SLC38A12

Summary

SLC38A12 (solute carrier family 38 member 12, HGNC:25984) is a protein-coding gene on chromosome 17q25.1, encoding Putative sodium-coupled neutral amino acid transporter 12 (Q8NE00).

Predicted to be located in membrane.

Source: NCBI Gene 54868 — RefSeq curated summary.

At a glance

• Gene–disease (curated): complex neurodevelopmental disorder (Limited, GenCC)
• GWAS associations: 2
• Clinical variants (ClinVar): 83 total
• MANE Select transcript: NM_017728

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25984
Approved symbol	SLC38A12
Name	solute carrier family 38 member 12
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20255, FLJ00021
Ensembl gene	ENSG00000109066
Ensembl biotype	protein_coding
Entrez	54868

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000335464, ENST00000417024, ENST00000578764, ENST00000582330, ENST00000582773, ENST00000584171, ENST00000584246, ENST00000872109, ENST00000872110, ENST00000915163, ENST00000915164, ENST00000915165

RefSeq mRNA: 2 — MANE Select: NM_017728 NM_001321264, NM_017728

CCDS: CCDS32723, CCDS82201

Canonical transcript exons

ENST00000335464 — 10 exons

Exon	Start	End
ENSE00000744092	74785482	74785603
ENSE00000744093	74788789	74788870
ENSE00000744094	74790200	74790296
ENSE00000744095	74790956	74791036
ENSE00000744214	74819750	74819843
ENSE00000908385	74795524	74795632
ENSE00000908386	74795012	74795111
ENSE00001343412	74776499	74776577
ENSE00002734811	74835927	74839753
ENSE00003678210	74777264	74777375

Expression profiles

Bgee: expression breadth ubiquitous, 211 present calls, max score 84.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.2160 / max 145.9400, expressed in 1812 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
162671	19.6157	1812
162672	0.6003	360

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	84.60	gold quality
granulocyte	CL:0000094	83.92	gold quality
monocyte	CL:0000576	82.92	gold quality
leukocyte	CL:0000738	82.64	gold quality
mononuclear cell	CL:0000842	82.62	gold quality
endothelial cell	CL:0000115	82.03	silver quality
parotid gland	UBERON:0001831	81.05	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	81.02	gold quality
blood	UBERON:0000178	79.82	gold quality
left adrenal gland cortex	UBERON:0035825	79.82	gold quality
left adrenal gland	UBERON:0001234	79.75	gold quality
right adrenal gland	UBERON:0001233	79.65	gold quality
right lobe of liver	UBERON:0001114	79.56	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.16	gold quality
spinal cord	UBERON:0002240	79.01	gold quality
right adrenal gland cortex	UBERON:0035827	78.88	gold quality
adrenal cortex	UBERON:0001235	78.42	gold quality
adenohypophysis	UBERON:0002196	78.42	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	78.40	silver quality
apex of heart	UBERON:0002098	78.26	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.77	gold quality
adrenal gland	UBERON:0002369	77.55	gold quality
upper lobe of left lung	UBERON:0008952	77.32	gold quality
mucosa of transverse colon	UBERON:0004991	77.23	gold quality
metanephros cortex	UBERON:0010533	77.10	gold quality
inferior olivary complex	UBERON:0002127	76.93	gold quality
right lobe of thyroid gland	UBERON:0001119	76.89	gold quality
pituitary gland	UBERON:0000007	76.87	gold quality
medial globus pallidus	UBERON:0002477	76.81	gold quality
ascending aorta	UBERON:0001496	76.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

156 targeting SLC38A12, 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-4283	100.00	66.42	2097
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem104	ENSDARG00000088560
mus_musculus	Tmem104	ENSMUSG00000045980
rattus_norvegicus	Tmem104	ENSRNOG00000025669
drosophila_melanogaster	CG5262	FBGN0036988
caenorhabditis_elegans		WBGENE00007267

Protein

Protein identifiers

Putative sodium-coupled neutral amino acid transporter 12 — Q8NE00 (reviewed: Q8NE00)

Alternative names: Solute carrier family 38 member 12

All UniProt accessions (3): Q8NE00, B4DKL7, J3QQK2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NE00-1	1	yes
Q8NE00-2	2

RefSeq proteins (2): NP_001308193, NP_060198* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013057	AA_transpt_TM	Domain

Pfam: PF01490

UniProt features (29 total): topological domain 12, transmembrane region 11, splice variant 2, sequence variant 2, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NE00-F1	81.33	0.36

Functional residue map

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

Glycosylation sites (1): 193

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): RRAGTTGT_UNKNOWN, CAGCTG_AP4_Q5, TTGCWCAAY_CEBPB_02, GTGCCTT_MIR506, KESHELAVA_MULTIPLE_DRUG_RESISTANCE, TGANTCA_AP1_C, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, CEBPB_02, MARTENS_BOUND_BY_PML_RARA_FUSION, DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP, BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP, BHAT_ESR1_TARGETS_VIA_AKT1_UP, TBK1.DF_UP, DACH1_TARGET_GENES

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (2): membrane (GO:0016020), cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

426 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC38A12	ANTKMT	Q9BQD7	557
SLC38A12	SVOP	Q8N4V2	489
SLC38A12	UNC93A	Q86WB7	470
SLC38A12	SVOPL	Q8N434	470
SLC38A12	TMEM94	Q12767	459
SLC38A12	SPNS3	Q6ZMD2	441
SLC38A12	FDXR	P22570	434
SLC38A12	SUPV3L1	Q8IYB8	418
SLC38A12	MFSD6	Q6ZSS7	394
SLC38A12	SYTL5	Q8TDW5	389
SLC38A12	MFSD8	Q8NHS3	387
SLC38A12	KIAA0513	O60268	374
SLC38A12	GPRASP3	Q6PI77	369
SLC38A12	BTBD16	Q32M84	355
SLC38A12	SPNS1	Q9H2V7	355

IntAct

8 interactions, top by confidence:

A	B	Type	Score
USP36	STK25	psi-mi:“MI:0914”(association)	0.350
CRELD1	TMEM223	psi-mi:“MI:0914”(association)	0.350
LRRC55	TMEM120B	psi-mi:“MI:0914”(association)	0.350
HTR3C	GET1	psi-mi:“MI:0914”(association)	0.350
DLK1	PLPP3	psi-mi:“MI:0914”(association)	0.350
GPR12	MGST3	psi-mi:“MI:0914”(association)	0.350
TMEM104	PSMD12	psi-mi:“MI:0914”(association)	0.350

BioGRID (24): TMEM104 (Affinity Capture-MS), TMEM104 (Affinity Capture-MS), TMEM104 (Affinity Capture-MS), TMEM104 (Proximity Label-MS), TMEM104 (Affinity Capture-RNA), TMEM104 (Affinity Capture-MS), TMEM104 (Affinity Capture-MS), TMEM104 (Affinity Capture-MS), TMEM104 (Co-fractionation), TMEM104 (Co-fractionation), ABCB10 (Affinity Capture-MS), FAF2 (Affinity Capture-MS), HLA-A (Affinity Capture-MS), NPLOC4 (Affinity Capture-MS), PSMA7 (Affinity Capture-MS)

ESM2 similar proteins: A6NFX1, B0JZE1, E2RFJ3, F1NCD6, F1NJ67, F1PZV2, P54219, P57057, Q01818, Q01827, Q05940, Q0IHM1, Q17QZ3, Q1JQC1, Q27963, Q2XWK0, Q32LQ6, Q3T9M1, Q3TIT8, Q3U481, Q58CV5, Q5F3N0, Q5R8G5, Q5TF39, Q5U3U7, Q5ZIT9, Q66H95, Q68F72, Q6DEJ6, Q6NUT3, Q7SY29, Q8BH31, Q8BRU6, Q8IVW8, Q8NA29, Q8NCC5, Q8NE00, Q8NHS3, Q8R070, Q8R090

Diamond homologs: Q17598, Q3TB48, Q5F3I6, Q5RCV1, Q610N4, Q8NE00, Q9VPF8, Q54S12

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	3
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2101 predictions. Top by Δscore:

Variant	Effect	Δscore
17:74777376:G:GG	donor_gain	1.0000
17:74788739:T:TA	acceptor_gain	1.0000
17:74788749:A:AG	acceptor_gain	1.0000
17:74788749:AACCT:A	acceptor_gain	1.0000
17:74788750:A:AG	acceptor_gain	1.0000
17:74788751:C:G	acceptor_gain	1.0000
17:74788753:T:A	acceptor_gain	1.0000
17:74788757:C:CA	acceptor_gain	1.0000
17:74788763:T:TA	acceptor_gain	1.0000
17:74788764:G:A	acceptor_gain	1.0000
17:74788766:C:CA	acceptor_gain	1.0000
17:74788774:ACTC:A	acceptor_gain	1.0000
17:74790159:T:TA	acceptor_gain	1.0000
17:74790178:C:CA	acceptor_gain	1.0000
17:74790183:A:AG	acceptor_gain	1.0000
17:74790184:T:G	acceptor_gain	1.0000
17:74790188:A:AG	acceptor_gain	1.0000
17:74790188:ACT:A	acceptor_gain	1.0000
17:74790188:ACTG:A	acceptor_gain	1.0000
17:74790189:C:G	acceptor_gain	1.0000
17:74790190:T:TA	acceptor_gain	1.0000
17:74790191:G:A	acceptor_gain	1.0000
17:74790197:CAG:C	acceptor_loss	1.0000
17:74790198:A:AG	acceptor_gain	1.0000
17:74790199:G:GG	acceptor_gain	1.0000
17:74790199:G:T	acceptor_loss	1.0000
17:74790293:G:GG	donor_gain	1.0000
17:74790294:TGC:T	donor_gain	1.0000
17:74790295:GC:G	donor_gain	1.0000
17:74790295:GCG:G	donor_gain	1.0000

AlphaMissense

3255 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:74795063:T:C	L160P	1.000
17:74836292:A:C	S366R	1.000
17:74836294:C:A	S366R	1.000
17:74836294:C:G	S366R	1.000
17:74836323:T:C	L376P	1.000
17:74785505:C:A	N23K	0.999
17:74785505:C:G	N23K	0.999
17:74785507:T:C	L24P	0.999
17:74785515:G:C	G27R	0.999
17:74785521:G:C	G29R	0.999
17:74785522:G:A	G29D	0.999
17:74785528:T:A	L31H	0.999
17:74785537:C:A	P34H	0.999
17:74785569:A:C	S45R	0.999
17:74785571:C:A	S45R	0.999
17:74785571:C:G	S45R	0.999
17:74795051:T:C	L156P	0.999
17:74795056:G:A	G158R	0.999
17:74795056:G:C	G158R	0.999
17:74795057:G:A	G158E	0.999
17:74795059:G:C	D159H	0.999
17:74795060:A:T	D159V	0.999
17:74836313:G:C	A373P	0.999
17:74836333:C:A	N379K	0.999
17:74836333:C:G	N379K	0.999
17:74836472:G:T	G426W	0.999
17:74836473:G:A	G426E	0.999
17:74836484:G:C	G430R	0.999
17:74836485:G:A	G430D	0.999
17:74836625:T:A	W477R	0.999

dbSNP variants (sampled 300 via entrez): RS1000012914 (17:74790439 CA>C), RS1000017639 (17:74809386 A>G), RS1000035700 (17:74808735 C>G), RS1000057800 (17:74784041 A>G), RS1000073831 (17:74839614 A>G), RS1000075606 (17:74804454 A>G), RS1000108121 (17:74784504 G>A), RS1000110255 (17:74827511 G>A), RS1000121616 (17:74827194 T>C), RS1000144322 (17:74792216 C>A,T), RS1000175461 (17:74775486 G>A), RS1000208795 (17:74811609 T>C), RS1000271461 (17:74786652 C>T), RS1000306313 (17:74817460 G>A), RS1000317044 (17:74799642 G>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
complex neurodevelopmental disorder	Limited	Autosomal dominant

Mondo (1): complex neurodevelopmental disorder (MONDO:0100038)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004721_20	Congenital heart disease (maternal effect)	4.000000e-06
GCST004723_22	Conotruncal heart defects (maternal effects)	7.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	3
Tretinoin	increases expression	2
dicrotophos	increases expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
bisphenol A	increases expression	1
ferrous chloride	decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Vehicle Emissions	decreases expression, increases abundance	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Estradiol	increases expression	1
Lead	affects expression	1
Ozone	affects cotreatment, decreases expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	decreases expression, increases abundance	1
Volatile Organic Compounds	affects cotreatment, decreases 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_D4R6	HCT116-TMEM104-KO-c4	Cancer cell line	Male
CVCL_D4R7	HCT116-TMEM104-KO-c5	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT06310681	Not specified	COMPLETED	Pilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049	Not specified	NOT_YET_RECRUITING	Cognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder