SLC38A3

Summary

SLC38A3 (solute carrier family 38 member 3, HGNC:18044) is a protein-coding gene on chromosome 3p21.31, encoding Sodium-coupled neutral amino acid transporter 3 (Q99624). Symporter that cotransports specific neutral amino acids and sodium ions, coupled to an H(+) antiporter activity.

Enables L-amino acid transmembrane transporter activity. Involved in carboxylic acid transport. Located in plasma membrane. Implicated in developmental and epileptic encephalopathy 102.

Source: NCBI Gene 10991 — RefSeq curated summary.

At a glance

• Gene–disease (curated): developmental and epileptic encephalopathy 102 (Strong, GenCC)
• GWAS associations: 8
• Clinical variants (ClinVar): 71 total — 6 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 68
• MANE Select transcript: NM_006841

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18044
Approved symbol	SLC38A3
Name	solute carrier family 38 member 3
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	G17, SN1, SNAT3
Ensembl gene	ENSG00000188338
Ensembl biotype	protein_coding
OMIM	604437
Entrez	10991

Gene structure

Transcript identifiers

Ensembl transcripts: 37 — 32 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000417121, ENST00000417851, ENST00000439524, ENST00000445096, ENST00000610458, ENST00000614032, ENST00000620404, ENST00000621456, ENST00000621714, ENST00000888661, ENST00000888662, ENST00000888663, ENST00000888664, ENST00000888665, ENST00000888666, ENST00000888667, ENST00000888668, ENST00000888669, ENST00000888670, ENST00000888671, ENST00000888672, ENST00000888673, ENST00000888674, ENST00000888675, ENST00000888676, ENST00000888677, ENST00000888678, ENST00000888679, ENST00000888680, ENST00000888681, ENST00000888682, ENST00000888683, ENST00000888684, ENST00000888685, ENST00000888686, ENST00000888687, ENST00000930045

RefSeq mRNA: 1 — MANE Select: NM_006841 NM_006841

CCDS: CCDS74940

Canonical transcript exons

ENST00000614032 — 16 exons

Exon	Start	End
ENSE00003551922	50217238	50217320
ENSE00003597182	50217917	50217996
ENSE00003630212	50217676	50217840
ENSE00003689530	50217415	50217473
ENSE00003716154	50218270	50218370
ENSE00003716244	50220073	50221486
ENSE00003729895	50215544	50215636
ENSE00003730775	50218593	50218717
ENSE00003738580	50218804	50218948
ENSE00003742871	50219881	50219984
ENSE00003745293	50215740	50215821
ENSE00003747004	50215386	50215459
ENSE00003993691	50214653	50214768
ENSE00003993695	50214402	50214483
ENSE00003993717	50214149	50214300
ENSE00003993720	50205271	50205348

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 98.53.

FANTOM5 (CAGE): breadth broad, TPM avg 5.8095 / max 663.4105, expressed in 537 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36697	5.3557	525
36698	0.2545	94
202757	0.1409	52
36699	0.0584	27

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	98.53	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.68	gold quality
liver	UBERON:0002107	94.36	gold quality
body of pancreas	UBERON:0001150	93.02	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.60	gold quality
ganglionic eminence	UBERON:0004023	87.92	gold quality
right frontal lobe	UBERON:0002810	87.45	gold quality
ventricular zone	UBERON:0003053	86.87	gold quality
spinal cord	UBERON:0002240	86.39	gold quality
gastrocnemius	UBERON:0001388	85.43	gold quality
caudate nucleus	UBERON:0001873	85.35	gold quality
muscle of leg	UBERON:0001383	85.08	gold quality
amygdala	UBERON:0001876	84.63	gold quality
putamen	UBERON:0001874	84.23	gold quality
cingulate cortex	UBERON:0003027	84.00	gold quality
anterior cingulate cortex	UBERON:0009835	83.93	gold quality
pancreas	UBERON:0001264	83.85	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.57	gold quality
apex of heart	UBERON:0002098	82.76	gold quality
prefrontal cortex	UBERON:0000451	82.69	gold quality
nucleus accumbens	UBERON:0001882	82.31	gold quality
muscle organ	UBERON:0001630	81.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.70	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.64	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.03	gold quality
neocortex	UBERON:0001950	80.54	gold quality
frontal cortex	UBERON:0001870	80.17	gold quality
hypothalamus	UBERON:0001898	79.66	gold quality
substantia nigra	UBERON:0002038	79.63	gold quality
telencephalon	UBERON:0001893	79.36	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting SLC38A3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-7515	99.31	68.22	1795

