TNPO1

gene
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Also known as MIPTRNIPO2MIP1

Summary

TNPO1 (transportin 1, HGNC:6401) is a protein-coding gene on chromosome 5q13.2, encoding Transportin-1 (Q92973). Functions in nuclear protein import as nuclear transport receptor. It is a selective cancer dependency (DepMap: 31.9% of cell lines).

This gene encodes the beta subunit of the karyopherin receptor complex which interacts with nuclear localization signals to target nuclear proteins to the nucleus. The karyopherin receptor complex is a heterodimer of an alpha subunit which recognizes the nuclear localization signal and a beta subunit which docks the complex at nucleoporins. Alternate splicing of this gene results in several transcript variants encoding different proteins.

Source: NCBI Gene 3842 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): cataract 15 multiple types (Definitive, GenCC) — +7 more curated relationships
  • GWAS associations: 28
  • Clinical variants (ClinVar): 227 total — 15 pathogenic, 7 likely-pathogenic
  • Phenotypes (HPO): 1
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 31.9% of screened cell lines
  • MANE Select transcript: NM_002270

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6401
Approved symbolTNPO1
Nametransportin 1
Location5q13.2
Locus typegene with protein product
StatusApproved
AliasesMIP, TRN, IPO2, MIP1
Ensembl geneENSG00000083312
Ensembl biotypeprotein_coding
OMIM602901
Entrez3842

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 12 protein_coding, 8 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000337273, ENST00000503084, ENST00000505082, ENST00000506351, ENST00000506528, ENST00000508762, ENST00000509030, ENST00000511754, ENST00000513944, ENST00000515483, ENST00000518279, ENST00000520850, ENST00000523768, ENST00000605210, ENST00000679378, ENST00000680025, ENST00000680111, ENST00000680533, ENST00000681711, ENST00000895477, ENST00000895478, ENST00000895479, ENST00000895480, ENST00000895481, ENST00000944758

RefSeq mRNA: 7 — MANE Select: NM_002270 NM_001364292, NM_001364293, NM_001364294, NM_001364295, NM_001364296, NM_002270, NM_153188

CCDS: CCDS4016, CCDS43329, CCDS93732, CCDS93733

Canonical transcript exons

ENST00000337273 — 25 exons

ExonStartEnd
ENSE000007524407286559672865729
ENSE000019252007290870972914388
ENSE000022126347289313972893246
ENSE000022221977288707072887222
ENSE000022313627288807872888303
ENSE000023057547289337772893535
ENSE000032350327290097472901073
ENSE000032535647289645872896556
ENSE000032925847288978672889957
ENSE000033179177289181072891896
ENSE000033507867289361672893703
ENSE000033660777289705672897151
ENSE000034314927290000672900081
ENSE000034738237287722872877346
ENSE000034778517287263972872720
ENSE000034846537285577472855923
ENSE000034919097287561572875737
ENSE000035137907290530372905445
ENSE000035284427286180872861914
ENSE000035376757288306472883232
ENSE000036027677288246772882527
ENSE000036150117290370972903783
ENSE000036310907284838572848498
ENSE000036479287285124472851319
ENSE000039179067281666172816752

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 105.8212 / max 499.4646, expressed in 1828 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
5701647.69381825
5700945.15941810
570178.42691738
570221.8971977
570151.4074767
570081.2366815

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
corpus epididymisUBERON:000435999.74gold quality
caput epididymisUBERON:000435899.73gold quality
cauda epididymisUBERON:000436099.73gold quality
pylorusUBERON:000116699.64gold quality
secondary oocyteCL:000065599.63gold quality
cranial nerve IIUBERON:000094199.56gold quality
cardia of stomachUBERON:000116299.44gold quality
renal medullaUBERON:000036299.41gold quality
cervix squamous epitheliumUBERON:000692299.39gold quality
pericardiumUBERON:000240799.35gold quality
nippleUBERON:000203099.29gold quality
visceral pleuraUBERON:000240199.27gold quality
trigeminal ganglionUBERON:000167599.23gold quality
dorsal motor nucleus of vagus nerveUBERON:000287099.23gold quality
mammary ductUBERON:000176599.18gold quality
superior surface of tongueUBERON:000737199.18gold quality
inferior olivary complexUBERON:000212799.16gold quality
mucosa of paranasal sinusUBERON:000503099.06gold quality
saphenous veinUBERON:000731899.04gold quality
parietal pleuraUBERON:000240099.01gold quality
trabecular bone tissueUBERON:000248398.98gold quality
medulla oblongataUBERON:000189698.97gold quality
epithelium of mammary glandUBERON:000324498.95gold quality
pharyngeal mucosaUBERON:000035598.86gold quality
ventral tegmental areaUBERON:000269198.86gold quality
germinal epithelium of ovaryUBERON:000130498.83gold quality
superficial temporal arteryUBERON:000161498.83gold quality
inferior vagus X ganglionUBERON:000536398.83gold quality
urethraUBERON:000005798.79gold quality
pleuraUBERON:000097798.78gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): IRF3, PITX3

miRNA regulators (miRDB)

