SLC17A2

gene
On this page

Also known as NPT3

Summary

SLC17A2 (solute carrier family 17 member 2, HGNC:10930) is a protein-coding gene on chromosome 6p22.2, encoding Sodium-dependent phosphate transport protein 3 (O00624). Acts as a membrane potential-dependent organic anion transporter, the transport requires a low concentration of chloride ions.

Predicted to enable urate transmembrane transporter activity. Predicted to be involved in phosphate-containing compound metabolic process and sodium ion transport. Predicted to be located in plasma membrane. Predicted to be active in apical plasma membrane.

Source: NCBI Gene 10246 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 66 total
  • Druggable target: yes
  • MANE Select transcript: NM_001286123

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10930
Approved symbolSLC17A2
Namesolute carrier family 17 member 2
Location6p22.2
Locus typegene with protein product
StatusApproved
AliasesNPT3
Ensembl geneENSG00000112337
Ensembl biotypeprotein_coding
OMIM611049
Entrez10246

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000265425, ENST00000360488, ENST00000377850, ENST00000882944, ENST00000882945, ENST00000882946, ENST00000882947, ENST00000882948, ENST00000882949, ENST00000882950, ENST00000882951, ENST00000882952

RefSeq mRNA: 3 — MANE Select: NM_001286123 NM_001286123, NM_001286125, NM_005835

CCDS: CCDS4567, CCDS69060

Canonical transcript exons

ENST00000377850 — 12 exons

ExonStartEnd
ENSE000007008632591573625915868
ENSE000007009402591668525916846
ENSE000007012102592100625921093
ENSE000007012972592117925921412
ENSE000009288882591696925917087
ENSE000009288892591848725918573
ENSE000010849852591549925915646
ENSE000011760692592369525923906
ENSE000012804642592576925925879
ENSE000022089092593027725930691
ENSE000035295392591275425913451
ENSE000036763202591458025914670

Expression profiles

Bgee: expression breadth broad, 22 present calls, max score 94.36.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1224 / max 72.4414, expressed in 11 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
722880.162710
722860.06448
722870.05809

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111494.36gold quality
liverUBERON:000210794.13gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.69gold quality
endometrium epitheliumUBERON:000481170.42gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099155.79gold quality
buccal mucosa cellCL:000233654.30silver quality
oocyteCL:000002353.14gold quality
endothelial cellCL:000011552.80gold quality
cranial nerve IIUBERON:000094150.79silver quality
frontal poleUBERON:000279550.41gold quality
middle frontal gyrusUBERON:000270250.30gold quality
paraflocculusUBERON:000535150.18gold quality
Brodmann (1909) area 10UBERON:001354150.18gold quality
quadriceps femorisUBERON:000137749.96gold quality
thymusUBERON:000237049.70gold quality
vastus lateralisUBERON:000137949.51gold quality
Brodmann (1909) area 46UBERON:000648349.30gold quality
blood vessel layerUBERON:000479749.29gold quality
cerebellar vermisUBERON:000472049.25gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
hair follicleUBERON:000207349.18gold quality
olfactory bulbUBERON:000226448.92gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
adult mammalian kidneyUBERON:000008248.87gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
oviduct epitheliumUBERON:000480448.82gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
nephron tubuleUBERON:000123148.37silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting SLC17A2, 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-5692A100.0074.406850
HSA-MIR-56899.9869.862084
HSA-MIR-23B-5P99.9866.07587
HSA-MIR-1213699.9872.815713
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-23A-5P99.9465.39468
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-430799.8270.453374
HSA-MIR-430699.7270.503630
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-6733-3P99.5467.801281
HSA-MIR-942-5P99.4168.401977
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-3191-5P99.2466.521722
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-807799.1766.67862
HSA-MIR-4758-3P99.1263.96869
HSA-MIR-4711-3P98.9766.871020
HSA-MIR-374A-3P98.8767.821531
HSA-MIR-3145-3P98.8569.072031
HSA-MIR-509498.6367.111062