Literature-anchored findings (GeneRIF, showing 8)

• SN1 is a target for the ubiquitin ligase Nedd4-2, which is inactivated by the serum and glucocorticoid inducible kinase SGK1, its isoform SGK3, and protein kinase B. (PMID:12788082)
• SNAT3 mRNA showed a 3-5 times stronger expression in gliomas than in metastases or control tissue, and was virtually absent from glioma cultures. Native glioblastoma immunostained positively with anti-SNAT3 antibody. (PMID:15094455)
• Transcription of the SLC38A3 gene was impaired in all 5 RCC cell lines analyzed. Our data indicate this gene as a putative tumour suppressor gene. (PMID:16432833)
• SNAT3 is expressed in the placenta in the early stage of pregnancy. (PMID:19892400)
• The regulation of SNAT3 gene expression by extracellular pH involves post-transcriptional and transcriptional mechanisms, the latter being distinct from the mechanisms that control the tissue-specific expression of the gene. (PMID:24854847)
• SLC38A3 activated PDK1/AKT signaling and promoted metastasis of non-small cell lung cancer cells through regulating glutamine and histidine transport. (PMID:28202352)
• Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy. (PMID:34605855)
• Glutamine transporter SLC38A3 promotes breast cancer metastasis via Gsk3beta/beta-catenin/EMT pathway. (PMID:38309615)

Cross-species orthologs

17 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc38a3a	ENSDARG00000027065
danio_rerio	slc38a3b	ENSDARG00000091061
mus_musculus	Slc38a3	ENSMUSG00000010064
rattus_norvegicus	Slc38a3	ENSRNOG00000016827
drosophila_melanogaster	CG16700	FBGN0030816
drosophila_melanogaster	CG4991	FBGN0030817
drosophila_melanogaster	polyph	FBGN0033572
drosophila_melanogaster	acs	FBGN0035300
drosophila_melanogaster	CG7888	FBGN0036116
drosophila_melanogaster	CG32079	FBGN0052079
drosophila_melanogaster	CG32081	FBGN0052081
caenorhabditis_elegans	slc-36.4	WBGENE00010421
caenorhabditis_elegans	Y18D10A.23	WBGENE00012487
caenorhabditis_elegans		WBGENE00012629
caenorhabditis_elegans		WBGENE00012804
caenorhabditis_elegans		WBGENE00019837
caenorhabditis_elegans		WBGENE00020837

Paralogs (15): SLC38A5 (ENSG00000017483), SLC32A1 (ENSG00000101438), SLC38A7 (ENSG00000103042), SLC38A1 (ENSG00000111371), SLC36A1 (ENSG00000123643), SLC38A2 (ENSG00000134294), SLC38A4 (ENSG00000139209), SLC38A6 (ENSG00000139974), SLC38A10 (ENSG00000157637), SLC38A8 (ENSG00000166558), SLC38A11 (ENSG00000169507), SLC38A9 (ENSG00000177058), SLC36A4 (ENSG00000180773), SLC36A3 (ENSG00000186334), SLC36A2 (ENSG00000186335)

Protein

Protein identifiers

Sodium-coupled neutral amino acid transporter 3 — Q99624 (reviewed: Q99624)

Alternative names: N-system amino acid transporter 1, Na(+)-coupled neutral amino acid transporter 3, Solute carrier family 38 member 3, System N amino acid transporter 1

All UniProt accessions (5): A0A087WVW8, A0A087WWS5, A0A087X175, A0A087X1Q4, Q99624

UniProt curated annotations — full annotation on UniProt →

Function. Symporter that cotransports specific neutral amino acids and sodium ions, coupled to an H(+) antiporter activity. Mainly participates in the glutamate-GABA-glutamine cycle in brain where it transports L-glutamine from astrocytes in the intercellular space for the replenishment of both neurotransmitters glutamate and gamma-aminobutyric acid (GABA) in neurons and also functions as the major influx transporter in ganglion cells mediating the uptake of glutamine. The transport activity is specific for L-glutamine, L-histidine and L-asparagine. The transport is electroneutral coupled to the cotransport of 1 Na(+) and the antiport of 1 H(+). The transport is pH dependent, saturable, Li(+) tolerant and functions in both direction depending on the concentration gradients of its substrates and cotransported ions. Also mediates an amino acid-gated H(+) conductance that is not stoichiometrically coupled to the amino acid transport but which influences the ionic gradients that drive the amino acid transport. In addition, may play a role in nitrogen metabolism, amino acid homeostasis, glucose metabolism and renal ammoniagenesis.