512 targeting TNPO1, 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-4262100.0073.263931
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-8485100.0077.574731
HSA-MIR-3646100.0073.565283
HSA-MIR-3163100.0077.238605
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-4533100.0069.482758
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4692100.0067.322066
HSA-MIR-4481100.0066.421669
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3924100.0072.092394
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-12118100.0065.881270
HSA-MIR-188-3P100.0068.761240
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3162-3P100.0065.37363
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-118499.9968.191458
HSA-MIR-366299.9973.825684

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 31.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • nuclear import of the HPV16 E6 oncoprotein in digitonin-permeabilized HeLa cells could be mediated by Kap beta2 (PMID:12551970)
  • 1 major capsid protein of human papillomavirus type 11 interacts with Kap beta2 nuclear import receptor (PMID:12620808)
  • HPV16 L2 interacts via its NLSs with a network of karyopherins and can enter the nucleus via several import pathways mediated by Kapalpha(2)beta(1) heterodimers, Kapbeta(2), and Kapbeta(3). (PMID:15507604)
  • Results describe four crystal structures of human transoprtin 1 in a substrate-free form as well as in the complex with three nuclear localization signals. (PMID:17936704)
  • the 3.0 A crystal structure of unliganded Kap beta2, which consists of a superhelix of 20 HEAT repeats (PMID:17997969)
  • TRN1-binding to CCR2 promotes its nuclear translocation in a TRN1-dependent manner. (PMID:18846510)
  • Data suggest that increased MIP-1alpha/beta production enhances multiple myeloma cell binding to stromal cells by VLA-4-VCAM-1 adhesion, forming a “vicious cycle” between MM cell adhesion to stromal cells and MIP-1 production via VLA-4-VCAM-1 interaction. (PMID:19057841)
  • we identify transportin-1 as the import receptor for ADAR1. (PMID:19124606)
  • Ran in complex with importin-beta has a higher affinity for GTP. This feature is responsible for the generation of Ran-GTP from Ran-GDP by importin-beta. (PMID:19549784)
  • The interplay of the two negative regulators, transportin and importin beta, along with the positive regulator RanGTP, allows precise choreography of multiple cell cycle assembly events. (PMID:19641022)
  • Results suggest that hnRNP H and F are nuclear shuttling proteins whose posttranslational modifications may alter interaction with transportin 1, nuclear localization, and hence function. (PMID:20308327)
  • Nuclear import of fused in sarcoma (FUS) is dependent on Transportin, and interference with this transport pathway leads to cytoplasmic redistribution and recruitment of fused in sarcoma (FUS) into stress granules. (PMID:20606625)
  • Data demonstrate that Importin beta2 is necessary for localization of retinitis pigmentosa 2 (RP2) to the primary cilium, and identify two distinct binding sites of RP2, which interact independently with Importin beta2. (PMID:21285245)
  • Transportin binding might delay methylation of PABPN1 until after nuclear import. (PMID:21808065)
  • These data imply a specific dysfunction in the interaction between Trn1 and FET proteins in the inclusion body formation in FTLD-FUS. (PMID:22842875)
  • C-terminal FUS mutations prevent TNPO 1 binding to the NLS, inhibiting nuclear import and promoting cytoplasmic aggregation. The presence of TNPO 1 in wild-type FUS aggregates in frontotemporal lobar degeneration-FUS distinguishes it from ALS. (PMID:22934812)
  • arginine methylation impairs TRN dependent nuclear import of FUS, by decreasing binding of TRN to a novel TRN-binding motif next to the proline-tyrosine nuclear localization signal of FUS. (PMID:22968170)
  • Identification of a karyopherin beta1/beta2 proline-tyrosine nuclear localization signal in huntingtin protein. (PMID:23012356)
  • The crystal structure of the FUS-NLS/Trn1 complex shows extensive contacts between the two proteins and a unique alpha-helical structure in the FUS-NLS. (PMID:23056579)
  • In case of L7, importin beta2 or importin beta3 are preferentially used by clusters with a high import efficiency. (PMID:23266416)
  • Disulfide formation with transportin-1 is required for nuclear localization and the activation of FOXO4 induced by reactive oxygen species. (PMID:23333309)
  • Crystal structure of human Karyopherin beta2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2 (PMID:23535894)
  • Data suggest the C-terminal nuclear localization domain (QYP) is critical for RAM (RNMT-activating mini protein) to enter the cell nucleus where RAM activates RNMT resulting in mRNA cap methylation; TNPO1/TNPO2 mediate RAM nuclear entry. (PMID:24200467)
  • ADAR1 carries a unique nuclear localization signal (NLS) that overlaps one of its double-stranded RNA-binding domains (dsRBDs). This dsRBD-NLS is recognized by nuclear import receptor transportin 1 (also called karyopherin-beta2) in an RNA-sensitive manner. (PMID:24753571)
  • Studies indicate potential roles of Tranportin-1 and Transportin-2 beyond protein nuclear import. (PMID:24780099)
  • Kapbeta2 interacts with ULK2 through ULK2’s putative PY-NLS motif, and facilitates transport from the cytoplasm to the nucleus, depending on its Ser1027 residue phosphorylation by PKA, thereby reducing autophagic activity. (PMID:26052940)
  • FGF2 nuclear translocation is regulated by Karyopherin-beta2 and Ran GTPase in human glioblastoma cells (PMID:26056081)
  • A molecular docking and dynamics study concluded that R521C and R521H mutations in FUS result in weak binding with Karyopherin-beta2 leading to amyotrophic lateral sclerosis. (PMID:27381509)
  • Importins, Impbeta, Kapbeta2, Imp4, Imp5, Imp7, Imp9, and Impalpha, show the H3 tail binding more tightly than the H4 tail. The H3 tail binds Kapbeta2 and Imp5 with KD values of 77 and 57 nm, respectively, and binds the other five Importins more weakly. (PMID:27528606)
  • Results show that Karyopherin-b2 binds to the N-terminal tail of histone H3 with high affinity even though H3 lacks a recognizable proline-tyrosine nuclear localization signal (PY-NLS). (PMID:27618664)
  • the TNPO1-Rab8-ciliary targeting signals complex mediates selective entry into and retention of cargos within cilia. (PMID:27633000)
  • Together, these results indicate that transportin-1 mediates YB-1 nuclear translocation. (PMID:27794479)
  • findings suggest that a new player, i.e., O-GlcNAcylation, regulates hnRNP A1 translocation and interaction with Trn1, possibly affecting its function (PMID:27913144)
  • Data suggest that micoRNA-128 targets the 3prime-untranslated region of nuclear import factor transportin 1 (TNPO1) mRNA. (PMID:28974576)
  • TNPO1-mediated nuclear import may constitute a novel input pathway of how cellular redox state signals to the clock, since redox stress increases binding of TNPO1 to PER1 and decreases its nuclear localization. TNPO1 is one of the novel players essential for normal circadian periods and potentially for redox regulation of the clock. (PMID:29377895)
  • high-affinity binding of karyopherin-beta2 to the FUS C-terminal proline-tyrosine nuclear localization signal tethers the proteins together, allowing multiple, distributed weak intermolecular contacts to disrupt FUS self-association, blocking liquid-liquid phase separation (PMID:29677513)
  • Transportin 1, a member of the importin-beta family proteins, binds to a PY-NLS(2) sequence motif close to the amino terminus of matrix protein (M1) exposed during acid priming of the viral core. (PMID:30692667)
  • Study provides evidence that TRN-1 mediates the timely release of the HIV-1 genome from the capsid protein shell and efficient viral nuclear import. (PMID:31611641)
  • The Renpenning syndrome-associated protein PQBP1 facilitates the nuclear import of splicing factor TXNL4A through the karyopherin beta2 receptor. (PMID:32041777)
  • Nup358 and Transportin 1 Cooperate in Adenoviral Genome Import. (PMID:32161167)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotnpo1ENSDARG00000035390
mus_musculusTnpo1ENSMUSG00000009470
rattus_norvegicusTnpo1ENSRNOG00000014999
drosophila_melanogasterCG8219FBGN0035693
caenorhabditis_elegansWBGENE00002076

