SLC7A13

Summary

SLC7A13 (solute carrier family 7 member 13, HGNC:23092) is a protein-coding gene on chromosome 8q21.3, encoding Solute carrier family 7 member 13 (Q8TCU3). Associates with SLC3A1/rBAT to form a functional heterodimeric complex that transports anionic and neutral amino acids across the apical plasma membrane of renal epithelium.

Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in apical plasma membrane.

Source: NCBI Gene 157724 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 164 total
• MANE Select transcript: NM_138817

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23092
Approved symbol	SLC7A13
Name	solute carrier family 7 member 13
Location	8q21.3
Locus type	gene with protein product
Status	Approved
Aliases	AGT-1, XAT2
Ensembl gene	ENSG00000164893
Ensembl biotype	protein_coding
OMIM	617256
Entrez	157724

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000297524, ENST00000419776, ENST00000520624

RefSeq mRNA: 1 — MANE Select: NM_138817 NM_138817

CCDS: CCDS34917

Canonical transcript exons

ENST00000297524 — 4 exons

Exon	Start	End
ENSE00001088325	86217470	86217831
ENSE00001088328	86229593	86230381
ENSE00002094566	86214063	86214646
ENSE00003672547	86222972	86223103

Expression profiles

Bgee: expression breadth broad, 32 present calls, max score 95.01.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0023 / max 3.4846, expressed in 1 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
93815	0.0023	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	95.01	gold quality
renal medulla	UBERON:0000362	69.28	gold quality
adult organism	UBERON:0007023	63.90	gold quality
kidney	UBERON:0002113	62.31	gold quality
adult mammalian kidney	UBERON:0000082	60.91	gold quality
ileal mucosa	UBERON:0000331	54.59	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
epithelial cell of pancreas	CL:0000083	53.69	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
pancreatic ductal cell	CL:0002079	52.05	silver quality
cortex of kidney	UBERON:0001225	51.80	gold quality
myocardium	UBERON:0002349	50.25	gold quality
tibialis anterior	UBERON:0001385	49.87	silver quality
deltoid	UBERON:0001476	49.67	gold quality
cerebellar vermis	UBERON:0004720	48.63	gold quality
quadriceps femoris	UBERON:0001377	47.33	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
metanephros cortex	UBERON:0010533	46.49	gold quality
lower lobe of lung	UBERON:0008949	46.34	silver quality
metanephros	UBERON:0000081	46.32	gold quality
skin of hip	UBERON:0001554	45.93	silver quality
vastus lateralis	UBERON:0001379	45.40	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
thymus	UBERON:0002370	42.26	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting SLC7A13, 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-568	99.98	69.86	2084
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-936	98.87	70.51	1124
HSA-MIR-6794-3P	98.76	66.99	894
HSA-MIR-222-5P	98.75	69.17	1242
HSA-MIR-34B-3P	98.70	67.40	1171
HSA-MIR-4766-3P	98.48	67.94	1347
HSA-MIR-4423-3P	97.98	69.66	912
HSA-MIR-4286	97.20	64.37	1587
HSA-MIR-4654	95.86	65.72	751
HSA-MIR-4522	95.76	66.23	742
HSA-MIR-4769-5P	95.37	66.09	570

Literature-anchored findings (GeneRIF, showing 1)

• data suggest that the cellular energetic deficit due to AGC1 impairment is associated with inappropriate aspartate levels to support neuronal proliferation when glutamine is not used as metabolic substrate (PMID:28235644)

Cross-species orthologs

21 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkeyp-120h9.1	ENSDARG00000020278
danio_rerio	slc7a2	ENSDARG00000037097
danio_rerio	si:ch73-352p4.8	ENSDARG00000040610
danio_rerio	slc7a11	ENSDARG00000071384
danio_rerio	zgc:175280	ENSDARG00000099111
mus_musculus	Slc7a13	ENSMUSG00000041052
rattus_norvegicus	Slc7a13	ENSRNOG00000024903
drosophila_melanogaster	mnd	FBGN0002778
drosophila_melanogaster	sbm	FBGN0030574
drosophila_melanogaster	CG7255	FBGN0036493
drosophila_melanogaster	CG5535	FBGN0036764
drosophila_melanogaster	CG13248	FBGN0036984
drosophila_melanogaster	slif	FBGN0037203
drosophila_melanogaster	CG1607	FBGN0039844
caenorhabditis_elegans		WBGENE00000002
caenorhabditis_elegans		WBGENE00000003
caenorhabditis_elegans		WBGENE00000005
caenorhabditis_elegans	aat-9	WBGENE00000010
caenorhabditis_elegans		WBGENE00015197
caenorhabditis_elegans		WBGENE00016806
caenorhabditis_elegans		WBGENE00017747

Paralogs (12): SLC7A2 (ENSG00000003989), SLC7A14 (ENSG00000013293), SLC7A9 (ENSG00000021488), SLC7A8 (ENSG00000092068), SLC7A4 (ENSG00000099960), SLC7A6 (ENSG00000103064), SLC7A5 (ENSG00000103257), SLC7A10 (ENSG00000130876), SLC7A1 (ENSG00000139514), SLC7A11 (ENSG00000151012), SLC7A7 (ENSG00000155465), SLC7A3 (ENSG00000165349)

Protein

Protein identifiers

Solute carrier family 7 member 13 — Q8TCU3 (reviewed: Q8TCU3)

Alternative names: Sodium-independent aspartate/glutamate transporter 1, X-amino acid transporter 2

All UniProt accessions (1): Q8TCU3

UniProt curated annotations — full annotation on UniProt →

Function. Associates with SLC3A1/rBAT to form a functional heterodimeric complex that transports anionic and neutral amino acids across the apical plasma membrane of renal epithelium. Preferentially mediates exchange transport, but can also operate via facilitated diffusion. May act as a major transporter for L-cystine in late proximal tubules, ensuring its reabsorption from the luminal fluid in exchange for cytosolic L-glutamate or L-aspartate.

Subunit / interactions. Disulfide-linked heterodimer composed of the catalytic light subunit SLC7A13 and the heavy subunit SLC3A1.

Subcellular location. Apical cell membrane.

Tissue specificity. Expressed in the kidney.

Similarity. Belongs to the amino acid-polyamine-organocation (APC) superfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8TCU3-1	1	yes
Q8TCU3-2	2

RefSeq proteins (1): NP_620172* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002293	AA/rel_permease1	Family
IPR050598	AminoAcid_Transporter	Family

Pfam: PF13520

Catalyzed reactions (Rhea), 10 shown:

• L-cystine(out) + L-aspartate(in) = L-cystine(in) + L-aspartate(out) (RHEA:76299)
• L-cystine(out) = L-cystine(in) (RHEA:76303)
• L-aspartate(in) + L-glutamate(out) = L-aspartate(out) + L-glutamate(in) (RHEA:76307)
• L-aspartate(in) + L-glutamine(out) = L-aspartate(out) + L-glutamine(in) (RHEA:76311)
• L-aspartate(in) + L-methionine(out) = L-aspartate(out) + L-methionine(in) (RHEA:76315)
• L-leucine(out) + L-aspartate(in) = L-leucine(in) + L-aspartate(out) (RHEA:76319)
• L-valine(out) + L-aspartate(in) = L-valine(in) + L-aspartate(out) (RHEA:76323)
• L-aspartate(in) + L-phenylalanine(out) = L-aspartate(out) + L-phenylalanine(in) (RHEA:76327)
• L-tyrosine(out) + L-aspartate(in) = L-tyrosine(in) + L-aspartate(out) (RHEA:76331)
• L-tryptophan(out) + L-aspartate(in) = L-tryptophan(in) + L-aspartate(out) (RHEA:76335)

UniProt features (33 total): topological domain 13, transmembrane region 12, sequence variant 4, splice variant 3, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8WK6	ELECTRON MICROSCOPY	2.64

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TCU3-F1	88.05	0.53

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (7): amino acid transmembrane transport (GO:0003333), aspartate transmembrane transport (GO:0015810), L-cystine transport (GO:0015811), L-glutamate transmembrane transport (GO:0015813), amino acid transport (GO:0006865), transmembrane transport (GO:0055085), L-alpha-amino acid transmembrane transport (GO:1902475)

GO Molecular Function (4): L-amino acid transmembrane transporter activity (GO:0015179), antiporter activity (GO:0015297), protein heterodimerization activity (GO:0046982), transmembrane transporter activity (GO:0022857)

GO Cellular Component (3): apical plasma membrane (GO:0016324), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transmembrane transport	2
amino acid transmembrane transport	2
carboxylic acid transmembrane transport	2
L-amino acid transport	2
L-alpha-amino acid transmembrane transport	2
transport	2
amino acid transport	1
C4-dicarboxylate transport	1
acidic amino acid transport	1
nitrogen compound transport	1
sulfur amino acid transport	1
neutral amino acid transport	1
modified amino acid transport	1
L-glutamate import	1
cellular process	1
amino acid transmembrane transporter activity	1
carboxylic acid transmembrane transporter activity	1
secondary active transmembrane transporter activity	1
protein dimerization activity	1
transporter activity	1
apical part of cell	1
plasma membrane region	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC7A13	SLC3A1	Q07837	818
SLC7A13	ACSM3	Q53FZ2	538
SLC7A13	SLC7A3	Q8WY07	531
SLC7A13	CPNE3	O75131	514
SLC7A13	SLC7A9	P82251	481
SLC7A13	SLC22A6	Q4U2R8	481
SLC7A13	SLC3A2	P08195	471
SLC7A13	CNGB3	Q9NQW8	447
SLC7A13	SLC22A10	Q63ZE4	429
SLC7A13	SLC35G4	P0C7Q5	425
SLC7A13	SLC9C2	Q5TAH2	420
SLC7A13	SLC5A2	P31639	418
SLC7A13	SLC1A1	P43005	410
SLC7A13	LRRCC1	Q9C099	402
SLC7A13	SLC22A11	Q9NSA0	393

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SLC7A13	ATL2	psi-mi:“MI:0915”(physical association)	0.400
SLC7A13		psi-mi:“MI:0915”(physical association)	0.370

BioGRID (3): SLC7A13 (Two-hybrid), SLC7A13 (Synthetic Lethality), ATL2 (Affinity Capture-MS)

ESM2 similar proteins: A1L3M3, A7MBD8, B3TP03, B5D5N9, D3ZMM8, O08812, O61369, P11170, P13866, P18581, P30823, P30825, P52569, P70423, P83740, Q01650, Q09143, Q1EHB4, Q22397, Q28I80, Q3ZMH1, Q49B93, Q59I64, Q5BL81, Q5PR34, Q5RAE3, Q5RAG7, Q5RKI7, Q63016, Q6DCE8, Q7SYH5, Q7T384, Q7YQK4, Q8BGK6, Q8BYF6, Q8N695, Q8TCU3, Q8WY07, Q91WN3, Q92536

Diamond homologs: A1L3M3, D3ZMM8, O34739, P63115, P63116, P82251, P82252, Q01650, Q22397, Q28I80, Q59I64, Q5RAE3, Q5RAG7, Q5RKI7, Q63016, Q7YQK4, Q8BGK6, Q8MH63, Q8TCU3, Q91WN3, Q92536, Q9GIP4, Q9N1Q4, Q9N1R6, Q9NS82, Q9QXA6, Q9QXW9, Q9R0S5, Q9UHI5, Q9UM01, Q9UPY5, Q9WTR6, Q9WVR6, Q9Z127, Q9Z1K8, Q8VIE6, A0JNI9, A8I499, B0UYF2, B3TP03

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	109
Likely benign	34
Benign	20

Top pathogenic / likely-pathogenic (0)

SpliceAI

667 predictions. Top by Δscore:

Variant	Effect	Δscore
8:86223038:CAG:C	donor_gain	0.9700
8:86230327:T:A	donor_gain	0.9600
8:86223040:G:C	donor_gain	0.9500
8:86228188:TTGGC:T	donor_gain	0.9500
8:86217551:C:T	acceptor_gain	0.9100
8:86230070:T:C	donor_gain	0.9100
8:86223035:C:CT	donor_gain	0.8900
8:86223036:T:TT	donor_gain	0.8900
8:86217779:AAT:A	donor_gain	0.8700
8:86230331:G:A	donor_gain	0.8600
8:86229309:C:CT	acceptor_gain	0.8400
8:86223099:CTCCC:C	acceptor_gain	0.8200
8:86228187:TTTGG:T	donor_gain	0.8200
8:86223101:CCC:C	acceptor_gain	0.8000
8:86223102:CCC:C	acceptor_gain	0.8000
8:86230309:A:AC	donor_gain	0.8000
8:86223104:C:CC	acceptor_gain	0.7800
8:86225785:G:C	donor_gain	0.7800
8:86230069:A:AC	donor_gain	0.7800
8:86230069:AT:A	donor_gain	0.7800
8:86223102:CC:C	acceptor_gain	0.7700
8:86223103:CC:C	acceptor_gain	0.7700
8:86230069:ATCT:A	donor_gain	0.7600
8:86217551:C:CT	acceptor_gain	0.7500
8:86217550:CCG:C	acceptor_gain	0.7200
8:86222967:CAAA:C	donor_loss	0.7200
8:86222968:AAACC:A	donor_loss	0.7200
8:86222969:AACC:A	donor_loss	0.7200
8:86222970:A:G	donor_loss	0.7200
8:86222971:C:CA	donor_loss	0.7200

AlphaMissense

3009 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:86229996:A:C	F94L	0.969
8:86229996:A:T	F94L	0.969
8:86229998:A:G	F94L	0.969
8:86230182:A:C	F32L	0.961
8:86230182:A:T	F32L	0.961
8:86230184:A:G	F32L	0.961
8:86229789:G:C	S163R	0.958
8:86229789:G:T	S163R	0.958
8:86229791:T:G	S163R	0.958
8:86230121:A:G	W53R	0.958
8:86230121:A:T	W53R	0.958
8:86217746:G:C	S301R	0.955
8:86217746:G:T	S301R	0.955
8:86217748:T:G	S301R	0.955
8:86230065:A:C	S71R	0.951
8:86230065:A:T	S71R	0.951
8:86230067:T:G	S71R	0.951
8:86229762:G:C	S172R	0.950
8:86229762:G:T	S172R	0.950
8:86229764:T:G	S172R	0.950
8:86229630:A:C	F216L	0.948
8:86229630:A:T	F216L	0.948
8:86229632:A:G	F216L	0.948
8:86230119:C:A	W53C	0.945
8:86230119:C:G	W53C	0.945
8:86223018:G:C	N257K	0.943
8:86223018:G:T	N257K	0.943
8:86223068:A:G	C241R	0.942
8:86229842:C:G	G146R	0.942
8:86229842:C:T	G146R	0.942

dbSNP variants (sampled 300 via entrez): RS1000175342 (8:86218610 T>G), RS1000187946 (8:86223389 T>A), RS1000189834 (8:86222920 A>C,G,T), RS1000205591 (8:86228792 G>A), RS1000219270 (8:86218925 C>G), RS1000305934 (8:86223119 G>A), RS1000490658 (8:86227598 C>A,G), RS1000504322 (8:86220157 C>T), RS1001047989 (8:86221823 C>T), RS1001097010 (8:86227368 A>G), RS1001406215 (8:86231740 T>A,G), RS1001873302 (8:86231692 C>G), RS1002029931 (8:86226533 C>A), RS1002176988 (8:86221402 T>G), RS1002314780 (8:86220695 T>C)

Disease associations

OMIM: gene MIM:617256 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008059_44	Estimated glomerular filtration rate	7.000000e-14

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 — SLC7 family

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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