SLC31A2

gene
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Also known as hCTR2CTR2

Summary

SLC31A2 (solute carrier family 31 member 2, HGNC:11017) is a protein-coding gene on chromosome 9q32, encoding Protein SLC31A2 (O15432). Does not function as a copper(1+) importer in vivo.

Enables copper ion transmembrane transporter activity. Involved in copper ion import. Located in late endosome membrane; lysosomal membrane; and plasma membrane.

Source: NCBI Gene 1318 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 9 total
  • Druggable target: yes
  • MANE Select transcript: NM_001860

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11017
Approved symbolSLC31A2
Namesolute carrier family 31 member 2
Location9q32
Locus typegene with protein product
StatusApproved
AliaseshCTR2, CTR2
Ensembl geneENSG00000136867
Ensembl biotypeprotein_coding
OMIM603088
Entrez1318

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000259392, ENST00000374220, ENST00000490809

RefSeq mRNA: 1 — MANE Select: NM_001860 NM_001860

CCDS: CCDS6788

Canonical transcript exons

ENST00000259392 — 4 exons

ExonStartEnd
ENSE00001666797113157727113157793
ENSE00001856316113151007113151080
ENSE00003474818113162749113164140
ENSE00003613561113161509113161698

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 98.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.2764 / max 546.2144, expressed in 1714 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
9806814.39901411
980675.02041534
980690.8571376

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183198.85gold quality
inferior vagus X ganglionUBERON:000536398.35gold quality
C1 segment of cervical spinal cordUBERON:000646997.51gold quality
spinal cordUBERON:000224097.11gold quality
corpus callosumUBERON:000233696.10gold quality
ponsUBERON:000098895.95gold quality
subthalamic nucleusUBERON:000190695.48gold quality
medulla oblongataUBERON:000189695.16gold quality
monocyteCL:000057694.97gold quality
mononuclear cellCL:000084294.84gold quality
superior vestibular nucleusUBERON:000722794.82gold quality
deciduaUBERON:000245094.74gold quality
leukocyteCL:000073894.65gold quality
ventral tegmental areaUBERON:000269194.58gold quality
seminal vesicleUBERON:000099894.48gold quality
saliva-secreting glandUBERON:000104494.45gold quality
bloodUBERON:000017893.69gold quality
inferior olivary complexUBERON:000212793.26gold quality
minor salivary glandUBERON:000183093.19gold quality
dorsal plus ventral thalamusUBERON:000189793.05gold quality
midbrainUBERON:000189192.97gold quality
skin of legUBERON:000151192.93gold quality
upper leg skinUBERON:000426292.91gold quality
substantia nigra pars reticulataUBERON:000196692.83gold quality
substantia nigraUBERON:000203892.74gold quality
skin of abdomenUBERON:000141692.68gold quality
zone of skinUBERON:000001492.56gold quality
mouth mucosaUBERON:000372992.23gold quality
upper arm skinUBERON:000426391.93gold quality
hair follicleUBERON:000207391.42gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-13yes24.96
E-ANND-3yes15.78
E-MTAB-5061no3.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

104 targeting SLC31A2, 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-9-5P100.0072.282361
HSA-MIR-340-5P100.0072.504437
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-450099.9972.722367
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548AW99.9972.573559
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-806899.9873.852376
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-391099.9571.132227
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-17-5P99.8973.832665

Literature-anchored findings (GeneRIF, showing 10)

  • hCTR2 is as an oligomeric membrane protein localized in lysosomes, which stimulates copper delivery to the cytosol of human cells at relatively high copper concentrations. (PMID:17617060)
  • Ctr2 promotes copper uptake at the plasma membrane and plays a role in regulating copper levels in COS-7 cells (PMID:17944601)
  • CTR2 functions by limiting drug accumulation, and its expression correlates with the sensitivity of human ovarian carcinoma cell lines to cisplatin. (PMID:19509135)
  • Increased CTR2 expression is associated with platinum resistance in epithelial ovarian cancer. (PMID:23564780)
  • Over-expression of CTR2 increased exchangeable Cu(+) by 150% and rendered the human epithelial 2008 cancer cell model 2.5-fold resistant to cisplatin. (PMID:24522273)
  • Data suggest that SLC31A1 and SLC31A2, despite being structurally closely related and sharing important amino acid motifs, play different roles in copper homeostasis and in platinum-based chemotherapy of neoplasms. [REVIEW] (PMID:24703712)
  • Studied the interaction of CTR1 and CTR2 in fully malignant HEK293T and OVCAR8 human ovarian cancer cells using a CRISPR-Cas9 knock out system. (PMID:26205368)
  • Decreased expression of CTR2 is associated with clear cell renal cell carcinoma. (PMID:26411550)
  • Gene duplication and neo-functionalization in the evolutionary and functional divergence of the metazoan copper transporters Ctr1 and Ctr2 (PMID:28507097)
  • 11 single-nucleotide polymorphisms (SNPs) in CTR1, CTR2, ATP7A, and ATP7B were genotyped in these patients. (PMID:28737129)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_rerioslc31a2ENSDARG00000076092
mus_musculusSlc31a2ENSMUSG00000066152
rattus_norvegicusSlc31a2ENSRNOG00000013631
drosophila_melanogasterCtr1CFBGN0062411
drosophila_melanogasterCtr1BFBGN0062412
drosophila_melanogasterCtr1AFBGN0062413
caenorhabditis_elegansWBGENE00010274
caenorhabditis_elegansF27C1.2WBGENE00017852
caenorhabditis_elegansK12C11.3WBGENE00019674
caenorhabditis_elegansWBGENE00044107
caenorhabditis_elegansK12C11.6WBGENE00045052

Paralogs (1): SLC31A1 (ENSG00000136868)

Protein

Protein identifiers

Protein SLC31A2O15432 (reviewed: O15432)

Alternative names: Copper transporter 2, Solute carrier family 31 member 2

All UniProt accessions (3): O15432, F2Z3D2, Q53X94

UniProt curated annotations — full annotation on UniProt →

Function. Does not function as a copper(1+) importer in vivo. However, in vitro functions as a low-affinity copper(1+) importer. Regulator of SLC31A1 which facilitates the cleavage of the SLC31A1 ecto-domain or which stabilizes the truncated form of SLC31A1 (Truncated CTR1 form), thereby drives the SLC31A1 truncated form-dependent endosomal copper export and modulates the copper and cisplatin accumulation via SLC31A1.

Subunit / interactions. Oligomer. Interacts with SLC31A1; this interaction stabilizes SLC31A2 and protects it from ubiquitination and the subsequent degradation.

Subcellular location. Membrane. Cytoplasmic vesicle membrane. Late endosome membrane. Lysosome membrane.

Tissue specificity. Ubiquitous with high expression in placenta and heart.

Post-translational modifications. Ubiquitinated; ubiquitination and the subsequent proteasomal degradation are prevent by SLC31A1 that stabilizes it.

Domain organisation. The N-terminal domain may be involved in Cu(2+) acquisition from potential degradation products of proteins in the lysosome.

Similarity. Belongs to the copper transporter (Ctr) (TC 1.A.56) family. SLC31A subfamily.

RefSeq proteins (1): NP_001851* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007274Cop_transporterFamily

Pfam: PF04145

UniProt features (11 total): topological domain 4, transmembrane region 3, mutagenesis site 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15432-F171.980.15

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 (1): 77

Mutagenesis-validated functional residues (2):

PositionPhenotype
4decreases almost 7 times the cu(2+) affinity at ph 7.4 compared to wild-type. decreases almost 10 times the cu(2+) affin
1–3slightly decreases cu(2+) affinity at ph 7.4. decreases about 3 times the cu(2+) affinity at ph 7.4 compared to wild-typ

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 292 (showing top): RRAGTTGT_UNKNOWN, GOCC_VACUOLAR_MEMBRANE, GOBP_TRANSITION_METAL_ION_TRANSPORT, MODULE_45, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, KYNG_DNA_DAMAGE_DN, RACCACAR_AML_Q6, TGACCTY_ERR1_Q2, RIZKI_TUMOR_INVASIVENESS_3D_DN, USF_C, GOBP_COPPER_ION_TRANSPORT, GOBP_MONOATOMIC_CATION_TRANSPORT, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN

GO Biological Process (6): copper ion transport (GO:0006825), intracellular copper ion homeostasis (GO:0006878), copper ion import (GO:0015677), regulation of copper ion transmembrane transport (GO:1902311), monoatomic ion transport (GO:0006811), copper ion transmembrane transport (GO:0035434)

GO Molecular Function (2): copper ion transmembrane transporter activity (GO:0005375), protein binding (GO:0005515)

GO Cellular Component (10): lysosomal membrane (GO:0005765), plasma membrane (GO:0005886), late endosome membrane (GO:0031902), recycling endosome (GO:0055037), lysosome (GO:0005764), endosome (GO:0005768), late endosome (GO:0005770), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
copper ion transport2
copper ion transmembrane transport2
endosome2
cytoplasmic vesicle2
transition metal ion transport1
intracellular monoatomic cation homeostasis1
copper ion homeostasis1
regulation of metal ion transport1
regulation of monoatomic cation transmembrane transport1
transport1
monoatomic cation transmembrane transport1
transition metal ion transmembrane transporter activity1
binding1
lysosome1
lytic vacuole membrane1
membrane1
cell periphery1
late endosome1
endosome membrane1
lytic vacuole1
endomembrane system1
cellular anatomical structure1
vesicle membrane1
cytoplasm1
intracellular vesicle1