Paralogs (5): IPO5 (ENSG00000065150), TNPO2 (ENSG00000105576), KPNB1 (ENSG00000108424), RANBP6 (ENSG00000137040), IPO4 (ENSG00000196497)

Protein

Protein identifiers

Transportin-1Q92973 (reviewed: Q92973)

Alternative names: Importin beta-2, Karyopherin beta-2, M9 region interaction protein

All UniProt accessions (7): Q92973, A0A7P0T944, A0A7P0T9C0, A0A7P0TBF0, A0A7P0Z4D3, E7EW37, S4R398

UniProt curated annotations — full annotation on UniProt →

Function. Functions in nuclear protein import as nuclear transport receptor. Serves as receptor for nuclear localization signals (NLS) in cargo substrates. May mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Involved in nuclear import of M9-containing proteins. In vitro, binds directly to the M9 region of the heterogeneous nuclear ribonucleoproteins (hnRNP), A1 and A2 and mediates their nuclear import. Involved in hnRNP A1/A2 nuclear export. Mediates the nuclear import of ribosomal proteins RPL23A, RPS7 and RPL5. In vitro, mediates nuclear import of H2A, H2B, H3 and H4 histones. In vitro, mediates nuclear import of SRP19. Mediates nuclear import of ADAR/ADAR1 isoform 1 and isoform 5 in a RanGTP-dependent manner. Main mediator of PR-DUB complex component BAP1 nuclear import; acts redundantly with the karyopherins KPNA1 and KPNA2. (Microbial infection) In case of HIV-1 infection, binds and mediates the nuclear import of HIV-1 Rev.

Subunit / interactions. Identified in a complex that contains TNPO1, RAN and RANBP1. Binds HNRPA1, HNRPA2, HNRNPDL, RPS7, RPL5 and RAN. Interacts with H2A, H2B, H3 and H4 histones. Interacts with isoform 1 and isoform 5 of ADAR/ADAR1 (via DRBM 3 domain). Interacts with SNAI1 (via zinc fingers); the interaction mediates SNAI1 nuclear import. Interacts with SNAI2 (via zinc fingers). Interacts with RPL23A (via BIB domain) and SRP19; this interaction is involved in RPL23A and SRP19 import into the nucleus. Interacts (via HEAT repeats 8-12) with BAP1 (via non-classical PY-NLS); this interaction is direct, is involved in BAP1 nuclear import and disrupts BAP1 homodimerization. (Microbial infection) Binds to HIV-1 Rev.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the importin beta family. Importin beta-2 subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
Q92973-11yes
Q92973-22
Q92973-33

RefSeq proteins (6): NP_001351221, NP_001351222, NP_001351223, NP_001351224, NP_002261, NP_694858 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001494Importin-beta_NDomain
IPR011989ARM-likeHomologous_superfamily
IPR016024ARM-type_foldHomologous_superfamily
IPR040122Importin_betaFamily
IPR057672TPR_IPO4/5Domain
IPR058584IMB1_TNPO1-like_TPRDomain

Pfam: PF03810, PF13513, PF25574, PF25780

UniProt features (121 total): helix 68, repeat 20, strand 9, turn 9, sequence conflict 4, site 2, splice variant 2, mutagenesis site 2, chain 1, modified residue 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

21 structures.

