disease

On this page

Also known as DEE102

Summary

Developmental and epileptic encephalopathy 102 (MONDO:0030881) is a disease caused by SLC38A3 (GenCC Strong), with 1 cohort gene.

At a glance

Causal gene: SLC38A3 (GenCC Strong)
Cohort genes: 1
ClinVar variants: 8

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	developmental and epileptic encephalopathy 102
Mondo ID	MONDO:0030881
OMIM	619881
DOID	DOID:0070388
UMLS	C5676991
MedGen	1812769
GARD	0025649
Is cancer (heuristic)	no

Also known as: DEE102 · developmental and epileptic encephalopathy 102

Data availability: 8 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 102

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

8 retrieved; paginated sample, class counts are floors:

6 pathogenic, 1 likely pathogenic, 1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
1687050	NM_006841.6(SLC38A3):c.855+1G>T	SLC38A3	Pathogenic	no assertion criteria provided
1687051	NM_006841.6(SLC38A3):c.1049C>A (p.Ser350Ter)	SLC38A3	Pathogenic	no assertion criteria provided
1687052	NM_006841.6(SLC38A3):c.1119del (p.Val373_Leu374insTer)	SLC38A3	Pathogenic	no assertion criteria provided
1687053	NM_006841.6(SLC38A3):c.1123A>C (p.Thr375Pro)	SLC38A3	Pathogenic	no assertion criteria provided
2444165	NM_006841.6(SLC38A3):c.187G>T (p.Glu63Ter)	SLC38A3	Pathogenic	criteria provided, single submitter
4292999	NM_006841.6(SLC38A3):c.856_859del	SLC38A3	Pathogenic	criteria provided, single submitter
1321101	NM_006841.6(SLC38A3):c.1212G>A (p.Trp404Ter)	SLC38A3	Likely pathogenic	criteria provided, single submitter
3589451	NM_006841.6(SLC38A3):c.806C>T (p.Pro269Leu)	SLC38A3	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · 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
SLC38A3	Strong	Autosomal recessive	developmental and epileptic encephalopathy 102	4

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
SLC38A3	Orphanet:442835	Non-specific early-onset epileptic encephalopathy

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
SLC38A3	HGNC:18044	ENSG00000188338	Q99624	Sodium-coupled neutral amino acid transporter 3	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC38A3	Sodium-coupled neutral amino acid transporter 3	Symporter that cotransports specific neutral amino acids and sodium ions, coupled to an H(+) antiporter activity.

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)
SLC38A3	Other/Unknown	no		AA_transpt_TM

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
hindlimb stylopod muscle	1
liver	1
right lobe of liver	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC38A3	164	broad	marker	right lobe of liver, hindlimb stylopod muscle, liver

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC38A3	1,374

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
SLC38A3	Q99624	78.62

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 4. 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
Amino acid transport across the plasma membrane	1	300.5×	0.013	SLC38A3
R-HSA-425393	1	129.8×	0.015	SLC38A3
SLC-mediated transmembrane transport	1	59.2×	0.023	SLC38A3
Transport of small molecules	1	25.1×	0.040	SLC38A3

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
L-asparagine import across plasma membrane	1	16852.0×	4e-04	SLC38A3
positive regulation of glutamine transport	1	16852.0×	4e-04	SLC38A3
L-glutamine secretion	1	8426.0×	4e-04	SLC38A3
histidine transport	1	8426.0×	4e-04	SLC38A3
L-histidine import across plasma membrane	1	8426.0×	4e-04	SLC38A3
asparagine transport	1	5617.3×	4e-04	SLC38A3
cellular response to potassium ion starvation	1	5617.3×	4e-04	SLC38A3
intracellular amino acid homeostasis	1	5617.3×	4e-04	SLC38A3
L-histidine transport	1	5617.3×	4e-04	SLC38A3
L-alanine transport	1	2407.4×	7e-04	SLC38A3
L-glutamine import across plasma membrane	1	2106.5×	8e-04	SLC38A3
L-glutamine transport	1	1404.3×	0.001	SLC38A3
response to acidic pH	1	1296.3×	0.001	SLC38A3
amino acid transmembrane transport	1	732.7×	0.002	SLC38A3
amino acid transport	1	312.1×	0.004	SLC38A3
female pregnancy	1	210.7×	0.005	SLC38A3
transport across blood-brain barrier	1	179.3×	0.006	SLC38A3
positive regulation of transcription by RNA polymerase II	1	14.9×	0.067	SLC38A3

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
SLC38A3	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	SLC38A3

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)
SLC38A3	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: SLC38A3