Protein interactions and networks

STRING

1352 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC31A2ATP7BP35670926
SLC31A2ATP7AQ04656905
SLC31A2ATOX1O00244810
SLC31A2COX17Q14061756
SLC31A2CCSO14618714
SLC31A2COX11Q9Y6N1582
SLC31A2SCO1O75880507
SLC31A2SOD1P00441504
SLC31A2SLC11A1P49279500
SLC31A2IER3IP1Q9Y5U9500
SLC31A2SLC11A2P49281498
SLC31A2ERG28Q9UKR5492
SLC31A2H3BSS0H3BSS0481
SLC31A2CPP00450478
SLC31A2ZFP37Q9Y6Q3478

IntAct

12 interactions, top by confidence:

ABTypeScore
SLC31A2BNIP3psi-mi:“MI:0915”(physical association)0.560
GLP1RSLC31A2psi-mi:“MI:0915”(physical association)0.510
SLC31A2GLP1Rpsi-mi:“MI:0915”(physical association)0.510
SLC31A2F2RL1psi-mi:“MI:0915”(physical association)0.370
SLC31A2GPR35psi-mi:“MI:0915”(physical association)0.370
SLC31A2HTR2Bpsi-mi:“MI:0915”(physical association)0.370
SLC31A2OPRL1psi-mi:“MI:0915”(physical association)0.370
SLC31A2PLSCR1psi-mi:“MI:0914”(association)0.350
SLC31A2SLC31A1psi-mi:“MI:0914”(association)0.350
BNIP3SLC31A2psi-mi:“MI:0915”(physical association)0.000

BioGRID (38): RAMP1 (Reconstituted Complex), RAMP2 (Reconstituted Complex), RAMP3 (Reconstituted Complex), SLC31A2 (Synthetic Lethality), BNIP3 (Two-hybrid), SLC31A2 (Two-hybrid), SLC31A2 (Two-hybrid), SLC31A2 (Two-hybrid), SLC31A2 (Two-hybrid), SLC6A8 (Affinity Capture-MS), PLSCR1 (Affinity Capture-MS), SLC9A6 (Affinity Capture-MS), AGPAT3 (Affinity Capture-MS), SLC20A2 (Affinity Capture-MS), CAV1 (Affinity Capture-MS)

ESM2 similar proteins: A0A142I735, A5DRE8, A8N1Z1, A9UY97, B0CQN9, B5XB24, F4JRE0, G4YM00, G4Z2L3, H1AE12, J9VLN4, J9VWN8, J9VX37, O13356, O15432, O94722, P0CS25, P30599, P38865, Q06686, Q12116, Q27783, Q2H0X9, Q39065, Q3T0K8, Q4W9R7, Q4WCY0, Q4WHY8, Q4WX45, Q4WYN3, Q52CS0, Q54LC9, Q59NP1, Q5J8M3, Q5RC35, Q61086, Q6GR43, Q6P011, Q6P6G5, Q6PBF7

Diamond homologs: O15431, O15432, P38865, Q4WHY8, Q4WX45, Q5RAS6, Q8K211, Q8WNR0, Q9CPU9, Q9JK41, Q9STG2, Q7XTF8, Q10KT6, Q39065, Q5ZD08, Q60EN8, Q69P80, Q8GWP3, Q8SAA5, Q93VM8, Q94EE4, Q9FGU8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance5
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

824 predictions. Top by Δscore:

VariantEffectΔscore
9:113151077:GGCG:Gdonor_gain1.0000
9:113151078:GCG:Gdonor_gain1.0000
9:113151078:GCGG:Gdonor_gain1.0000
9:113151080:GGTA:Gdonor_loss1.0000
9:113151081:G:GGdonor_gain1.0000
9:113151081:GTA:Gdonor_loss1.0000
9:113151082:T:Gdonor_loss1.0000
9:113151076:TGGCG:Tdonor_gain0.9900
9:113151077:GGCGG:Gdonor_gain0.9900
9:113151079:CG:Cdonor_gain0.9900
9:113151080:GG:Gdonor_gain0.9900
9:113161503:TGACA:Tacceptor_loss0.9900
9:113161504:GACAG:Gacceptor_loss0.9900
9:113161505:ACAGG:Aacceptor_loss0.9900
9:113161506:CAGGC:Cacceptor_loss0.9900
9:113161507:A:Tacceptor_loss0.9900
9:113161508:GGC:Gacceptor_gain0.9900
9:113161508:GGCAT:Gacceptor_gain0.9900
9:113161662:GC:Gdonor_gain0.9900
9:113161700:T:Cdonor_loss0.9900
9:113161704:GGCA:Gdonor_gain0.9900
9:113161705:GCAG:Gdonor_gain0.9900
9:113162747:AGGT:Aacceptor_gain0.9900
9:113162748:GGTG:Gacceptor_gain0.9900
9:113151759:G:GTdonor_gain0.9800
9:113161507:A:AGacceptor_gain0.9800
9:113161508:G:GGacceptor_gain0.9800
9:113161708:G:GGdonor_gain0.9800
9:113162745:CTAG:Cacceptor_loss0.9800
9:113162746:TAG:Tacceptor_loss0.9800

AlphaMissense

923 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:113162830:G:AM115I0.993
9:113162830:G:CM115I0.993
9:113162830:G:TM115I0.993
9:113162839:C:AN118K0.990
9:113162839:C:GN118K0.990
9:113162818:G:AM111I0.989
9:113162818:G:CM111I0.989
9:113162818:G:TM111I0.989
9:113157763:T:CF15L0.988
9:113157765:T:AF15L0.988
9:113157765:T:GF15L0.988
9:113162855:G:CG124R0.988
9:113157772:T:AW18R0.984
9:113157772:T:CW18R0.984
9:113162867:G:CG128R0.984
9:113162868:G:AG128D0.984
9:113162880:G:AG132D0.982
9:113162838:A:TN118I0.981
9:113162856:G:AG124D0.980
9:113162843:T:AW120R0.978
9:113162843:T:CW120R0.978
9:113162879:G:CG132R0.977
9:113157733:T:CF5L0.975
9:113157735:C:AF5L0.975
9:113157735:C:GF5L0.975
9:113162804:G:CG107R0.975
9:113161557:A:TE41V0.974
9:113162837:A:TN118Y0.974
9:113161567:G:CK44N0.972
9:113161567:G:TK44N0.972

dbSNP variants (sampled 300 via entrez): RS1000118432 (9:113162019 G>C), RS1000317304 (9:113160294 T>C), RS1000372828 (9:113153740 T>C), RS1000462913 (9:113149277 G>A), RS1000974677 (9:113155067 T>G), RS1001137094 (9:113155296 A>C), RS1001185470 (9:113161047 A>G), RS1001591562 (9:113159065 T>C), RS1001622162 (9:113152173 G>A), RS1001638039 (9:113160694 TC>T), RS1001965519 (9:113158696 G>C), RS1002928533 (9:113159364 C>A,T), RS1003011469 (9:113151060 C>A,T), RS1003236818 (9:113157338 C>T), RS1003294738 (9:113150893 G>A,C,T)

Disease associations

OMIM: gene MIM:603088 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST90002385_392High light scatter reticulocyte count6.000000e-11
GCST90002386_435High light scatter reticulocyte percentage of red cells9.000000e-10
GCST90002390_397Mean corpuscular hemoglobin7.000000e-20
GCST90002392_544Mean corpuscular volume8.000000e-23
GCST90002396_414Mean reticulocyte volume5.000000e-32
GCST90002397_692Mean spheric corpuscular volume1.000000e-40
GCST90002398_158Neutrophil count1.000000e-13

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007986reticulocyte count
EFO:0004527mean corpuscular hemoglobin
EFO:0010701mean reticulocyte volume
EFO:0004833neutrophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724592 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — SLC31 family of copper transporters

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects expression, affects cotreatment7
Cisplatinincreases response to substance, increases uptake, affects localization, decreases degradation, affects uptake (+5 more)5
Copperdecreases abundance, decreases expression, increases response to substance, increases uptake, decreases reaction (+1 more)3
Cyclosporinedecreases expression3
Estradiolincreases reaction, decreases expression2
Tretinoinincreases expression2
Particulate Matterdecreases expression, increases abundance2
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
zinc chloridedecreases expression, increases expression1
sodium arseniteincreases abundance, increases expression1
tetrathiomolybdatedecreases response to substance1
bathocuproine sulfonateaffects localization, decreases abundance, decreases expression, increases response to substance, increases uptake1
aflatoxin B2increases methylation1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
monomethylarsonous acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases abundance, increases expression1
Benzo(a)pyrenedecreases expression1
Calcitriolincreases expression, affects cotreatment1
Carbamazepineaffects expression1
Dexamethasonedecreases expression1
Ethyl Methanesulfonateincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5723786BindingRLU of HCTR2 at 1.0 µM in the Aequorin PRESTO-Tango GPCRome screenData for DCP probe T-10430

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D4LPHCT116-SLC31A2-KO-c1Cancer cell lineMale
CVCL_D4LQHCT116-SLC31A2-KO-c9Cancer cell lineMale
CVCL_E0NVUbigene HeLa SLC31A2 KOCancer cell lineFemale
CVCL_TM98HAP1 SLC31A2 (-) 1Cancer cell lineMale
CVCL_XT17HAP1 SLC31A2 (-) 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.