PDBMethodResolution (Å)
4FDDX-RAY DIFFRACTION2.3
2Z5KX-RAY DIFFRACTION2.6
4OO6X-RAY DIFFRACTION2.7
7CYLX-RAY DIFFRACTION2.7
5YVIX-RAY DIFFRACTION2.9
1QBKX-RAY DIFFRACTION3
2QMRX-RAY DIFFRACTION3
2Z5MX-RAY DIFFRACTION3
4FQ3X-RAY DIFFRACTION3
5TQCX-RAY DIFFRACTION3
2H4MX-RAY DIFFRACTION3.05
4JLQX-RAY DIFFRACTION3.05
5J3VX-RAY DIFFRACTION3.05
2OT8X-RAY DIFFRACTION3.1
5YVHX-RAY DIFFRACTION3.15
8SGHELECTRON MICROSCOPY3.17
2Z5NX-RAY DIFFRACTION3.2
2Z5OX-RAY DIFFRACTION3.2
2Z5JX-RAY DIFFRACTION3.4
7VPWX-RAY DIFFRACTION3.76
5YVGX-RAY DIFFRACTION4.05

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92973-F192.240.83

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 468 (important for interaction with cargo nuclear localization signals); 738 (important for interaction with cargo nuclear localization signals)

Post-translational modifications (1): 1

Mutagenesis-validated functional residues (2):

PositionPhenotype
468abolishes interaction with the adar nuclear localization signal. abolishes adar nuclear import.
738abolishes interaction with the adar nuclear localization signal. abolishes adar nuclear import.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-450513Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-HSA-5620924Intraflagellar transport
R-HSA-9615933Postmitotic nuclear pore complex (NPC) reformation

MSigDB gene sets: 514 (showing top): WENDT_COHESIN_TARGETS_UP, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, JI_RESPONSE_TO_FSH_UP, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, SP3_Q3, TACAATC_MIR508, MODULE_352, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOMF_GTPASE_BINDING, PATIL_LIVER_CANCER, GOBP_NUCLEAR_TRANSPORT, GOBP_CELL_CELL_ADHESION, GOBP_WATER_TRANSPORT, ONKEN_UVEAL_MELANOMA_UP

GO Biological Process (3): protein import into nucleus (GO:0006606), intracellular protein transport (GO:0006886), protein transport (GO:0015031)

GO Molecular Function (5): RNA binding (GO:0003723), nuclear localization sequence binding (GO:0008139), small GTPase binding (GO:0031267), nuclear import signal receptor activity (GO:0061608), protein binding (GO:0005515)

GO Cellular Component (8): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), cilium (GO:0005929), extracellular exosome (GO:0070062), nuclear lumen (GO:0031981)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Regulation of mRNA stability by proteins that bind AU-rich elements1
Assembly of the 9+0 primary cilium1
Nuclear Envelope (NE) Reassembly1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
import into nucleus2
intracellular protein localization2
nuclear lumen2
intracellular protein transport1
protein localization to nucleus1
establishment of protein localization to organelle1
protein transport1
intracellular transport1
transport1
establishment of protein localization1
nucleic acid binding1
signal sequence receptor activity1
GTPase binding1
nucleocytoplasmic carrier activity1
binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
intracellular anatomical structure1
cytoplasm1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1
extracellular vesicle1
nucleus1
intracellular organelle lumen1

Protein interactions and networks

STRING

2562 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TNPO1HNRNPA1P09651995
TNPO1TNPO3Q9Y5L0955
TNPO1PHGDHO43175913
TNPO1FUSP35637867
TNPO1KIF17Q9P2E2822
TNPO1RGPD5Q99666814
TNPO1IPO7O95373800
TNPO1CSE1LP55060794
TNPO1NUP153P49790794
TNPO1FOXO4P98177779
TNPO1IPO9Q96P70778
TNPO1RANBP2P49792763
TNPO1NUP62P37198747
TNPO1IPO8O15397745
TNPO1XPO1O14980742
TNPO1RANP17080742

IntAct

172 interactions, top by confidence:

