SLC39A3

gene
On this page

Also known as ZIP3

Summary

SLC39A3 (solute carrier family 39 member 3, HGNC:17128) is a protein-coding gene on chromosome 19p13.3, encoding Zinc transporter ZIP3 (Q9BRY0). Transporter for the divalent cation Zn(2+).

Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to act upstream of or within several processes, including T cell homeostasis; chordate embryonic development; and zinc ion transport. Predicted to be located in hippocampal mossy fiber to CA3 synapse. Predicted to be active in plasma membrane.

Source: NCBI Gene 29985 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 73 total
  • Druggable target: yes
  • MANE Select transcript: NM_144564

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17128
Approved symbolSLC39A3
Namesolute carrier family 39 member 3
Location19p13.3
Locus typegene with protein product
StatusApproved
AliasesZIP3
Ensembl geneENSG00000141873
Ensembl biotypeprotein_coding
OMIM612168
Entrez29985

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 13 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000269740, ENST00000455372, ENST00000545664, ENST00000589166, ENST00000589363, ENST00000590875, ENST00000909979, ENST00000909980, ENST00000909981, ENST00000909982, ENST00000909983, ENST00000959861, ENST00000959862, ENST00000959863

RefSeq mRNA: 2 — MANE Select: NM_144564 NM_144564, NM_213568

CCDS: CCDS12093, CCDS45909

Canonical transcript exons

ENST00000269740 — 3 exons

ExonStartEnd
ENSE0000115002327325242733485
ENSE0000225713527399452740017
ENSE0000360313227370482737379

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 96.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.4424 / max 275.0111, expressed in 1803 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
17820311.61721775
1782045.40661734
1782020.4186169

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453396.42gold quality
right testisUBERON:000453496.26gold quality
testisUBERON:000047393.37gold quality
stromal cell of endometriumCL:000225592.57gold quality
prefrontal cortexUBERON:000045191.28gold quality
apex of heartUBERON:000209890.02gold quality
islet of LangerhansUBERON:000000689.75gold quality
smooth muscle tissueUBERON:000113589.49gold quality
Brodmann (1909) area 9UBERON:001354089.15gold quality
monocyteCL:000057689.10gold quality
leukocyteCL:000073888.94gold quality
adenohypophysisUBERON:000219688.65gold quality
anterior cingulate cortexUBERON:000983588.65gold quality
right adrenal glandUBERON:000123388.64gold quality
right frontal lobeUBERON:000281088.61gold quality
left adrenal glandUBERON:000123488.59gold quality
left adrenal gland cortexUBERON:003582588.37gold quality
right adrenal gland cortexUBERON:003582788.25gold quality
pancreatic ductal cellCL:000207988.13silver quality
mucosa of transverse colonUBERON:000499187.82gold quality
hindlimb stylopod muscleUBERON:000425287.05gold quality
granulocyteCL:000009487.00gold quality
pituitary glandUBERON:000000786.96gold quality
right lobe of liverUBERON:000111486.79gold quality
adrenal glandUBERON:000236986.79gold quality
neocortexUBERON:000195086.77gold quality
adrenal cortexUBERON:000123586.73gold quality
dorsolateral prefrontal cortexUBERON:000983486.65gold quality
frontal cortexUBERON:000187086.64gold quality
gastrocnemiusUBERON:000138886.53gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-GEOD-130473yes531.63
E-MTAB-7407yes287.16
E-HCAD-6yes54.97
E-CURD-112yes35.84
E-MTAB-9067yes22.28
E-MTAB-10042yes14.32
E-ANND-3yes8.73
E-MTAB-6379no114.62
E-MTAB-9801no2.55

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): RREB1

miRNA regulators (miRDB)

8 targeting SLC39A3, 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-1213699.9872.815713
HSA-MIR-365899.9673.874379
HSA-MIR-808799.9069.551351
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-7161-5P99.6868.921592
HSA-MIR-548U99.6567.781463
HSA-MIR-4649-3P99.5666.901783
HSA-MIR-2467-5P97.3667.71991

Literature-anchored findings (GeneRIF, showing 6)

  • ZIP1, ZIP2 and ZIP3 may play cell-specific roles in zinc homeostasis rather than primary roles in the acquisition of dietary zinc (PMID:14525987)
  • ZiP2 and Zip3 are down regulated in malignant cells (PMID:17550612)
  • Gene expression regulation of ZIPs after zinc supplementation. (PMID:18279033)
  • The metallothionein gene had a higher expression in the blood, when compared to zinc transporters ZnT-1, Zip-1, and Zip-3 (p=0.01 in obese patients. (PMID:21053094)
  • Data show that the combination of concurrent zinc, ZIP3, and RREB-1 changes represent early events in the development of adenocarcinoma. (PMID:21613827)
  • These results support a concept that downregulation of RREB-1 causes downregulation of ZIP3, which results in decreased zinc in pancreatic premalignant and carcinoma cells (PMID:22427155)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusSlc39a3ENSMUSG00000046822
rattus_norvegicusSlc39a3ENSRNOG00000045524
drosophila_melanogasterZip42C.1FBGN0033096
caenorhabditis_elegansWBGENE00015940

Paralogs (2): SLC39A1 (ENSG00000143570), SLC39A2 (ENSG00000165794)

Protein

Protein identifiers

Zinc transporter ZIP3Q9BRY0 (reviewed: Q9BRY0)

Alternative names: Solute carrier family 39 member 3, Zrt- and Irt-like protein 3

All UniProt accessions (4): Q9BRY0, F5H385, K7EJZ1, K7ENJ1

UniProt curated annotations — full annotation on UniProt →

Function. Transporter for the divalent cation Zn(2+). Mediates the influx of Zn(2+) into cells from extracellular space. Controls Zn(2+) accumulation into dentate gyrus granule cells in the hippocampus. Mediates Zn(2+) reuptake from the secreted milk within the alveolar lumen.

Subcellular location. Cell membrane. Apical cell membrane.

Similarity. Belongs to the ZIP transporter (TC 2.A.5) family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BRY0-11yes
Q9BRY0-22

RefSeq proteins (2): NP_653165, NP_998733 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003689ZIPFamily

Pfam: PF02535

Catalyzed reactions (Rhea), 1 shown:

  • Zn(2+)(in) = Zn(2+)(out) (RHEA:29351)

UniProt features (24 total): topological domain 9, transmembrane region 8, modified residue 2, splice variant 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BRY0-F181.290.54

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 (2): 125, 129

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-442380Zinc influx into cells by the SLC39 gene family
R-HSA-382551Transport of small molecules
R-HSA-425366
R-HSA-425407SLC-mediated transmembrane transport
R-HSA-425410Metal ion SLC transporters
R-HSA-435354Zinc transporters

MSigDB gene sets: 204 (showing top): RNGTGGGC_UNKNOWN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_TRANSITION_METAL_ION_TRANSPORT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, CMYB_01, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_T_CELL_HOMEOSTASIS, GOBP_LYMPHOCYTE_HOMEOSTASIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_MONOATOMIC_CATION_TRANSPORT, MARTINEZ_RB1_TARGETS_UP

GO Biological Process (10): cell morphogenesis (GO:0000902), in utero embryonic development (GO:0001701), T cell homeostasis (GO:0043029), embryonic cranial skeleton morphogenesis (GO:0048701), limb development (GO:0060173), zinc ion transmembrane transport (GO:0071577), monoatomic ion transport (GO:0006811), zinc ion transport (GO:0006829), metal ion transport (GO:0030001), transmembrane transport (GO:0055085)

GO Molecular Function (3): zinc ion transmembrane transporter activity (GO:0005385), protein binding (GO:0005515), metal ion transmembrane transporter activity (GO:0046873)

GO Cellular Component (4): plasma membrane (GO:0005886), apical plasma membrane (GO:0016324), hippocampal mossy fiber to CA3 synapse (GO:0098686), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Zinc transporters1
Transport of small molecules1
SLC-mediated transmembrane transport1
Metal ion SLC transporters1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport2
anatomical structure morphogenesis1
chordate embryonic development1
lymphocyte homeostasis1
embryonic skeletal system morphogenesis1
cranial skeletal system development1
appendage development1
zinc ion transport1
monoatomic cation transmembrane transport1
transition metal ion transport1
monoatomic cation transport1
cellular process1
transition metal ion transmembrane transporter activity1
zinc ion transmembrane transport1
binding1
monoatomic cation transmembrane transporter activity1
metal ion transport1
membrane1
cell periphery1
apical part of cell1
plasma membrane region1
thorny excrescence1
neuron to neuron synapse1
hippocampal mossy fiber expansion1
cellular anatomical structure1

Protein interactions and networks

STRING

774 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC39A3SLC39A11Q8N1S5747
SLC39A3SLC39A4Q6P5W5716
SLC39A3SLC39A9Q9NUM3693
SLC39A3SLC39A7Q92504688
SLC39A3SLC39A5Q6ZMH5656
SLC39A3SLC39A12Q504Y0650
SLC39A3SLC39A13Q96H72649
SLC39A3SLC39A10Q9ULF5621
SLC39A3SLC39A6Q13433612
SLC39A3SLC39A8Q9C0K1611
SLC39A3SLC30A9Q6PML9607
SLC39A3SLC39A14Q15043573
SLC39A3SLC30A6Q6NXT4546
SLC39A3SLC30A1Q9Y6M5542
SLC39A3SLC30A7Q8NEW0520

IntAct

32 interactions, top by confidence:

ABTypeScore
TNFSF8TOR1Bpsi-mi:“MI:0914”(association)0.640
MANSC1KLRG2psi-mi:“MI:0914”(association)0.530
EVA1CUPK3BL1psi-mi:“MI:0914”(association)0.530
HLA-BLTN1psi-mi:“MI:0914”(association)0.530
TNFSF8LGALS8psi-mi:“MI:0914”(association)0.530
SEC22BNBASpsi-mi:“MI:0914”(association)0.350
TMPRSS11Bpsi-mi:“MI:0914”(association)0.350
TNFSF8NME4psi-mi:“MI:0914”(association)0.350
BSCL2B4GAT1psi-mi:“MI:0914”(association)0.350
PMELMAN1A2psi-mi:“MI:0914”(association)0.350
BSCL2TMEM223psi-mi:“MI:0914”(association)0.350
HIDE1TMEM120Bpsi-mi:“MI:0914”(association)0.350
SLC39A3PLEKHG3psi-mi:“MI:0914”(association)0.350
TMPRSS11BADAM10psi-mi:“MI:0914”(association)0.350
PCDHB3ESYT2psi-mi:“MI:0914”(association)0.350
CLEC2DESYT2psi-mi:“MI:0914”(association)0.350
HLA-CTMEM131Lpsi-mi:“MI:0914”(association)0.350
KLRD1TMEM131Lpsi-mi:“MI:0914”(association)0.350
GPR45VWA8psi-mi:“MI:0914”(association)0.350
OPALINFAM171A2psi-mi:“MI:0914”(association)0.350
CLEC4Apsi-mi:“MI:0914”(association)0.350
SPINT2psi-mi:“MI:0914”(association)0.350
LRRC25SCAMP3psi-mi:“MI:0914”(association)0.350
RAMP3MGST3psi-mi:“MI:0914”(association)0.350
HLA-BRAB29psi-mi:“MI:0914”(association)0.350
P2RY8BTAF1psi-mi:“MI:0914”(association)0.350
AIFM1HSPA12Apsi-mi:“MI:0914”(association)0.350
CA14ORC4psi-mi:“MI:0914”(association)0.350
TMEM25CRLF1psi-mi:“MI:0914”(association)0.350
SLC39A3AMY1Apsi-mi:“MI:0914”(association)0.350

BioGRID (128): SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-MS), SLC39A3 (Affinity Capture-RNA), TRAPPC13 (Negative Genetic), SLC39A3 (Negative Genetic), TRAPPC2L (Negative Genetic), VPS51 (Negative Genetic)

ESM2 similar proteins: A0A0G2KQY6, A0A3Q7ZPG5, A4IFD7, A4IIC5, A5PMX1, A8WMY3, A8X482, O04089, O45923, O64738, O82643, O94639, P40544, P59889, Q12067, Q12436, Q28J44, Q2YDD4, Q3KR82, Q52KD7, Q54LY6, Q5BJM8, Q5BL29, Q5E960, Q5MNV6, Q5RE57, Q5U1X7, Q5ZIU9, Q640S1, Q6NRI1, Q6NRM1, Q6NTL1, Q6P3N9, Q6P6S2, Q6QQT1, Q8BFU1, Q8BWY7, Q8LE59, Q8N1S5, Q8NEW0

Diamond homologs: A4IIC5, Q55EA1, Q5E960, Q5U1X7, Q99K24, Q9BRY0, G3X943, P59889, Q3SYU3, Q6QQT1, Q9NP94, Q9NY26, Q9QZ03, Q54MB9, C6KST8, A3BI11, O04089, O23039, O81123, O82643, Q0DHE3, Q38856, Q5Z653, Q6L8F7, Q6ZJ91, Q7XLD4, Q8LE59, Q8S3W4, Q8W246, Q9SLG3, Q852F6, Q94DG6, Q9LTH9, Q94EG9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance70
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

534 predictions. Top by Δscore:

VariantEffectΔscore
19:2733503:C:CTacceptor_gain1.0000
19:2733503:C:Tacceptor_gain1.0000
19:2733504:G:Tacceptor_gain1.0000
19:2739941:CTA:Cdonor_loss1.0000
19:2739942:TA:Tdonor_loss1.0000
19:2739943:A:Cdonor_loss1.0000
19:2739944:C:Adonor_loss1.0000
19:2733486:C:CCacceptor_gain0.9900
19:2733493:C:CTacceptor_gain0.9900
19:2733493:C:Tacceptor_gain0.9900
19:2733502:C:CTacceptor_gain0.9900
19:2739943:ACCT:Adonor_gain0.9900
19:2739943:ACCTC:Adonor_gain0.9900
19:2739944:CCT:Cdonor_gain0.9900
19:2739944:CCTC:Cdonor_gain0.9900
19:2739944:CCTCC:Cdonor_gain0.9900
19:2733484:AG:Aacceptor_gain0.9800
19:2733485:GC:Gacceptor_loss0.9800
19:2733486:CT:Cacceptor_loss0.9800
19:2733487:T:Cacceptor_loss0.9800
19:2733499:C:CTacceptor_gain0.9800
19:2737199:A:Tacceptor_gain0.9800
19:2737380:C:CCacceptor_gain0.9800
19:2739943:A:ACdonor_gain0.9800
19:2739944:C:CCdonor_gain0.9800
19:2733483:GAG:Gacceptor_gain0.9700
19:2733485:GCTG:Gacceptor_loss0.9700
19:2733494:G:Tacceptor_gain0.9700
19:2733481:TGGAG:Tacceptor_gain0.9600
19:2733490:A:Tacceptor_gain0.9600

AlphaMissense

2018 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:2733049:C:TG216D0.994
19:2733050:C:GG216R0.994
19:2732985:G:CS237R0.993
19:2732985:G:TS237R0.993
19:2732987:T:GS237R0.993
19:2733143:C:GG185R0.991
19:2732791:C:TG302D0.989
19:2732897:C:GG267R0.988
19:2733416:C:GG94R0.988
19:2733049:C:AG216V0.987
19:2737100:C:TG53E0.987
19:2732792:C:GG302R0.986
19:2732871:G:CF275L0.986
19:2732871:G:TF275L0.986
19:2732873:A:GF275L0.986
19:2732974:G:CP241R0.985
19:2733415:C:TG94D0.985
19:2732968:C:TG243D0.984
19:2737083:A:GC59R0.984
19:2737101:C:AG53W0.984
19:2737101:C:GG53R0.984
19:2737101:C:TG53R0.984
19:2732884:C:TG271D0.983
19:2733169:G:TA176E0.983
19:2733131:C:GG189R0.981
19:2732885:C:GG271R0.980
19:2732969:C:GG243R0.980
19:2733143:C:AG185C0.980
19:2737088:G:TA57D0.980
19:2737094:A:GF55S0.980

dbSNP variants (sampled 300 via entrez): RS1000349816 (19:2734961 G>A), RS1000602627 (19:2735692 G>A,T), RS1000777222 (19:2732114 C>G,T), RS1000806149 (19:2740411 T>A), RS1000852306 (19:2732105 A>G), RS1000906659 (19:2740753 C>G,T), RS1001387606 (19:2738296 T>C), RS1002127120 (19:2739665 G>A,T), RS1002280272 (19:2734577 C>T), RS1002341601 (19:2737326 G>A,C,T), RS1002423503 (19:2734780 C>A,T), RS1002736383 (19:2734039 T>C), RS1003262229 (19:2738495 G>A,C), RS1003393189 (19:2733154 G>A,C), RS1003692958 (19:2734015 C>T)

Disease associations

OMIM: gene MIM:612168 | 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): CHEMBL6066510 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — SLC39 family of metal ion transporters

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.50Kd31.67nMCHEMBL5653589
7.48ED5033.26nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149425: Binding affinity to human SLC39A3 incubated for 45 mins by Kinobead based pull down assaykd0.0317uM

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

ChemicalActions (top 5)PubMed papers
Zincincreases transport, affects expression, decreases expression4
Valproic Acidincreases expression, increases methylation3
sodium arseniteincreases expression2
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
14-deoxy-11,12-didehydroandrographolidedecreases expression1
Grape Seed Proanthocyanidinsdecreases expression1
bis-N,N-dimethylamino-2-(N-methylpyrrolyl)methyl cyclopentadienyl titanium (IV)decreases expression1
Sunitinibincreases expression1
Benzo(a)pyreneincreases methylation1
Caffeinedecreases phosphorylation1
Calcitrioldecreases expression1
Plant Extractsdecreases expression1
Smokedecreases expression1
Dronabinolincreases expression1
Tretinoindecreases expression1
Cadmium Chlorideincreases expression1
Okadaic Acidincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652467BindingBinding affinity to human SLC39A3 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D4NIHCT116-SLC39A3-KO-c2Cancer cell lineMale
CVCL_D4NJHCT116-SLC39A3-KO-c4Cancer cell lineMale
CVCL_TN56HAP1 SLC39A3 (-) 1Cancer cell lineMale
CVCL_TN57HAP1 SLC39A3 (-) 2Cancer 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.