Literature-anchored findings (GeneRIF, showing 2)

  • Association was detected in premenopausal women of European descent between percent iron saturation and variants in the chromosome 6 region containing both HFE and SLC17A2 genes. (PMID:26852655)
  • a novel gout-associated gene, SLC17A2, was identified (OR = 0.83, PFDR = 0.017).The common variant rs2071299 is an expression associated SNP and SLC17A2 mRNA expression is modified by different genotypes of this variant. the mRNA expression and protein levels of SLC17A2 between healthy individuals and hyperuricemia patients were significantly different (PMID:29497127)

Cross-species orthologs

56 orthologs

OrganismSymbolGene ID
danio_rerioslc17a5ENSDARG00000055190
danio_rerioslc37a4bENSDARG00000077180
danio_reriosi:ch1073-513e17.1ENSDARG00000086739
danio_rerioslc37a4blENSDARG00000093531
mus_musculusSlc17a2ENSMUSG00000036110
rattus_norvegicusSlc17a2ENSRNOG00000017180
drosophila_melanogasterdmGlutFBGN0010497
drosophila_melanogasterMFS14FBGN0010651
drosophila_melanogasterPicotFBGN0024315
drosophila_melanogasterCG9254FBGN0028513
drosophila_melanogasterCG6978FBGN0029727
drosophila_melanogasterVGlutFBGN0031424
drosophila_melanogasterCG7881FBGN0033048
drosophila_melanogasterMFS12FBGN0033234
drosophila_melanogasterMFS15FBGN0034392
drosophila_melanogasterCG15096FBGN0034394
drosophila_melanogasterMFS16FBGN0034611
drosophila_melanogasterCG12490FBGN0034782
drosophila_melanogasterCG9825FBGN0034783
drosophila_melanogasterCG9826FBGN0034784
drosophila_melanogasterCG3649FBGN0034785
drosophila_melanogasterCG2003FBGN0039886
drosophila_melanogasterCG30265FBGN0050265
drosophila_melanogasterMFS1FBGN0050272
caenorhabditis_elegansWBGENE00001135
caenorhabditis_elegansWBGENE00007669
caenorhabditis_elegansWBGENE00008000
caenorhabditis_elegansWBGENE00008677
caenorhabditis_elegansWBGENE00010755
caenorhabditis_elegansWBGENE00010931
caenorhabditis_elegansWBGENE00011185
caenorhabditis_elegansWBGENE00011349
caenorhabditis_elegansWBGENE00011556
caenorhabditis_elegansWBGENE00011688
caenorhabditis_elegansWBGENE00012443
caenorhabditis_elegansWBGENE00015271
caenorhabditis_elegansWBGENE00015272
caenorhabditis_elegansWBGENE00016003
caenorhabditis_elegansWBGENE00018429
caenorhabditis_elegansWBGENE00018918
caenorhabditis_elegansWBGENE00018920
caenorhabditis_elegansWBGENE00019187
caenorhabditis_elegansWBGENE00019655
caenorhabditis_elegansWBGENE00020583
caenorhabditis_elegansWBGENE00020584
caenorhabditis_elegansWBGENE00020697
caenorhabditis_elegansWBGENE00020698
caenorhabditis_elegansWBGENE00020699
caenorhabditis_elegansWBGENE00020700
caenorhabditis_elegansWBGENE00021157
caenorhabditis_elegansWBGENE00021158
caenorhabditis_elegansWBGENE00021219
caenorhabditis_elegansWBGENE00021220
caenorhabditis_elegansWBGENE00021223
caenorhabditis_elegansWBGENE00021226
caenorhabditis_elegansWBGENE00302978

Paralogs (12): SLC17A6 (ENSG00000091664), SLC17A9 (ENSG00000101194), SLC17A7 (ENSG00000104888), SLC17A5 (ENSG00000119899), SLC17A3 (ENSG00000124564), SLC17A1 (ENSG00000124568), SLC37A2 (ENSG00000134955), SLC37A4 (ENSG00000137700), SLC17A4 (ENSG00000146039), SLC37A3 (ENSG00000157800), SLC37A1 (ENSG00000160190), SLC17A8 (ENSG00000179520)

Protein

Protein identifiers

Sodium-dependent phosphate transport protein 3O00624 (reviewed: O00624)

Alternative names: Na(+)/PI cotransporter 3, Sodium/phosphate cotransporter 3, Solute carrier family 17 member 2

All UniProt accessions (1): O00624

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a membrane potential-dependent organic anion transporter, the transport requires a low concentration of chloride ions. Mediates chloride-dependent transport of urate. Can actively transport inorganic phosphate into cells via Na(+) cotransport.

Subcellular location. Apical cell membrane.

Tissue specificity. Expressed in the small intestine, kidney, spleen and testis. Not detected in fetal brain, bone marrow, and mammary gland.

Similarity. Belongs to the major facilitator superfamily. Sodium/anion cotransporter family.

Isoforms (3)

UniProt IDNamesCanonical?
O00624-11yes
O00624-22
O00624-33

RefSeq proteins (3): NP_001273052, NP_001273054, NP_005826 (=MANE)

Domains & families (InterPro)

IDNameType
IPR011701MFSFamily
IPR020846MFS_domDomain
IPR036259MFS_trans_sfHomologous_superfamily
IPR050382MFS_Na/Anion_cotransporterFamily

Pfam: PF07690

Catalyzed reactions (Rhea), 2 shown:

  • 3 Na(+)(out) + phosphate(out) = 3 Na(+)(in) + phosphate(in) (RHEA:71255)
  • urate(out) + n chloride(in) = urate(in) + n chloride(out) (RHEA:72319)

UniProt features (16 total): transmembrane region 9, glycosylation site 4, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O00624-F183.340.50

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 (4): 47, 56, 68, 69

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 97 (showing top): MODULE_162, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GOBP_MONOATOMIC_CATION_TRANSPORT, TCF4_Q5, MODULE_368, RGTTAMWNATT_HNF1_01, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GOBP_ORGANIC_ANION_TRANSPORT, GOCC_APICAL_PLASMA_MEMBRANE, GCM_TEC, HNF1_C, USF_02, LEF1_Q6, GCM_CDH5, GOBP_TRANSMEMBRANE_TRANSPORT

GO Biological Process (7): phosphate-containing compound metabolic process (GO:0006796), sodium ion transport (GO:0006814), monoatomic ion transport (GO:0006811), inorganic anion transport (GO:0015698), urate transport (GO:0015747), sodium ion transmembrane transport (GO:0035725), transmembrane transport (GO:0055085)

GO Molecular Function (4): sodium:phosphate symporter activity (GO:0005436), urate transmembrane transporter activity (GO:0015143), transmembrane transporter activity (GO:0022857), symporter activity (GO:0015293)

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport3
metabolic process1
metal ion transport1
nitrogen compound transport1
sodium ion transport1
monoatomic cation transmembrane transport1
cellular process1
phosphate transmembrane transporter activity1
solute:sodium symporter activity1
urate transport1
salt transmembrane transporter activity1
transporter activity1
transmembrane transport1
secondary active transmembrane transporter activity1
membrane1
cell periphery1
cellular anatomical structure1
apical part of cell1
plasma membrane region1

Protein interactions and networks

STRING

604 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC17A2SLC34A1Q06495742
SLC17A2SLC20A1Q8WUM9637
SLC17A2SLC20A2Q08357585
SLC17A2HFEQ30201544
SLC17A2SLC34A3Q8N130430
SLC17A2SLC18B1Q6NT16389
SLC17A2SLC2A9Q9NRM0335
SLC17A2ITPK1Q13572327
SLC17A2KRT38O76015320
SLC17A2LGI4Q8N135307
SLC17A2SASH1O94885296
SLC17A2PPCDCQ96CD2290
SLC17A2SLC22A11Q9NSA0288
SLC17A2SLC18A3Q16572282
SLC17A2SLC22A9Q8IVM8271

IntAct

2 interactions, top by confidence:

ABTypeScore
SLC17A2ABCD4psi-mi:“MI:0914”(association)0.350

BioGRID (94): LRRC8D (Affinity Capture-MS), KCNT2 (Affinity Capture-MS), UBB (Affinity Capture-MS), ABCD4 (Affinity Capture-MS), ANO10 (Affinity Capture-MS), ABCB9 (Affinity Capture-MS), TAP2 (Affinity Capture-MS), SARAF (Affinity Capture-MS), ABCC10 (Affinity Capture-MS), SLC16A13 (Affinity Capture-MS), ATP8A1 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), KIAA0195 (Affinity Capture-MS), KCNJ11 (Affinity Capture-MS), RHBDD3 (Affinity Capture-MS)

ESM2 similar proteins: A4FV52, A6QLI1, O00476, O00624, O61369, O62786, P34272, P34644, P38142, Q03567, Q05B21, Q10046, Q14916, Q1L8X9, Q21455, Q28722, Q2QWW7, Q32LF0, Q3TXX4, Q3UHK1, Q5NCM1, Q5SZA1, Q5W8I7, Q5W8I8, Q61983, Q62634, Q62795, Q66KG0, Q6INC8, Q7TSF2, Q7ZX53, Q8BFU8, Q8BLE7, Q8NDX2, Q921A2, Q95R48, Q961J5, Q96QE2, Q9C757, Q9FKV1

Diamond homologs: A4FV52, A6QLI1, O00476, O00624, O61369, O82390, P34644, Q03567, Q05B21, Q0IZQ3, Q10046, Q14916, Q1L8X9, Q28722, Q2QWW7, Q32LF0, Q3E9A0, Q3TXX4, Q53P54, Q5NCM1, Q5Q0U0, Q5SZA1, Q5W8I7, Q5W8I8, Q61983, Q62634, Q62795, Q652N5, Q66GI9, Q6INC8, Q7TSF2, Q8BFU8, Q8BLE7, Q8BN82, Q8GX78, Q8NDX2, Q9FKV1, Q9JI12, Q9MZD1, Q9NRA2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance58
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1328 predictions. Top by Δscore:

VariantEffectΔscore
6:25918482:CTCA:Cdonor_loss1.0000
6:25918483:TCA:Tdonor_loss1.0000
6:25918484:CACCA:Cdonor_loss1.0000
6:25918485:A:ACdonor_gain1.0000
6:25918486:C:CCdonor_gain1.0000
6:25918570:GACCC:Gacceptor_gain1.0000
6:25918571:ACCC:Aacceptor_loss1.0000
6:25918571:ACCCT:Aacceptor_gain1.0000
6:25918572:CC:Cacceptor_gain1.0000
6:25918573:CC:Cacceptor_gain1.0000
6:25918574:C:Aacceptor_loss1.0000
6:25918574:C:CCacceptor_gain1.0000
6:25918575:T:Aacceptor_loss1.0000
6:25921092:CC:Cacceptor_gain1.0000
6:25921093:CC:Cacceptor_gain1.0000
6:25923692:TAC:Tdonor_loss1.0000
6:25923693:A:ACdonor_gain1.0000
6:25923693:AC:Adonor_gain1.0000
6:25923693:ACCTT:Adonor_loss1.0000
6:25923694:C:CGdonor_gain1.0000
6:25923694:CC:Cdonor_gain1.0000
6:25923694:CCT:Cdonor_gain1.0000
6:25923694:CCTT:Cdonor_gain1.0000
6:25923694:CCTTT:Cdonor_gain1.0000
6:25923905:ACC:Aacceptor_loss1.0000
6:25923907:C:CCacceptor_gain1.0000
6:25913449:ATCCT:Aacceptor_loss0.9900
6:25913450:TCC:Tacceptor_loss0.9900
6:25913451:CCT:Cacceptor_loss0.9900
6:25913452:CTA:Cacceptor_loss0.9900

AlphaMissense

3107 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:25921054:A:GW172R0.996
6:25921054:A:TW172R0.996
6:25921052:C:AW172C0.994
6:25921052:C:GW172C0.994
6:25915532:C:TG393E0.991
6:25915533:C:AG393W0.990
6:25915736:C:GG355R0.987
6:25915736:C:TG355R0.987
6:25921063:A:GW169R0.987
6:25921063:A:TW169R0.987
6:25915519:G:CN397K0.986
6:25915519:G:TN397K0.986
6:25915756:C:GR348P0.986
6:25916763:G:CS284R0.984
6:25916763:G:TS284R0.984
6:25916765:T:GS284R0.984
6:25917058:A:GW227R0.984
6:25917058:A:TW227R0.984
6:25921395:C:AW86C0.984
6:25921395:C:GW86C0.984
6:25921397:A:GW86R0.984
6:25921397:A:TW86R0.984
6:25915533:C:GG393R0.983
6:25915533:C:TG393R0.983
6:25918497:G:CF213L0.983
6:25918497:G:TF213L0.983
6:25918499:A:GF213L0.983
6:25921031:G:CS179R0.983
6:25921031:G:TS179R0.983
6:25921033:T:GS179R0.983

dbSNP variants (sampled 300 via entrez): RS1000080460 (6:25913069 G>A,T), RS1000144806 (6:25930520 A>G), RS1000327892 (6:25925861 T>C), RS1000443996 (6:25926247 G>A), RS1000603671 (6:25932495 A>T), RS1000946174 (6:25922444 A>G), RS1000996792 (6:25922123 G>A,C), RS1001121629 (6:25928712 T>G), RS1001437905 (6:25927750 G>A), RS1001574218 (6:25920886 A>G), RS1001794292 (6:25931975 G>A), RS1001968200 (6:25916103 C>A,T), RS1002082816 (6:25916332 C>T), RS1002223713 (6:25932277 G>A), RS1002973031 (6:25917958 G>C)

Disease associations

OMIM: gene MIM:611049 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3769300 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — Type I sodium-phosphate co-transporters

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression4
Cyclosporineaffects expression, increases expression4
Aflatoxin B1affects expression, decreases expression, increases methylation4
Acetaminophendecreases expression2
Tetrachlorodibenzodioxindecreases expression2
OTX015decreases expression1
mivebresibdecreases expression1
uranyl acetateaffects expression1
bisphenol Aaffects cotreatment, increases methylation, decreases methylation1
kojic aciddecreases expression1
3,4,3’,4’-tetrachlorobiphenylaffects expression1
resorcinoldecreases expression1
CGP 52608affects binding, increases reaction1
(+)-JQ1 compounddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Estradioldecreases expression1
Hydrogen Peroxideaffects expression1
Plant Extractsaffects cotreatment, decreases expression1
Quercetindecreases expression1
Smokeincreases expression1
Uraniumaffects expression1
Urethanedecreases expression1
Valproic Aciddecreases expression, decreases methylation1
2,4-Dichlorophenoxyacetic Aciddecreases expression1
Zidovudinedecreases expression1
Copper Sulfateincreases expression1
tert-Butylhydroperoxideaffects expression1
Vitamin K 3affects expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3773489BindingInhibition of NaPiA3 (unknown origin)Optimization of a Dicarboxylic Series for in Vivo Inhibition of Citrate Transport by the Solute Carrier 13 (SLC13) Family. — J Med Chem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D4RYHuH7-SLC17A2-KO-c2Cancer cell lineMale
CVCL_D4RZHuH7-SLC17A2-KO-c3Cancer 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.