ABTypeScore
NUP153KPNB1psi-mi:“MI:0914”(association)0.820
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
TNPO1HNRNPMpsi-mi:“MI:0407”(direct interaction)0.620
FAM234BABCD4psi-mi:“MI:0914”(association)0.620
LRRK2PSMD11psi-mi:“MI:0914”(association)0.600
RANTNPO1psi-mi:“MI:0407”(direct interaction)0.590
FUSTNPO1psi-mi:“MI:0407”(direct interaction)0.590
TNPO1psi-mi:“MI:0407”(direct interaction)0.560
TNPO1HNRNPA1psi-mi:“MI:0407”(direct interaction)0.560
TNPO1CIRBPpsi-mi:“MI:0407”(direct interaction)0.560
CIRBPTNPO1psi-mi:“MI:0407”(direct interaction)0.560
NXF1TNPO1psi-mi:“MI:0407”(direct interaction)0.540
NXF1TNPO1psi-mi:“MI:0915”(physical association)0.540
EGFRNDUFA4psi-mi:“MI:0914”(association)0.530
KPNB1POM121Cpsi-mi:“MI:0914”(association)0.530
TMA16TNPO2psi-mi:“MI:0914”(association)0.530
EPHA1EXOC5psi-mi:“MI:0914”(association)0.530
FAM174ABLTP3Bpsi-mi:“MI:0914”(association)0.530
VAMP5NBASpsi-mi:“MI:0914”(association)0.530
CD40EXOC5psi-mi:“MI:0914”(association)0.530

BioGRID (413): TNPO1 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), IPO7 (Co-fractionation), IPO8 (Co-fractionation), IPO9 (Co-fractionation), RAN (Co-fractionation), RANBP6 (Co-fractionation), TNPO1 (Co-fractionation), TNPO1 (Co-fractionation), TNPO1 (Co-fractionation)

ESM2 similar proteins: A0JN27, C9WPN6, F1LTR1, F1QGW6, O14787, O14980, O15294, P17427, P18484, P20461, P41091, P52296, P52297, P56558, P61201, P61202, P61203, P70168, P81436, P81795, Q13888, Q14974, Q27HV0, Q28D01, Q2KHU8, Q2TBV5, Q2VIR3, Q3SYU7, Q5F398, Q5HZM6, Q5R797, Q5RIC0, Q5SP67, Q5ZHS1, Q5ZMS3, Q6IQT4, Q6IR75, Q6NVL5, Q6P1K8, Q6P5F9

Diamond homologs: B8ARW2, B9FDR3, O14089, O14787, Q3SYU7, Q55CQ7, Q8BFY9, Q8H0U4, Q92973, Q99LG2, P38217, P52296, P70168

SIGNOR signaling

5 interactions.

AEffectBMechanism
TNPO1“up-regulates activity”PER1relocalization
RANBP2“up-regulates activity”TNPO1binding
TNPO1“up-regulates activity”HNRNPA1relocalization
TNPO1“up-regulates activity”NUP153relocalization
TNPO1“up-regulates activity”FUSrelocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 178 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
GRB2 events in EGFR signaling534.6×4e-05
SHC1 events in EGFR signaling532.4×4e-05
Constitutive Signaling by EGFRvIII532.4×4e-05
Signaling by ERBB2 ECD mutants530.5×5e-05
GRB2 events in ERBB2 signaling528.8×6e-05
Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants525.9×7e-05
SHC1 events in ERBB2 signaling521.6×1e-04
Signaling by ERBB2 TMD/JMD mutants521.6×1e-04

GO biological processes:

GO termPartnersFoldFDR
RNA export from nucleus533.2×2e-04
NLS-bearing protein import into nucleus528.5×3e-04
protein import into nucleus1212.3×3e-07
Ras protein signal transduction68.8×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic15
Likely pathogenic7
Uncertain significance116
Likely benign18
Benign25

Top pathogenic / likely-pathogenic (22)

Variant IDHGVSClassification
1069403NM_012064.4(MIP):c.606+1G>CPathogenic
14354NM_012064.4(MIP):c.413C>G (p.Thr138Arg)Pathogenic
14355NM_012064.4(MIP):c.401A>G (p.Glu134Gly)Pathogenic
1806189NM_012064.4(MIP):c.616_632del (p.Val206fs)Pathogenic
217342NM_012064.4(MIP):c.97C>T (p.Arg33Cys)Pathogenic
217345NM_012064.4(MIP):c.597_598insGGGAACATTCCACT (p.Asn200fs)Pathogenic
252956NM_012064.4(MIP):c.631G>T (p.Gly211Ter)Pathogenic
2629509NM_012064.4(MIP):c.605G>A (p.Trp202Ter)Pathogenic
2722298NM_012064.4(MIP):c.606+1G>TPathogenic
377392NM_012064.4(MIP):c.508dup (p.Leu170fs)Pathogenic
432015NM_012064.4(MIP):c.698G>A (p.Arg233Lys)Pathogenic
4727827NM_012064.4(MIP):c.162dup (p.Leu55fs)Pathogenic
4734471NM_012064.4(MIP):c.530_531del (p.Tyr177fs)Pathogenic
474241NM_012064.4(MIP):c.623del (p.Pro208fs)Pathogenic
992878NM_012064.4(MIP):c.615G>A (p.Trp205Ter)Pathogenic
1176948NM_012064.4(MIP):c.698_699del (p.Arg233fs)Likely pathogenic
1703071NM_012064.4(MIP):c.559del (p.Arg187fs)Likely pathogenic
3061915NM_012064.4(MIP):c.493_494insT (p.Gly165fs)Likely pathogenic
3345576NM_012064.4(MIP):c.494G>A (p.Gly165Asp)Likely pathogenic
391974NM_012064.4(MIP):c.401A>C (p.Glu134Ala)Likely pathogenic
392878NM_012064.4(MIP):c.526-2A>CLikely pathogenic
944316NM_012064.4(MIP):c.525+1G>ALikely pathogenic

SpliceAI

4057 predictions. Top by Δscore:

VariantEffectΔscore
5:72855768:TTACA:Tacceptor_loss1.0000
5:72855769:TACA:Tacceptor_loss1.0000
5:72855770:ACAG:Aacceptor_loss1.0000
5:72855771:CA:Cacceptor_loss1.0000
5:72855772:A:ACacceptor_loss1.0000
5:72855772:A:AGacceptor_gain1.0000
5:72855772:AGAT:Aacceptor_gain1.0000
5:72855773:G:GTacceptor_gain1.0000
5:72855773:GA:Gacceptor_gain1.0000
5:72855773:GAT:Gacceptor_gain1.0000
5:72855773:GATG:Gacceptor_gain1.0000
5:72855773:GATGA:Gacceptor_gain1.0000
5:72855920:GTTG:Gdonor_gain1.0000
5:72855922:TGG:Tdonor_loss1.0000
5:72855924:G:GGdonor_gain1.0000
5:72855924:GT:Gdonor_loss1.0000
5:72855925:TAA:Tdonor_loss1.0000
5:72860503:T:Gacceptor_gain1.0000
5:72865590:TTACA:Tacceptor_loss1.0000
5:72865591:TACAG:Tacceptor_loss1.0000
5:72865593:CAGG:Cacceptor_loss1.0000
5:72865594:A:AGacceptor_gain1.0000
5:72865594:A:Tacceptor_loss1.0000
5:72865594:AG:Aacceptor_gain1.0000
5:72865595:G:GGacceptor_gain1.0000
5:72865595:GG:Gacceptor_gain1.0000
5:72865595:GGGA:Gacceptor_gain1.0000
5:72865725:ATAAG:Adonor_loss1.0000
5:72865726:TAAG:Tdonor_loss1.0000
5:72865727:AAGG:Adonor_loss1.0000

AlphaMissense

5990 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:72848446:T:CL26P1.000
5:72848449:T:CL27S1.000
5:72851248:T:CL45P1.000
5:72851257:T:CL48P1.000
5:72851274:T:CF54L1.000
5:72851276:T:AF54L1.000
5:72851276:T:GF54L1.000
5:72851287:T:CL58S1.000
5:72851287:T:GL58W1.000
5:72851296:T:AV61D1.000
5:72851299:T:CL62P1.000
5:72855785:A:GR73G1.000
5:72855786:G:CR73T1.000
5:72855786:G:TR73I1.000
5:72855787:A:CR73S1.000
5:72855787:A:TR73S1.000
5:72855794:A:CS76R1.000
5:72855796:T:AS76R1.000
5:72855796:T:GS76R1.000
5:72855797:G:CG77R1.000
5:72855798:G:AG77D1.000
5:72855798:G:TG77V1.000
5:72855801:T:AL78H1.000
5:72855801:T:CL78P1.000
5:72855807:T:GL80W1.000
5:72855809:A:GK81E1.000
5:72855810:A:CK81T1.000
5:72855810:A:TK81M1.000
5:72855811:G:CK81N1.000
5:72855811:G:TK81N1.000

dbSNP variants (sampled 300 via entrez): RS1000015732 (5:72853444 A>C), RS1000025311 (5:72816723 C>T), RS1000026623 (5:72895834 T>A), RS1000063573 (5:72876601 A>C), RS1000088832 (5:72853188 C>G,T), RS1000092416 (5:72816964 A>G), RS1000100922 (5:72891324 G>C), RS1000150455 (5:72815059 C>A,T), RS1000157424 (5:72898034 A>G), RS1000185856 (5:72823330 A>G), RS1000211668 (5:72823559 T>C), RS1000228275 (5:72858749 A>G), RS1000251709 (5:72856112 A>G,T), RS1000321923 (5:72847916 A>G), RS1000331018 (5:72908168 A>G)

Disease associations

OMIM: gene MIM:602901 | disease phenotypes: MIM:615274, MIM:221900

GenCC curated gene-disease

DiseaseClassificationInheritance
cataract 15 multiple typesDefinitiveAutosomal dominant
early-onset lamellar cataractSupportiveAutosomal dominant
early-onset sutural cataractSupportiveAutosomal dominant
cerulean cataractSupportiveAutosomal dominant
early-onset nuclear cataractSupportiveAutosomal dominant
early-onset posterior polar cataractSupportiveAutosomal dominant
total early-onset cataractSupportiveAutosomal dominant
Tourette syndromeNo Known Disease RelationshipUnknown

Mondo (11): cataract 15 multiple types (MONDO:0014110), persistent hyperplastic primary vitreous (MONDO:0019631), pathologic nystagmus (MONDO:0004843), microphthalmia (MONDO:0021129), Tourette syndrome (MONDO:0007661), early-onset lamellar cataract (MONDO:0018611), early-onset sutural cataract (MONDO:0020372), cerulean cataract (MONDO:0020374), early-onset nuclear cataract (MONDO:0020376), early-onset posterior polar cataract (MONDO:0020378), total early-onset cataract (MONDO:0021548)

Orphanet (2): Early onset non-syndromic cataract (Orphanet:91492), Persistent hyperplastic primary vitreous (Orphanet:91495)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0000568Microphthalmia

GWAS associations

28 associations (top):

StudyTraitp-value
GCST002115_16Axial length4.000000e-07
GCST004599_100Mean platelet volume4.000000e-16
GCST004603_228Platelet count9.000000e-10
GCST004605_73Mean corpuscular hemoglobin concentration6.000000e-15
GCST005988_5Serum albumin levels1.000000e-08
GCST005992_7Mean corpuscular hemoglobin concentration5.000000e-09
GCST006804_62Red cell distribution width4.000000e-12
GCST007445_42Factor VIII levels2.000000e-10
GCST007445_8Factor VIII levels5.000000e-10
GCST007446_2vWF levels6.000000e-13
GCST007446_41vWF levels1.000000e-12
GCST007446_61vWF levels3.000000e-12
GCST007446_81vWF levels1.000000e-12
GCST007692_81Chronic obstructive pulmonary disease3.000000e-08
GCST007932_52Medication use (thyroid preparations)2.000000e-08
GCST008839_17Height1.000000e-15
GCST012020_368Serum metabolite levels5.000000e-16
GCST012020_369Serum metabolite levels2.000000e-26
GCST012232_21Lipoprotein (a) levels2.000000e-08
GCST90002384_108Hemoglobin2.000000e-17
GCST90002390_130Mean corpuscular hemoglobin6.000000e-15
GCST90002391_33Mean corpuscular hemoglobin concentration3.000000e-28
GCST90002395_670Mean platelet volume3.000000e-28
GCST90002400_686Plateletcrit3.000000e-20
GCST90002402_767Platelet count9.000000e-22
GCST90002402_768Platelet count4.000000e-09
GCST90002404_207Red cell distribution width1.000000e-42
GCST90013407_57Liver enzyme levels (gamma-glutamyl transferase)7.000000e-17

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0005318axial length measurement
EFO:0004309platelet count
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0009188Red cell distribution width
EFO:0004630factor VIII measurement
EFO:0009933Thyroid preparation use measurement
EFO:0006925lipoprotein A measurement
EFO:0004509hemoglobin measurement
EFO:0004527mean corpuscular hemoglobin
EFO:0007985platelet crit
EFO:0004532serum gamma-glutamyl transferase measurement

MeSH disease descriptors (6)

DescriptorNameTree numbers
D008850MicrophthalmosC11.250.566; C16.131.384.666
D009759Nystagmus, PathologicC10.292.562.675; C11.590.400
D054514Persistent Hyperplastic Primary VitreousC11.250.616; C16.131.384.725
D005879Tourette SyndromeC10.228.140.079.898; C10.228.662.825.800; C10.574.500.850; C16.320.400.820; F03.625.992.850
C563333Cataract, Age-Related Nuclear (supp.)
C537955Cerulean cataract (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725070 (SINGLE PROTEIN)

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

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.33Kd463.8nMCHEMBL5653589
6.33ED50463.8nMCHEMBL5653589
5.42Kd3814nMCHEMBL3752910
5.42ED503814nMCHEMBL3752910

PubChem BioAssay actives

2 with measured affinity, of 10 total; 2 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]benzamide2149628: Binding affinity to human TNPO1 incubated for 45 mins by Kinobead based pull down assaykd0.4638uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149628: Binding affinity to human TNPO1 incubated for 45 mins by Kinobead based pull down assaykd3.8136uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, affects expression, decreases expression3
methylmercuric chlorideincreases expression, decreases expression2
bisphenol Adecreases expression, increases expression2
sodium arseniteincreases abundance, increases expression2
cadmium sulfateincreases expression2
Acetaminophenincreases expression2
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, decreases expression2
Benzo(a)pyreneaffects methylation, increases methylation2
Calcitriolincreases activity, decreases activity, decreases expression, affects binding, increases reaction2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
Tretinoindecreases expression, affects expression2
Cyclosporineincreases expression2
Aflatoxin B1decreases methylation2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
uranyl acetateaffects expression1
arseniteaffects binding, decreases reaction1
afimoxifenedecreases expression1
cobaltous chlorideincreases expression1
butyraldehydedecreases expression1
aflatoxin B2decreases methylation1
1-nitropyreneincreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
beta-methylcholineaffects expression1
manumycindecreases expression, decreases reaction1
tamibarotenedecreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652670BindingBinding affinity to human TNPO1 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_TT18HAP1 TNPO1 (-) 1Cancer cell lineMale
CVCL_TT19HAP1 TNPO1 (-) 2Cancer cell lineMale
CVCL_TT20HAP1 TNPO1 (-) 3Cancer cell lineMale
CVCL_XU62HAP1 TNPO1 (-) 4Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00152750PHASE4UNKNOWNStudy of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00226824PHASE4TERMINATEDSafety Study of Galantamine in Tic Disorders
NCT00241176PHASE4COMPLETEDOpen Label Trial of Aripiprazole in Children and Adolescents With Tourette’s Disorder
NCT00370838PHASE4COMPLETEDComparison of Keppra and Clonidine in the Treatment of Tics
NCT01018056PHASE4COMPLETEDDeveloping New Treatments for Tourette Syndrome: Therapeutic Trials With Modulators of Glutamatergic Neurotransmission
NCT01547000PHASE4COMPLETEDGuanfacine in Children With Tic Disorders
NCT03239210PHASE4COMPLETEDEffects of Ondansetron in Obsessive-compulsive and Tic Disorders
NCT00004376PHASE3COMPLETEDPhase III Randomized, Double-Blind, Placebo-Controlled Study of Guanfacine for Tourette Syndrome and Attention Deficit Hyperactivity Disorder
NCT00206323PHASE3COMPLETEDA Randomized, Placebo-controlled, Tourette Syndrome Study.
NCT00206336PHASE3COMPLETEDAn Open-label Study to Determine the Efficacy and Safety of Topiramate in the Treatment of Tourette Syndrome.
NCT00478842PHASE3COMPLETEDPallidal Stimulation and Gilles de la Tourette Syndrome
NCT00681863PHASE3TERMINATEDOpen-label Extension Study of Pramipexole in the Treatment of Children and Adolescents With Tourette Syndrome
NCT01501695PHASE3COMPLETEDPhase III Study of 5LGr to Treat Tic Disorder
NCT03087201PHASE3COMPLETEDCANNAbinoids in the Treatment of TICS (CANNA-TICS)
NCT03487783PHASE3COMPLETEDAripiprazole Oral Solution in the Treatment of Children and Adolescents With Tourette’s Syndrome
NCT03567291PHASE3TERMINATEDEvaluation of Safety and Tolerability of Long-term TEV-50717 (Deutetrabenazine) for Treatment of Tourette Syndrome in Children and Adolescents
NCT03571256PHASE3COMPLETEDA Study to Test if TEV-50717 is Effective in Relieving Tics Associated With Tourette Syndrome (TS)
NCT06021522PHASE3ACTIVE_NOT_RECRUITINGA Study to Evaluate Long-term Safety of Ecopipam Tablets in Children, Adolescents and Adults With Tourette’s Disorder
NCT00004393PHASE2COMPLETEDPhase II Double Blind Placebo Controlled Trial of Risperidone in Tourette Syndrome
NCT00004652PHASE2COMPLETEDPhase II Pilot Controlled Study of Short Vs Longer Term Pimozide (Orap) Therapy in Tourette Syndrome
NCT00231985PHASE2COMPLETEDEffectiveness of Behavior Therapy and Psychosocial Therapy for the Treatment of Tourette Syndrome and Chronic Tic Disorder
NCT00311909PHASE2COMPLETEDThalamic Deep Brain Stimulation for Tourette Syndrome
NCT00529308PHASE2COMPLETEDTranscranial Magnetic Stimulation (TMS) for Individuals With Tourette’s Syndrome
NCT00558467PHASE2COMPLETEDPramipexole Pilot Phase II Study in Children and Adolescents With Tourette Disorder According to DSM-IV Criteria
NCT01043549PHASE2TERMINATEDRepetitive Transcranial Magnetic Stimulation of the Posterior Parietal Cortex in Patients Suffering From Gilles de la Tourette Syndrome
NCT01133353PHASE2WITHDRAWNA Study of the Effectiveness and Safety of Tetrabenazine MR in Pediatric Subjects With Tourette’s Syndrome
NCT01475383PHASE2WITHDRAWNStudy Evaluating The Safety And Efficacy Of PF-03654746 In Adult Subjects With Tourette’s Syndrome
NCT01647269PHASE2COMPLETEDA Trial of Bilateral Deep Brain Stimulation to the Globus Pallidus Internum in Tourette Syndrome
NCT01904773PHASE2COMPLETEDSafety, Tolerability, Pharmacokinetic, and Efficacy Study of AZD5213 in Adolescents With Tourette’s Disorder
NCT02102698PHASE2COMPLETEDEcopipam Treatment of Tourette’s Syndrome in Subjects 7-17 Years
NCT02217007PHASE2WITHDRAWNA Trial Evaluating the Efficacy, Safety, and Pharmacokinetics of SNC-102 in Subjects With Tourette Syndrome
NCT02247206PHASE2COMPLETEDVoIP Delivered Behavior Therapy for Tourette Syndrome
NCT02581865PHASE2COMPLETEDSafety and Efficacy Study of NBI-98854 in Adults With Tourette Syndrome
NCT02619084PHASE2COMPLETEDSubthalamic Stimulation in Tourette’s Syndrome
NCT02679079PHASE2COMPLETEDSafety and Efficacy Study of NBI-98854 in Children and Adolescents With Tourette Syndrome
NCT02879578PHASE2COMPLETEDSafety and Tolerability Study of NBI-98854 for the Treatment of Subjects With Tourette Syndrome
NCT03066193PHASE2COMPLETEDEfficacy of a Therapeutic Combination of Dronabinol and PEA for Tourette Syndrome
NCT03247244PHASE2TERMINATEDSafety and Efficacy of Cannabis in Tourette Syndrome
NCT03325010PHASE2COMPLETEDSafety, Tolerability, and Efficacy of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome
NCT03444038PHASE2COMPLETEDOpen-Label Safety and Tolerability Study of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome