SLC38A10

Summary

SLC38A10 (solute carrier family 38 member 10, HGNC:28237) is a protein-coding gene on chromosome 17q25.3, encoding Solute carrier family 38 member 10 (Q9HBR0). Facilitates bidirectional transport of amino acids.

Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport. Predicted to act upstream of or within bone development. Located in Golgi apparatus.

Source: NCBI Gene 124565 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 159 total
• MANE Select transcript: NM_001037984

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28237
Approved symbol	SLC38A10
Name	solute carrier family 38 member 10
Location	17q25.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC15523, PP1744, SNAT10
Ensembl gene	ENSG00000157637
Ensembl biotype	protein_coding
OMIM	616525
Entrez	124565

Gene structure

Transcript identifiers

Ensembl transcripts: 44 — 39 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000288439, ENST00000374759, ENST00000539643, ENST00000539748, ENST00000540233, ENST00000540966, ENST00000542075, ENST00000543204, ENST00000546352, ENST00000573058, ENST00000576151, ENST00000899481, ENST00000899482, ENST00000899483, ENST00000899484, ENST00000899485, ENST00000899486, ENST00000899487, ENST00000899488, ENST00000899489, ENST00000899490, ENST00000899491, ENST00000899492, ENST00000899493, ENST00000899494, ENST00000899495, ENST00000918313, ENST00000918314, ENST00000918315, ENST00000918316, ENST00000918317, ENST00000947959, ENST00000947960, ENST00000947961, ENST00000947962, ENST00000947963, ENST00000947964, ENST00000947965, ENST00000947966, ENST00000947967, ENST00000947968, ENST00000947969, ENST00000947970, ENST00000947971

RefSeq mRNA: 2 — MANE Select: NM_001037984 NM_001037984, NM_138570

CCDS: CCDS11780, CCDS42397

Canonical transcript exons

ENST00000374759 — 16 exons

Exon	Start	End
ENSE00001111965	81284850	81284895
ENSE00001309561	81244811	81246673
ENSE00001327519	81294823	81295307
ENSE00003474284	81260238	81260394
ENSE00003513671	81283409	81283502
ENSE00003517749	81275969	81276151
ENSE00003525043	81251493	81251612
ENSE00003553514	81272516	81272627
ENSE00003573240	81289691	81289808
ENSE00003639256	81270918	81271024
ENSE00003650757	81246885	81247061
ENSE00003657474	81252195	81252683
ENSE00003671324	81253073	81253240
ENSE00003674503	81277031	81277133
ENSE00003687788	81280609	81280733
ENSE00003791312	81282189	81282332

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 97.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.9196 / max 907.3634, expressed in 1820 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168684	33.4646	1818
168683	2.0509	1116
168685	1.3933	1041
168682	0.7625	420
168681	0.2483	113

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	97.93	gold quality
body of pancreas	UBERON:0001150	97.67	gold quality
pituitary gland	UBERON:0000007	97.52	gold quality
right lobe of liver	UBERON:0001114	97.47	gold quality
right lobe of thyroid gland	UBERON:0001119	96.35	gold quality
mucosa of transverse colon	UBERON:0004991	96.22	gold quality
apex of heart	UBERON:0002098	95.94	gold quality
right uterine tube	UBERON:0001302	95.90	gold quality
right coronary artery	UBERON:0001625	95.85	gold quality
left lobe of thyroid gland	UBERON:0001120	95.82	gold quality
lower esophagus mucosa	UBERON:0035834	95.77	gold quality
granulocyte	CL:0000094	95.70	gold quality
body of stomach	UBERON:0001161	95.37	gold quality
thyroid gland	UBERON:0002046	95.27	gold quality
stromal cell of endometrium	CL:0002255	95.21	gold quality
sural nerve	UBERON:0015488	95.19	gold quality
right ovary	UBERON:0002118	95.04	gold quality
spleen	UBERON:0002106	94.98	gold quality
lower esophagus	UBERON:0013473	94.87	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.87	gold quality
ascending aorta	UBERON:0001496	94.84	gold quality
thoracic aorta	UBERON:0001515	94.79	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.79	gold quality
endocervix	UBERON:0000458	94.78	gold quality
left ovary	UBERON:0002119	94.76	gold quality
fundus of stomach	UBERON:0001160	94.66	gold quality
right adrenal gland	UBERON:0001233	94.64	gold quality
left adrenal gland cortex	UBERON:0035825	94.64	gold quality
left coronary artery	UBERON:0001626	94.63	gold quality
coronary artery	UBERON:0001621	94.54	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.26
E-GEOD-70580	no	157.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting SLC38A10, 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-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-6501-3P	98.71	67.45	1480
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-6515-5P	97.08	65.48	1219
HSA-MIR-6875-5P	96.87	65.49	958
HSA-MIR-3126-5P	96.87	65.83	912

Literature-anchored findings (GeneRIF, showing 1)

• A Fragment of S38AA is a Novel Plasma Biomarker of Alzheimer’s Disease. (PMID:31524172)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc38a10	ENSDARG00000077081
mus_musculus	Slc38a10	ENSMUSG00000061306
rattus_norvegicus	Slc38a10	ENSRNOG00000004604
drosophila_melanogaster	CG30394	FBGN0050394
caenorhabditis_elegans	Y51F10.4	WBGENE00021765

Paralogs (15): SLC38A5 (ENSG00000017483), SLC32A1 (ENSG00000101438), SLC38A7 (ENSG00000103042), SLC38A1 (ENSG00000111371), SLC36A1 (ENSG00000123643), SLC38A2 (ENSG00000134294), SLC38A4 (ENSG00000139209), SLC38A6 (ENSG00000139974), SLC38A8 (ENSG00000166558), SLC38A11 (ENSG00000169507), SLC38A9 (ENSG00000177058), SLC36A4 (ENSG00000180773), SLC36A3 (ENSG00000186334), SLC36A2 (ENSG00000186335), SLC38A3 (ENSG00000188338)

Protein

Protein identifiers

Solute carrier family 38 member 10 — Q9HBR0 (reviewed: Q9HBR0)

Alternative names: Amino acid transporter SLC38A10

All UniProt accessions (5): Q9HBR0, F5H3T4, H0YF92, H0YGS1, I3L0Q8

UniProt curated annotations — full annotation on UniProt →

Function. Facilitates bidirectional transport of amino acids. May act as a glutamate sensor that regulates glutamate-glutamine cycle and mTOR signaling in the brain. The transport mechanism remains to be elucidated.

Subcellular location. Membrane.

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

Isoforms (3)

UniProt ID	Names	Canonical?
Q9HBR0-1	1	yes
Q9HBR0-2	2
Q9HBR0-3	3

RefSeq proteins (2): NP_001033073, NP_612637 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013057	AA_transpt_TM	Domain

Pfam: PF01490

Catalyzed reactions (Rhea), 5 shown:

• L-serine(in) = L-serine(out) (RHEA:35031)
• L-glutamate(out) = L-glutamate(in) (RHEA:66336)
• L-alanine(in) = L-alanine(out) (RHEA:70719)
• L-leucine(in) = L-leucine(out) (RHEA:73011)
• L-glutamine(out) = L-glutamine(in) (RHEA:73419)

UniProt features (42 total): compositionally biased region 15, transmembrane region 10, modified residue 6, splice variant 5, region of interest 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HBR0-F1	54.71	0.13

Functional residue map

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

Post-translational modifications (6): 612, 772, 802, 889, 965, 997

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 141 (showing top): YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, DARWICHE_PAPILLOMA_PROGRESSION_RISK, GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, GOBP_ORGANIC_ACID_TRANSPORT, GOBP_BONE_DEVELOPMENT, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, GOBP_AMINO_ACID_TRANSPORT, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GOBP_ORGANIC_ANION_TRANSPORT, MODULE_88, BASAKI_YBX1_TARGETS_UP, HAN_SATB1_TARGETS_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON

GO Biological Process (4): amino acid transmembrane transport (GO:0003333), bone development (GO:0060348), amino acid transport (GO:0006865), L-alpha-amino acid transmembrane transport (GO:1902475)

GO Molecular Function (1): L-amino acid transmembrane transporter activity (GO:0015179)

GO Cellular Component (2): Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
amino acid transport	1
transmembrane transport	1
skeletal system development	1
animal organ development	1
transport	1
amino acid transmembrane transport	1
L-amino acid transport	1
carboxylic acid transmembrane transport	1
amino acid transmembrane transporter activity	1
carboxylic acid transmembrane transporter activity	1
L-alpha-amino acid transmembrane transport	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1185 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC38A10	SLC38A9	Q8NBW4	542
SLC38A10	TBC1D22A	Q8WUA7	461
SLC38A10	PRPSAP2	O60256	446
SLC38A10	ZNF516	Q92618	446
SLC38A10	CTAGE8	P0CG41	438
SLC38A10	KIF26B	Q2KJY2	429
SLC38A10	KIF18A	Q8NI77	406
SLC38A10	MIGA2	Q7L4E1	400
SLC38A10	NEK6	Q9HC98	400
SLC38A10	SLC7A8	Q9UHI5	390
SLC38A10	BBX	Q8WY36	386
SLC38A10	HERC5	Q9UII4	381
SLC38A10	ERICH4	A6NGS2	380
SLC38A10	SLC36A2	Q495M3	374
SLC38A10	NPEPL1	Q8NDH3	372

IntAct

87 interactions, top by confidence:

A	B	Type	Score
QRSL1	GATB	psi-mi:“MI:0914”(association)	0.790
TOR1AIP2	TMEM223	psi-mi:“MI:0914”(association)	0.530
HLA-DPA1	TYW5	psi-mi:“MI:0914”(association)	0.530
SYP	APBB1	psi-mi:“MI:0914”(association)	0.530
HAX1	CHEK1	psi-mi:“MI:0914”(association)	0.530
NCEH1	CLGN	psi-mi:“MI:0914”(association)	0.530
ARMC6	SLC27A2	psi-mi:“MI:0914”(association)	0.530
B4GAT1	ADCY6	psi-mi:“MI:0914”(association)	0.530
HFE	ADAM10	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
SLC38A10	PPIB	psi-mi:“MI:0915”(physical association)	0.400
Tpx2	NFKBIE	psi-mi:“MI:0914”(association)	0.350
Cep135		psi-mi:“MI:0914”(association)	0.350
Papss1	TCOF1	psi-mi:“MI:0914”(association)	0.350
Rab7a		psi-mi:“MI:0914”(association)	0.350
NCAPH	SCAMP2	psi-mi:“MI:0914”(association)	0.350
KIF5B	TRAK1	psi-mi:“MI:0914”(association)	0.350
Sass6	MACF1	psi-mi:“MI:0914”(association)	0.350
	ESYT2	psi-mi:“MI:0914”(association)	0.350
E5	ESYT2	psi-mi:“MI:0914”(association)	0.350
	HAX1	psi-mi:“MI:0914”(association)	0.350
HTR3C	TMEM223	psi-mi:“MI:0914”(association)	0.350
HLA-DPA1	GXYLT2	psi-mi:“MI:0914”(association)	0.350
EDEM2	HACD1	psi-mi:“MI:0914”(association)	0.350
SYP	APBB1	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
CCDC47	ESYT2	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
MGARP	BTAF1	psi-mi:“MI:0914”(association)	0.350

BioGRID (93): SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS), SLC38A10 (Affinity Capture-MS)

ESM2 similar proteins: A2AMT1, A8MU46, E9PT23, H3JU05, O54963, O70318, O88422, P10636, P10637, P15304, P19332, P46087, P51954, Q13438, Q14028, Q28181, Q3MHX6, Q3UH66, Q3UIZ8, Q3UVR3, Q4ZHG4, Q5I012, Q5RC98, Q5RKH6, Q5S6V2, Q5TCY1, Q5YCV9, Q5YCW0, Q5YCW1, Q6PCF9, Q6PCN3, Q7Z7M9, Q811D2, Q811Q2, Q8BHB9, Q8BWQ5, Q8C102, Q8K2C7, Q91XA2, Q91Z96

Diamond homologs: E9PT23, Q5I012, Q5RC98, Q6PCF9, Q9HBR0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	117
Likely benign	20
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3129 predictions. Top by Δscore:

Variant	Effect	Δscore
17:81252681:TCC:T	acceptor_gain	1.0000
17:81252682:CCC:C	acceptor_gain	1.0000
17:81253072:C:G	donor_loss	1.0000
17:81253096:G:A	donor_gain	1.0000
17:81253099:T:TA	donor_gain	1.0000
17:81253111:T:TA	donor_gain	1.0000
17:81253116:G:A	donor_gain	1.0000
17:81260233:CATA:C	donor_loss	1.0000
17:81260234:ATACC:A	donor_loss	1.0000
17:81260235:TA:T	donor_loss	1.0000
17:81260236:A:T	donor_loss	1.0000
17:81260237:CCTG:C	donor_loss	1.0000
17:81270913:CGCA:C	donor_loss	1.0000
17:81270914:GCAC:G	donor_loss	1.0000
17:81270915:CACCT:C	donor_loss	1.0000
17:81270916:A:C	donor_loss	1.0000
17:81270917:C:CG	donor_loss	1.0000
17:81271020:CTCCA:C	acceptor_gain	1.0000
17:81271021:TCCA:T	acceptor_gain	1.0000
17:81271022:CCA:C	acceptor_gain	1.0000
17:81271022:CCAC:C	acceptor_gain	1.0000
17:81271023:CA:C	acceptor_gain	1.0000
17:81271023:CAC:C	acceptor_gain	1.0000
17:81271025:C:CC	acceptor_gain	1.0000
17:81271025:CT:C	acceptor_loss	1.0000
17:81271026:T:A	acceptor_loss	1.0000
17:81271030:A:AC	acceptor_gain	1.0000
17:81271030:A:C	acceptor_gain	1.0000
17:81272628:C:CC	acceptor_gain	1.0000
17:81272630:G:C	acceptor_gain	1.0000

AlphaMissense

7259 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:81270984:G:C	S355R	0.999
17:81270984:G:T	S355R	0.999
17:81270986:T:G	S355R	0.999
17:81282267:G:C	S141R	0.999
17:81282267:G:T	S141R	0.999
17:81282269:T:G	S141R	0.999
17:81283502:G:C	S88R	0.999
17:81283502:G:T	S88R	0.999
17:81284851:T:G	S88R	0.999
17:81294853:A:C	S23R	0.999
17:81294853:A:T	S23R	0.999
17:81294855:T:G	S23R	0.999
17:81260356:G:C	S390R	0.998
17:81260356:G:T	S390R	0.998
17:81260358:T:G	S390R	0.998
17:81282228:G:C	S154R	0.998
17:81282228:G:T	S154R	0.998
17:81282230:T:G	S154R	0.998
17:81294868:G:C	S18R	0.998
17:81294868:G:T	S18R	0.998
17:81294870:T:G	S18R	0.998
17:81270989:C:G	G354R	0.997
17:81270989:C:T	G354R	0.997
17:81283491:A:G	L92P	0.997
17:81294871:G:C	N17K	0.997
17:81294871:G:T	N17K	0.997
17:81246962:A:G	L722P	0.996
17:81276002:C:A	R293S	0.996
17:81276002:C:G	R293S	0.996
17:81276003:C:A	R293M	0.996

dbSNP variants (sampled 300 via entrez): RS1000002655 (17:81296681 A>G), RS1000021319 (17:81264625 T>C), RS1000039174 (17:81253798 A>G), RS1000100224 (17:81264812 T>C), RS1000138603 (17:81246803 C>A,G,T), RS1000170523 (17:81255995 T>A), RS1000210709 (17:81281165 G>C), RS1000228025 (17:81292830 C>T), RS1000296912 (17:81274852 T>G), RS1000301052 (17:81244524 G>T), RS1000355842 (17:81251808 C>T), RS1000375304 (17:81283433 G>T), RS1000392572 (17:81264858 T>C), RS1000442959 (17:81260133 A>G), RS1000465762 (17:81248484 T>C)

Disease associations

OMIM: gene MIM:616525 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST000785_39	Longevity	1.000000e-06
GCST001848_270	IgG glycosylation	3.000000e-08
GCST009860_8	IgG N-glycosylation phenotypes (multivariate analysis)	1.000000e-15

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005193	serum IgG glycosylation measurement

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 — Orphan SLC38 transporters

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	7
sodium arsenite	increases expression	2
Air Pollutants	increases abundance, increases expression, affects expression	2
Nickel	increases expression	2
Ozone	affects cotreatment, increases expression, affects expression, increases abundance	2
Phenylmercuric Acetate	increases expression, affects cotreatment	2
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
manganese chloride	increases expression	1
ferrous chloride	decreases expression	1
cupric chloride	increases expression	1
methacrylaldehyde	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
bisphenol B	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
MT19c compound	decreases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases expression	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Caffeine	increases phosphorylation	1

Cellosaurus cell lines

5 cell lines: 4 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3HG	Abcam HEK293T SLC38A10 KO	Transformed cell line	Female
CVCL_D4N0	HCT116-SLC38A10-KO-c5	Cancer cell line	Male
CVCL_D4N1	HCT116-SLC38A10-KO-c6	Cancer cell line	Male
CVCL_TN40	HAP1 SLC38A10 (-) 1	Cancer cell line	Male
CVCL_TN41	HAP1 SLC38A10 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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