SLC43A1

gene
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Also known as R00504PB39

Summary

SLC43A1 (solute carrier family 43 member 1, HGNC:9225) is a protein-coding gene on chromosome 11q12.1, encoding Large neutral amino acids transporter small subunit 3 (O75387). Uniport that mediates the transport of neutral amino acids such as L-leucine, L-isoleucine, L-valine, and L-phenylalanine.

SLC43A1 belongs to the system L family of plasma membrane carrier proteins that transports large neutral amino acids (Babu et al., 2003 [PubMed 12930836]).

Source: NCBI Gene 8501 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 107 total
  • Druggable target: yes
  • MANE Select transcript: NM_003627

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9225
Approved symbolSLC43A1
Namesolute carrier family 43 member 1
Location11q12.1
Locus typegene with protein product
StatusApproved
AliasesR00504, PB39
Ensembl geneENSG00000149150
Ensembl biotypeprotein_coding
OMIM603733
Entrez8501

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 33 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000278426, ENST00000524995, ENST00000525764, ENST00000528450, ENST00000529452, ENST00000530159, ENST00000533066, ENST00000533263, ENST00000533515, ENST00000534105, ENST00000901378, ENST00000901379, ENST00000901380, ENST00000901381, ENST00000901382, ENST00000901383, ENST00000901384, ENST00000901385, ENST00000901386, ENST00000901387, ENST00000901388, ENST00000901389, ENST00000930667, ENST00000930668, ENST00000930669, ENST00000930670, ENST00000930671, ENST00000930672, ENST00000930673, ENST00000930674, ENST00000930675, ENST00000930676, ENST00000930677, ENST00000967927, ENST00000967928, ENST00000967929, ENST00000967930, ENST00000967931

RefSeq mRNA: 2 — MANE Select: NM_003627 NM_001198810, NM_003627

CCDS: CCDS7958

Canonical transcript exons

ENST00000278426 — 15 exons

ExonStartEnd
ENSE000010272825751395857514124
ENSE000010272835748709557487218
ENSE000021463645748453457485242
ENSE000021670735751544457515702
ENSE000034900195749603157496164
ENSE000035002205749775357497845
ENSE000035541075750077957500855
ENSE000036055085749171657491862
ENSE000036139265750098857501043
ENSE000036560195748925157489392
ENSE000036617395749159157491626
ENSE000036627755748891657488989
ENSE000036854365749122457491362
ENSE000037890825750115257501329
ENSE000037894535749399357494171

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 98.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.2562 / max 289.7168, expressed in 1543 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1197928.74151476
1197890.9927391
1197870.8917363
1197880.3360154
1197910.175258
1197900.119146

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
body of pancreasUBERON:000115098.75gold quality
right lobe of liverUBERON:000111496.81gold quality
liverUBERON:000210792.98gold quality
pancreasUBERON:000126491.71gold quality
mucosa of stomachUBERON:000119991.29gold quality
body of stomachUBERON:000116190.66gold quality
right ovaryUBERON:000211889.84gold quality
left ovaryUBERON:000211988.86gold quality
gall bladderUBERON:000211088.79gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.16gold quality
stomachUBERON:000094587.96gold quality
hindlimb stylopod muscleUBERON:000425287.46gold quality
stromal cell of endometriumCL:000225586.79gold quality
esophagogastric junction muscularis propriaUBERON:003584186.56gold quality
muscle layer of sigmoid colonUBERON:003580586.08gold quality
body of uterusUBERON:000985386.00gold quality
lower esophagus muscularis layerUBERON:003583385.99gold quality
lower esophagusUBERON:001347385.94gold quality
apex of heartUBERON:000209885.91gold quality
gastrocnemiusUBERON:000138885.57gold quality
muscle of legUBERON:000138385.47gold quality
fundus of stomachUBERON:000116085.21gold quality
ovaryUBERON:000099284.67gold quality
endocervixUBERON:000045884.38gold quality
trabecular bone tissueUBERON:000248384.38gold quality
right lobe of thyroid glandUBERON:000111984.35gold quality
skin of legUBERON:000151184.15gold quality
right lungUBERON:000216784.12gold quality
omental fat padUBERON:001041484.07gold quality
peritoneumUBERON:000235884.02gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-81547yes21.36
E-ANND-3yes19.93

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

32 targeting SLC43A1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-62399.7668.161170
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-6832-3P99.5270.441726
HSA-MIR-806499.4566.92875
HSA-MIR-670-3P99.0368.882404
HSA-MIR-4650-3P99.0168.391062
HSA-MIR-320A-5P98.8866.751248
HSA-MIR-6895-3P98.7965.69996
HSA-MIR-6868-3P98.6369.642259
HSA-MIR-1212598.5967.541044
HSA-MIR-1237-3P98.5567.651423
HSA-MIR-124898.4767.541314
HSA-MIR-6516-5P98.4270.191551
HSA-MIR-6831-5P98.2667.20990
HSA-MIR-805797.6466.54897
HSA-MIR-6514-3P97.5266.50808
HSA-MIR-214-5P97.3466.50617
HSA-MIR-364996.8564.10340
HSA-MIR-6822-3P96.6066.06680
HSA-MIR-6888-5P95.8963.78831
HSA-MIR-6805-5P95.7964.86670
HSA-MIR-1237-5P95.3862.21451

Literature-anchored findings (GeneRIF, showing 1)

  • LAT3 is a transporter subserving system L2 and should denote a new family of organic solute transporters (PMID:12930836)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioslc43a1aENSDARG00000037393
danio_rerioslc43a1bENSDARG00000037748
mus_musculusSlc43a1ENSMUSG00000027075
rattus_norvegicusSlc43a1ENSRNOG00000008243

Paralogs (1): SLC43A2 (ENSG00000167703)

Protein

Protein identifiers

Large neutral amino acids transporter small subunit 3O75387 (reviewed: O75387)

Alternative names: L-type amino acid transporter 3, Prostate cancer overexpressed gene 1 protein, Solute carrier family 43 member 1

All UniProt accessions (6): O75387, E9PJ68, E9PJT8, E9PR87, E9PRF0, H0YEH0

UniProt curated annotations — full annotation on UniProt →

Function. Uniport that mediates the transport of neutral amino acids such as L-leucine, L-isoleucine, L-valine, and L-phenylalanine. The transport activity is sodium ions-independent, electroneutral and mediated by a facilitated diffusion.

Subcellular location. Cell membrane. Apical cell membrane. Endoplasmic reticulum membrane.

Tissue specificity. Ubiquitously expressed in fetus and adult. Highest expression in adult pancreas, liver, skeletal muscle. In fetus, highest expression in liver and lower levels in kidney, and lung. Exclusively expressed in the glomeruli along the glomerular capillary walls.

Similarity. Belongs to the SLC43A transporter (TC 2.A.1.44) family.

Isoforms (2)

UniProt IDNamesCanonical?
O75387-11, 2.3kbyes
O75387-22, 5kb

RefSeq proteins (2): NP_001185739, NP_003618* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011701MFSFamily
IPR036259MFS_trans_sfHomologous_superfamily

Pfam: PF07690

Catalyzed reactions (Rhea), 6 shown:

  • L-phenylalanine(in) = L-phenylalanine(out) (RHEA:27950)
  • L-valine(in) = L-valine(out) (RHEA:29703)
  • L-methionine(in) = L-methionine(out) (RHEA:70939)
  • L-isoleucine(in) = L-isoleucine(out) (RHEA:70943)
  • L-leucine(in) = L-leucine(out) (RHEA:73011)
  • D-leucine(in) = D-leucine(out) (RHEA:73015)

UniProt features (22 total): transmembrane region 12, modified residue 3, glycosylation site 3, sequence variant 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75387-F179.710.53

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 (3): 237, 262, 267

Glycosylation sites (3): 57, 212, 229

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

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

MSigDB gene sets: 214 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOBP_NEGATIVE_REGULATION_OF_TRANSMEMBRANE_TRANSPORT, GOBP_REGULATION_OF_ORGANIC_ACID_TRANSPORT, MODULE_255, XU_GH1_AUTOCRINE_TARGETS_UP, MODULE_45, MODULE_317, MODULE_16, GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, GOBP_ORGANIC_ACID_TRANSPORT, KANG_FLUOROURACIL_RESISTANCE_DN, NFKB_C, GOBP_NEGATIVE_REGULATION_OF_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_AMINE_TRANSPORT, MYCMAX_01

GO Biological Process (9): amino acid transport (GO:0006865), neutral amino acid transport (GO:0015804), isoleucine transport (GO:0015818), L-leucine transport (GO:0015820), negative regulation of amino acid transport (GO:0051956), L-valine transmembrane transport (GO:1903785), negative regulation of L-leucine import across plasma membrane (GO:1905533), L-amino acid transport (GO:0015807), transmembrane transport (GO:0055085)

GO Molecular Function (8): L-valine transmembrane transporter activity (GO:0005304), amino acid transmembrane transporter activity (GO:0015171), neutral L-amino acid transmembrane transporter activity (GO:0015175), L-amino acid transmembrane transporter activity (GO:0015179), L-isoleucine transmembrane transporter activity (GO:0015188), L-leucine transmembrane transporter activity (GO:0015190), protein binding (GO:0005515), transmembrane transporter activity (GO:0022857)

GO Cellular Component (6): endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), apical plasma membrane (GO:0016324), podocyte foot (GO:0098846), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
SLC-mediated transport of amino acids1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
amino acid transport3
neutral amino acid transport3
neutral L-amino acid transmembrane transporter activity3
L-amino acid transmembrane transporter activity3
branched-chain amino acid transmembrane transporter activity3
transport2
branched-chain amino acid transport2
L-alpha-amino acid transmembrane transport2
amino acid transmembrane transporter activity2
L-amino acid transport1
negative regulation of amine transport1
regulation of amino acid transport1
valine transport1
negative regulation of organic acid transport1
negative regulation of transmembrane transport1
negative regulation of amino acid transport1
L-leucine import across plasma membrane1
regulation of L-leucine import across plasma membrane1
carboxylic acid transport1
nitrogen compound transport1
cellular process1
L-valine transmembrane transport1
amino acid transmembrane transport1
transmembrane transporter activity1
carboxylic acid transmembrane transporter activity1
binding1
transporter activity1
transmembrane transport1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
apical part of cell1
plasma membrane region1
plasma membrane bounded cell projection1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

710 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC43A1SLC7A8Q9UHI5943
SLC43A1SLC3A2P08195937
SLC43A1SLC7A5Q01650913
SLC43A1SLC7A6Q92536647
SLC43A1SLC1A5Q15758548
SLC43A1SLC38A2Q96QD8543
SLC43A1SLC38A1Q9H2H9506
SLC43A1SLC16A10Q8TF71490
SLC43A1SLC6A15Q9H2J7489
SLC43A1SLC7A9P82251455
SLC43A1SLC7A7Q9UM01455
SLC43A1SLC2A4RGQ9NR83418
SLC43A1SLC7A2P52569416
SLC43A1SLC1A4P43007412
SLC43A1SLC36A1Q7Z2H8410

IntAct

14 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
SLC43A1BACH2psi-mi:“MI:0915”(physical association)0.560
YIPF3TMEM120Bpsi-mi:“MI:0914”(association)0.530
CD81STX3psi-mi:“MI:0914”(association)0.350
ZACNFAM234Bpsi-mi:“MI:0914”(association)0.350
SLC22A4RTL8Cpsi-mi:“MI:0914”(association)0.350
KCNE3PIK3R2psi-mi:“MI:0914”(association)0.350
SLC17A2ABCD4psi-mi:“MI:0914”(association)0.350
OR10H2ABCD4psi-mi:“MI:0914”(association)0.350
SLC43A1PLPP1psi-mi:“MI:0914”(association)0.350
KCNK3ESYT2psi-mi:“MI:2364”(proximity)0.270
SLC43A1BACH2psi-mi:“MI:0915”(physical association)0.000

BioGRID (53): SLC43A1 (Affinity Capture-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Proximity Label-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Two-hybrid), SLC43A1 (Proximity Label-MS), SLC43A1 (Proximity Label-MS), SLC43A1 (Proximity Label-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Affinity Capture-MS), SLC43A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A125YQS6, A0A125YY03, A0A7J6K338, A1Z7R6, A4IHK6, A5K9W3, G4SDH4, J9UD11, O43306, O60266, O75387, O76269, O76343, P14773, P30804, P48768, Q01341, Q03343, Q04400, Q0C8L9, Q0VCM6, Q41706, Q4D3E8, Q4X251, Q57VW6, Q5B0V6, Q5BKX6, Q5RF58, Q5ZMT9, Q6C520, Q6CGU8, Q7Z8U2, Q8BIV7, Q8BSM7, Q8CGA3, Q8K4S3, Q8K596, Q8N370, Q93380, Q93Z75

Diamond homologs: A4IHK6, O75387, Q0VCM6, Q5RF58, Q8BSM7, Q8CGA3, Q8N370, Q8NBI5, Q1JPD8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance79
Likely benign7
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2833 predictions. Top by Δscore:

VariantEffectΔscore
11:57487107:T:Adonor_gain1.0000
11:57488915:CA:Cdonor_gain1.0000
11:57491358:CCCAA:Cacceptor_gain1.0000
11:57491359:CCAAC:Cacceptor_gain1.0000
11:57491712:TCA:Tdonor_loss1.0000
11:57491713:CAC:Cdonor_loss1.0000
11:57491714:A:ACdonor_gain1.0000
11:57491714:ACCAT:Adonor_loss1.0000
11:57491715:C:Adonor_loss1.0000
11:57491715:C:CCdonor_gain1.0000
11:57491715:CCATG:Cdonor_gain1.0000
11:57491859:GACC:Gacceptor_gain1.0000
11:57491861:CC:Cacceptor_gain1.0000
11:57491862:CC:Cacceptor_gain1.0000
11:57491863:C:CCacceptor_gain1.0000
11:57491863:C:Tacceptor_gain1.0000
11:57493987:ACTC:Adonor_loss1.0000
11:57493988:CTCAC:Cdonor_loss1.0000
11:57493989:T:TCdonor_loss1.0000
11:57493990:C:CGdonor_loss1.0000
11:57493991:A:ACdonor_gain1.0000
11:57493991:AC:Adonor_loss1.0000
11:57493991:ACT:Adonor_gain1.0000
11:57493991:ACTCT:Adonor_gain1.0000
11:57493992:C:CAdonor_gain1.0000
11:57493992:CT:Cdonor_gain1.0000
11:57493992:CTC:Cdonor_gain1.0000
11:57493992:CTCT:Cdonor_gain1.0000
11:57493992:CTCTC:Cdonor_gain1.0000
11:57494025:T:TAdonor_gain1.0000

AlphaMissense

3634 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:57487167:A:CS487R0.996
11:57487167:A:TS487R0.996
11:57487169:T:GS487R0.996
11:57491813:G:CS307R0.995
11:57491813:G:TS307R0.995
11:57491815:T:GS307R0.995
11:57497793:C:TG173D0.995
11:57497794:C:GG173R0.994
11:57501043:A:CS111R0.993
11:57501043:A:TS111R0.993
11:57501153:T:GS111R0.993
11:57501220:G:CS88R0.992
11:57501220:G:TS88R0.992
11:57501222:T:GS88R0.992
11:57514015:A:GW33R0.992
11:57514015:A:TW33R0.992
11:57501236:C:TG83D0.990
11:57501244:G:CF80L0.990
11:57501244:G:TF80L0.990
11:57501246:A:GF80L0.990
11:57487215:G:CF471L0.989
11:57487215:G:TF471L0.989
11:57487217:A:GF471L0.989
11:57488958:C:GR456P0.989
11:57491321:A:GC366R0.989
11:57514013:C:AW33C0.989
11:57514013:C:GW33C0.989
11:57514018:C:GG32R0.989
11:57487192:A:GL479P0.988
11:57491296:C:TG374D0.988

dbSNP variants (sampled 300 via entrez): RS1000013983 (11:57496429 T>A), RS1000068436 (11:57499842 C>A), RS1000200734 (11:57489920 G>A), RS1000332266 (11:57497233 G>A), RS1000343231 (11:57504057 C>T), RS1000473018 (11:57510308 A>C), RS1000493497 (11:57490263 C>T), RS1000534054 (11:57492060 C>T), RS1000672534 (11:57498443 C>A,T), RS1000780207 (11:57507681 C>G), RS1000911718 (11:57515910 T>G), RS1000969891 (11:57516543 T>A,C), RS1001025330 (11:57494897 G>C), RS1001030607 (11:57485344 A>T), RS1001046251 (11:57485035 C>G,T)

Disease associations

OMIM: gene MIM:603733 | 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):

StudyTraitp-value
GCST004748_22Lung cancer5.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4148 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — SLC43 family of large neutral amino acid transporters

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression4
bisphenol Aincreases expression2
sodium arsenitedecreases expression, increases expression2
entinostatincreases expression, affects cotreatment2
Panobinostataffects cotreatment, increases expression2
Benzo(a)pyrenedecreases expression2
Tetrachlorodibenzodioxindecreases expression2
Tunicamycinincreases expression2
Cyclosporineaffects expression, increases expression2
Aflatoxin B1decreases expression, affects expression2
allyl 2,4,6-tribromophenyl etherincreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
trichostatin Aincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
tri-o-cresyl phosphateincreases expression1
ochratoxin Adecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
perfluoro-n-nonanoic acidincreases expression1
motexafin gadoliniumincreases expression, affects cotreatment1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
belinostatincreases expression1
abrinedecreases expression1
quinocetonedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
dorsomorphinaffects cotreatment, increases expression1
2,3-dibromopropyl-2,4,6-tribromophenyl etherincreases expression1
(+)-JQ1 compounddecreases expression1
Sunitinibincreases expression1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3854167BindingInhibition of LAT3 in human LNCAP cells assessed as inhibition of [3H]L-leucine uptake at 10 uM after 15 mins by liquid scintillation counting method relative to controlBioactive Dihydro-β-agarofuran Sesquiterpenoids from the Australian Rainforest Plant Maytenus bilocularis. — J Nat Prod

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D4TRHuH7-SLC43A1-KO-c1Cancer cell lineMale
CVCL_D4TSHuH7-SLC43A1-KO-c12Cancer cell lineMale
CVCL_TN70HAP1 SLC43A1 (-)Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.