Subcellular location. Cell membrane. Basolateral cell membrane.

Disease relevance. Developmental and epileptic encephalopathy 102 (DEE102) [MIM:619881] A form of epileptic encephalopathy, a heterogeneous group of early-onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. DEE102 is an autosomal recessive form characterized by onset of variable types of seizures in infancy. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the amino acid/polyamine transporter 2 family.

RefSeq proteins (1): NP_006832* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013057	AA_transpt_TM	Domain

Pfam: PF01490

Catalyzed reactions (Rhea), 3 shown:

• L-glutamine(out) + Na(+)(out) + H(+)(in) = L-glutamine(in) + Na(+)(in) + H(+)(out) (RHEA:71127)
• L-asparagine(out) + Na(+)(out) + H(+)(in) = L-asparagine(in) + Na(+)(in) + H(+)(out) (RHEA:71131)
• L-histidine(out) + Na(+)(out) + H(+)(in) = L-histidine(in) + Na(+)(in) + H(+)(out) (RHEA:71135)

UniProt features (25 total): transmembrane region 10, sequence variant 6, glycosylation site 5, chain 1, site 1, disulfide bond 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99624-F1	78.62	0.48

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 77 (modulates l-glutamine-induced conductances and na(+) binding)

Disulfide bonds (1): 240–275

Glycosylation sites (5): 74, 247, 248, 252, 323

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-352230	Amino acid transport across the plasma membrane
R-HSA-382551	Transport of small molecules
R-HSA-425393
R-HSA-425407	SLC-mediated transmembrane transport

MSigDB gene sets: 324 (showing top): AP1_01, FREAC2_01, PAX4_01, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_REGULATION_OF_ORGANIC_ACID_TRANSPORT, GNF2_GSTM1, GNF2_HPN, TATTATA_MIR374, TGACCTY_ERR1_Q2, GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, CAGCTG_AP4_Q5, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_ORGANIC_ACID_TRANSPORT, CAGCAGG_MIR370, AP1_Q4_01

GO Biological Process (20): amino acid transmembrane transport (GO:0003333), amino acid transport (GO:0006865), asparagine transport (GO:0006867), L-glutamine transport (GO:0006868), female pregnancy (GO:0007565), response to acidic pH (GO:0010447), L-glutamine secretion (GO:0010585), L-alanine transport (GO:0015808), histidine transport (GO:0015817), positive regulation of transcription by RNA polymerase II (GO:0045944), cellular response to potassium ion starvation (GO:0051365), intracellular amino acid homeostasis (GO:0080144), transport across blood-brain barrier (GO:0150104), L-histidine transport (GO:1902024), L-glutamine import across plasma membrane (GO:1903803), L-histidine import across plasma membrane (GO:1903810), L-asparagine import across plasma membrane (GO:1903811), positive regulation of glutamine transport (GO:2000487), monoatomic ion transport (GO:0006811), sodium ion transport (GO:0006814)

GO Molecular Function (11): L-histidine transmembrane transporter activity (GO:0005290), neutral L-amino acid:sodium symporter activity (GO:0005295), amino acid transmembrane transporter activity (GO:0015171), L-alanine transmembrane transporter activity (GO:0015180), L-asparagine transmembrane transporter activity (GO:0015182), L-glutamine transmembrane transporter activity (GO:0015186), L-glutamine, sodium:proton antiporter activity (GO:0140830), L-asparagine, sodium:proton antiporter activity (GO:0140831), L-histidine, sodium:proton antiporter activity (GO:0140832), symporter activity (GO:0015293), antiporter activity (GO:0015297)

GO Cellular Component (4): plasma membrane (GO:0005886), basolateral plasma membrane (GO:0016323), apical plasma membrane (GO:0016324), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
SLC-mediated transport of amino acids	1
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
L-glutamine transport	4
L-amino acid transmembrane transporter activity	4
L-amino acid transport	3
amino acid import across plasma membrane	3
neutral L-amino acid transmembrane transporter activity	3
sodium:proton antiporter activity	3
amino acid:monoatomic cation antiporter activity	3
transport	2
neutral amino acid transport	2
basic amino acid transport	2
L-alpha-amino acid transmembrane transport	2
L-histidine transmembrane transport	2
asparagine transport	2
secondary active transmembrane transporter activity	2
plasma membrane region	2
amino acid transport	1
transmembrane transport	1
carboxylic acid transport	1
nitrogen compound transport	1
multi-organism reproductive process	1
multi-multicellular organism process	1
response to pH	1
secretion by cell	1
alanine transport	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
cellular response to starvation	1
intracellular chemical homeostasis	1
vascular transport	1
aromatic amino acid transport	1
asparagine transmembrane transport	1
positive regulation of organic acid transport	1
positive regulation of amino acid transport	1
regulation of glutamine transport	1
metal ion transport	1
aromatic amino acid transmembrane transporter activity	1
basic amino acid transmembrane transporter activity	1
azole transmembrane transporter activity	1
amino acid:sodium symporter activity	1

Protein interactions and networks

STRING

1352 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC38A3	SCN11A	Q9UI33	855
SLC38A3	SLC1A3	P43003	754
SLC38A3	SLC32A1	Q9H598	749
SLC38A3	SLC1A5	Q15758	617
SLC38A3	ADGRL3	Q9HAR2	553
SLC38A3	SLC1A2	P43004	546
SLC38A3	ZNF77	Q15935	546
SLC38A3	SLC7A6	Q92536	533
SLC38A3	SLC1A1	P43005	495
SLC38A3	SLC7A8	Q9UHI5	495
SLC38A3	CCDC28B	Q9BUN5	485
SLC38A3	GLUL	P15104	484
SLC38A3	AANAT	Q16613	475
SLC38A3	SLC38A9	Q8NBW4	475
SLC38A3	TECR	Q9NZ01	471

IntAct

12 interactions, top by confidence:

A	B	Type	Score
SCN3B	ABCC5	psi-mi:“MI:0914”(association)	0.530
SLC38A3	COL6A2	psi-mi:“MI:0915”(physical association)	0.370
SLC38A3	HMGN1	psi-mi:“MI:0915”(physical association)	0.370
CD81	STX3	psi-mi:“MI:0914”(association)	0.350
CD81	PVR	psi-mi:“MI:0914”(association)	0.350
CD81	CD276	psi-mi:“MI:0914”(association)	0.350
TSPAN15	TMEM223	psi-mi:“MI:0914”(association)	0.350
CACNG6	TSPAN3	psi-mi:“MI:0914”(association)	0.350
SLC38A3	SETDB1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): SLC38A3 (Affinity Capture-MS), SETDB1 (Two-hybrid), SLC38A3 (Affinity Capture-MS), SLC38A3 (Affinity Capture-MS), SLC38A3 (Affinity Capture-MS), SLC38A3 (Affinity Capture-MS), SLC38A3 (Proximity Label-MS), NEDD4 (Affinity Capture-Western), SLC38A3 (Two-hybrid), SLC38A3 (Two-hybrid)

ESM2 similar proteins: A1YG32, A2VCW5, A2VE31, D3Z813, F4KBM7, G3UVW3, O80668, P38176, P39981, P40074, P40501, P47082, Q08AI6, Q0WQJ3, Q17598, Q19425, Q28HE5, Q28I47, Q3U1J0, Q3USY0, Q503G8, Q54S12, Q5E9S9, Q5EA97, Q5F468, Q5R443, Q5RE87, Q5SPB1, Q5XH90, Q610N4, Q6DEL1, Q6DFE7, Q6WWW3, Q8CFE6, Q8HXI3, Q8IZM9, Q8K2P7, Q8R1S9, Q8WUX1, Q969I6

Diamond homologs: A1YG32, A2VCW5, A2VE31, G3UVW3, Q28HE5, Q3U1J0, Q503G8, Q5E9S9, Q5F468, Q5R443, Q5RE87, Q5SPB1, Q5XH90, Q6WWW3, Q8CFE6, Q8IZM9, Q8K2P7, Q8R1S9, Q8WUX1, Q969I6, Q96QD8, Q99624, Q9DCP2, Q9EQ25, Q9H2H9, Q9JHE5, Q9JHZ9, Q9JM15, F4J1Q9, A6NNN8, Q5HZH7, Q9LXF8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

71 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	6
Likely pathogenic	1
Uncertain significance	55
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
1687050	NM_006841.6(SLC38A3):c.855+1G>T	Pathogenic
1687051	NM_006841.6(SLC38A3):c.1049C>A (p.Ser350Ter)	Pathogenic
1687052	NM_006841.6(SLC38A3):c.1119del (p.Val373_Leu374insTer)	Pathogenic
1687053	NM_006841.6(SLC38A3):c.1123A>C (p.Thr375Pro)	Pathogenic
2444165	NM_006841.6(SLC38A3):c.187G>T (p.Glu63Ter)	Pathogenic
4292999	NM_006841.6(SLC38A3):c.856_859del	Pathogenic
1321101	NM_006841.6(SLC38A3):c.1212G>A (p.Trp404Ter)	Likely pathogenic

SpliceAI

2109 predictions. Top by Δscore:

Variant	Effect	Δscore
3:50205360:G:GT	donor_gain	1.0000
3:50214397:TACA:T	acceptor_loss	1.0000
3:50214399:CAGG:C	acceptor_loss	1.0000
3:50214401:A:AC	acceptor_loss	1.0000
3:50214479:CTGAC:C	donor_gain	1.0000
3:50214480:TGAC:T	donor_gain	1.0000
3:50214481:G:GT	donor_gain	1.0000
3:50214481:GAC:G	donor_gain	1.0000
3:50214482:AC:A	donor_gain	1.0000
3:50214484:G:GG	donor_gain	1.0000
3:50214493:G:T	donor_gain	1.0000
3:50214637:A:AG	acceptor_gain	1.0000
3:50214637:ATTCT:A	acceptor_gain	1.0000
3:50214638:T:G	acceptor_gain	1.0000
3:50214641:T:A	acceptor_gain	1.0000
3:50214642:G:A	acceptor_gain	1.0000
3:50214648:TGCA:T	acceptor_loss	1.0000
3:50214650:CAG:C	acceptor_loss	1.0000
3:50214651:A:AG	acceptor_gain	1.0000
3:50214652:G:GA	acceptor_gain	1.0000
3:50214652:GTTC:G	acceptor_gain	1.0000
3:50214743:GCCAA:G	donor_gain	1.0000
3:50214764:TTCCT:T	donor_gain	1.0000
3:50214765:TCCTG:T	donor_loss	1.0000
3:50214766:CCTGT:C	donor_loss	1.0000
3:50214767:CTGT:C	donor_loss	1.0000
3:50214768:TG:T	donor_loss	1.0000
3:50214769:G:GG	donor_gain	1.0000
3:50214769:GTGA:G	donor_loss	1.0000
3:50215539:T:A	acceptor_gain	1.0000

AlphaMissense

3299 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:50214693:T:C	L75P	1.000
3:50214710:G:C	G81R	1.000
3:50214691:C:A	N74K	0.999
3:50214691:C:G	N74K	0.999
3:50214710:G:T	G81C	0.999
3:50214711:G:A	G81D	0.999
3:50214713:A:C	S82R	0.999
3:50214715:C:A	S82R	0.999
3:50214715:C:G	S82R	0.999
3:50214716:G:C	G83R	0.999
3:50214723:T:A	L85Q	0.999
3:50215433:T:C	L116P	0.999
3:50215436:T:C	L117P	0.999
3:50215439:T:C	L118P	0.999
3:50215629:C:A	N153K	0.999
3:50215629:C:G	N153K	0.999
3:50215633:G:A	G155R	0.999
3:50215633:G:C	G155R	0.999
3:50215748:A:C	S159R	0.999
3:50215750:C:A	S159R	0.999
3:50215750:C:G	S159R	0.999
3:50217445:T:C	L221P	0.999
3:50217450:T:C	C223R	0.999
3:50217944:T:C	F295L	0.999
3:50217946:C:A	F295L	0.999
3:50217946:C:G	F295L	0.999
3:50217990:T:C	L310P	0.999
3:50218677:T:C	L374P	0.999
3:50218692:T:C	L379P	0.999
3:50218701:C:A	P382H	0.999

dbSNP variants (sampled 300 via entrez): RS1000055371 (3:50213267 T>C), RS1000248319 (3:50215885 T>G), RS1000306153 (3:50216400 G>T), RS1000329778 (3:50209737 T>C), RS1000591862 (3:50215856 G>A), RS1000643430 (3:50214933 A>G), RS1000888586 (3:50210033 C>A), RS1000891323 (3:50204195 C>T), RS1001340699 (3:50203496 A>G), RS1001387866 (3:50203938 G>A), RS1001491722 (3:50211334 T>G), RS1001530690 (3:50210015 A>C,G), RS1001734552 (3:50211141 C>T), RS1002099346 (3:50216189 C>T), RS1002246172 (3:50205155 C>G)

Disease associations

OMIM: gene MIM:604437 | disease phenotypes: MIM:619881

GenCC curated gene-disease

Disease	Classification	Inheritance
developmental and epileptic encephalopathy 102	Strong	Autosomal recessive

Mondo (1): developmental and epileptic encephalopathy 102 (MONDO:0030881)

Orphanet (0):

HPO phenotypes

68 total (30 of 68 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000252	Microcephaly
HP:0000348	High forehead
HP:0000494	Downslanted palpebral fissures
HP:0000504	Abnormality of vision
HP:0000505	Visual impairment
HP:0000508	Ptosis
HP:0000546	Retinal degeneration
HP:0000639	Nystagmus
HP:0000648	Optic atrophy
HP:0000668	Hypodontia
HP:0000708	Atypical behavior
HP:0000717	Autism
HP:0000750	Delayed speech and language development
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001257	Spasticity
HP:0001263	Global developmental delay
HP:0001265	Hyporeflexia
HP:0001268	Mental deterioration
HP:0001273	Abnormal corpus callosum morphology
HP:0001288	Gait disturbance
HP:0001290	Generalized hypotonia
HP:0001298	Encephalopathy
HP:0001315	Reduced tendon reflexes
HP:0001336	Myoclonus
HP:0001337	Tremor
HP:0001344	Absent speech
HP:0001347	Hyperreflexia

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST004723_21	Conotruncal heart defects (maternal effects)	4.000000e-07
GCST005951_49	Body mass index	1.000000e-08
GCST007327_38	Smoking status (ever vs never smokers)	8.000000e-09
GCST007559_24	Sleep duration (short sleep)	3.000000e-08
GCST012227_988	Hip circumference adjusted for BMI	1.000000e-12
GCST90002386_547	High light scatter reticulocyte percentage of red cells	3.000000e-12
GCST90002387_73	Immature fraction of reticulocytes	2.000000e-09
GCST90002406_33	Reticulocyte fraction of red cells	7.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004318	smoking behavior
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — System N-like transporters

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation, increases methylation	4
sodium arsenite	decreases expression, increases abundance, increases expression	3
Aflatoxin B1	affects expression, decreases expression	3
perfluorooctane sulfonic acid	decreases expression, increases expression	2
methyleugenol	decreases expression	1
bisphenol A	affects expression	1
deoxynivalenol	decreases expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
potassium chromate(VI)	increases expression	1
periodate-oxidized adenosine	affects expression	1
aflatoxin B2	increases methylation	1
nickel sulfate	decreases expression	1
benazol P	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
Rosiglitazone	decreases expression	1
Sunitinib	decreases expression	1
Troglitazone	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	increases abundance, increases expression	1
Cadmium	increases expression, increases response to substance	1
Caffeine	decreases phosphorylation	1
Carbamazepine	increases expression	1
Doxorubicin	decreases expression	1
Endosulfan	affects cotreatment, decreases expression	1
Estradiol	decreases expression	1
Quercetin	decreases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1
Valproic Acid	decreases expression	1
Zidovudine	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D4TF	HuH7-SLC38A3-KO-c2	Cancer cell line	Male
CVCL_D4TG	HuH7-SLC38A3-KO-c3	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.