UBXN7

gene
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Also known as KIAA0794

Summary

UBXN7 (UBX domain protein 7, HGNC:29119) is a protein-coding gene on chromosome 3q29, encoding UBX domain-containing protein 7 (O94888). Ubiquitin-binding adapter that links a subset of NEDD8-associated cullin ring ligases (CRLs) to the segregase VCP/p97, to regulate turnover of their ubiquitination substrates.

Enables RNA polymerase II-specific DNA-binding transcription factor binding activity; ubiquitin binding activity; and ubiquitin protein ligase binding activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Located in nucleoplasm. Part of VCP-NPL4-UFD1 AAA ATPase complex.

Source: NCBI Gene 26043 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 42 total
  • MANE Select transcript: NM_015562

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29119
Approved symbolUBXN7
NameUBX domain protein 7
Location3q29
Locus typegene with protein product
StatusApproved
AliasesKIAA0794
Ensembl geneENSG00000163960
Ensembl biotypeprotein_coding
OMIM616379
Entrez26043

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000296328, ENST00000381887, ENST00000413584, ENST00000428095, ENST00000429160, ENST00000493566, ENST00000897727, ENST00000897728, ENST00000938274

RefSeq mRNA: 1 — MANE Select: NM_015562 NM_015562

CCDS: CCDS43191

Canonical transcript exons

ENST00000296328 — 11 exons

ExonStartEnd
ENSE00001265446196347662196356846
ENSE00001747224196391813196391925
ENSE00003528738196402952196403019
ENSE00003553873196407246196407393
ENSE00003595619196432327196432427
ENSE00003600928196393554196393619
ENSE00004035133196371896196372042
ENSE00004035135196362294196362687
ENSE00004035136196368028196368155
ENSE00004035137196369421196369511
ENSE00004035138196361844196361923

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 91.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.9351 / max 348.1546, expressed in 1811 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
4635227.48491810
2030770.4502233

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endometrium epitheliumUBERON:000481191.78gold quality
colonic epitheliumUBERON:000039791.68gold quality
nippleUBERON:000203091.61gold quality
spermCL:000001991.31gold quality
cranial nerve IIUBERON:000094190.99gold quality
cartilage tissueUBERON:000241890.20gold quality
cervix squamous epitheliumUBERON:000692289.86gold quality
cortical plateUBERON:000534389.71gold quality
hair follicleUBERON:000207389.70gold quality
corpus epididymisUBERON:000435989.64gold quality
sural nerveUBERON:001548889.63gold quality
mammary ductUBERON:000176589.51gold quality
calcaneal tendonUBERON:000370189.47gold quality
ganglionic eminenceUBERON:000402389.44gold quality
ventricular zoneUBERON:000305389.19gold quality
caput epididymisUBERON:000435889.06gold quality
endothelial cellCL:000011588.96gold quality
male germ cellCL:000001588.80gold quality
corpus callosumUBERON:000233688.52gold quality
epithelium of mammary glandUBERON:000324488.43gold quality
paraflocculusUBERON:000535188.34gold quality
cauda epididymisUBERON:000436088.05gold quality
buccal mucosa cellCL:000233687.67gold quality
adrenal tissueUBERON:001830387.17gold quality
bone marrow cellCL:000209286.97gold quality
mucosa of paranasal sinusUBERON:000503086.78gold quality
tonsilUBERON:000237286.68gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.54gold quality
saphenous veinUBERON:000731886.29gold quality
inferior vagus X ganglionUBERON:000536385.99gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no5.58
E-HCAD-5no2.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

162 targeting UBXN7, 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-98-3P100.0074.083907
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-3163100.0077.238605
HSA-MIR-3646100.0073.565283
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-4425100.0067.591049
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-9-5P100.0072.282361
HSA-MIR-318599.9968.121959
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-3688-3P99.9772.022834

Literature-anchored findings (GeneRIF, showing 9)

  • UBXD7 links p97 to the ubiquitin ligase CUL2/VHL and its substrate hypoxia-inducible factor 1alpha (HIF1alpha). (PMID:18775313)
  • FAF1 and UBXD7 only bind to p97-UFD1/NPL4, but not free p97, thus demonstrating for the first time a hierarchy in p97-cofactor interactions (PMID:21645854)
  • Study finds that UBXN7 over-expression converts CUL2 to its neddylated form and causes the accumulation of non-ubiquitylated HIF1alpha. (PMID:22537386)
  • Data suggest that dimerization of UBX domain protein 7 (UBXD7) could affect the formation of the p97 ATPase-UBXD7 complex. (PMID:28274878)
  • [Circular RNA-UBXN7 promotes proliferation, migration and suppresses apoptosis in hepatocellular cancer]. (PMID:32536059)
  • UBXN7 cofactor of CRL3(KEAP1) and CRL2(VHL) ubiquitin ligase complexes mediates reciprocal regulation of NRF2 and HIF-1alpha proteins. (PMID:33444648)
  • HBV X Protein Induces Degradation of UBXN7, a Novel Negative Regulator of NF-kappaB Signaling, to Promote HBV Replication. (PMID:36096451)
  • CircUBXN7 suppresses cell proliferation and facilitates cell apoptosis in lipopolysaccharide-induced cell injury by sponging miR-622 and regulating the IL6ST/JAK1/STAT3 axis. (PMID:36257578)
  • CircUBXN7 promotes macrophage infiltration and renal fibrosis associated with the IGF2BP2-dependent SP1 mRNA stability in diabetic kidney disease. (PMID:37744330)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioubxn7ENSDARG00000009436
mus_musculusUbxn7ENSMUSG00000053774
rattus_norvegicusAABR07034438.1ENSRNOG00000046969

Paralogs (4): UBXN8 (ENSG00000104691), FAF2 (ENSG00000113194), UBXN10 (ENSG00000162543), FAF1 (ENSG00000185104)

Protein

Protein identifiers

UBX domain-containing protein 7O94888 (reviewed: O94888)

All UniProt accessions (5): C9JAT7, C9JD50, O94888, F8WB69, H7BYF4

UniProt curated annotations — full annotation on UniProt →

Function. Ubiquitin-binding adapter that links a subset of NEDD8-associated cullin ring ligases (CRLs) to the segregase VCP/p97, to regulate turnover of their ubiquitination substrates.

Subunit / interactions. Interacts with neddylated CUL2, ubiquitinated HIF1A, and VCP/p97.

Subcellular location. Nucleus.

Domain organisation. The UIM (ubiquitin-interacting motif) is required to engage the NEDD8 modification on cullins. The UBX domain mediates interaction with VCP/p97. The UBA domain is required for binding ubiquitinated-protein substrates.

RefSeq proteins (1): NP_056377* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001012UBX_domDomain
IPR006577UASDomain
IPR009060UBA-like_sfHomologous_superfamily
IPR017346UBX_7/2Family
IPR029071Ubiquitin-like_domsfHomologous_superfamily
IPR036249Thioredoxin-like_sfHomologous_superfamily
IPR050730UBX_domain-proteinFamily
IPR054109UBA_8Domain

Pfam: PF00789, PF13899, PF22566

UniProt features (49 total): helix 11, strand 9, turn 7, modified residue 6, cross-link 3, mutagenesis site 3, domain 3, compositionally biased region 3, region of interest 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
5X3PX-RAY DIFFRACTION2
5X4LX-RAY DIFFRACTION2.4
1WJ4SOLUTION NMR
2DALSOLUTION NMR
2DLXSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O94888-F173.780.44

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 (9): 2, 278, 280, 285, 288, 306, 84, 99, 134

Mutagenesis-validated functional residues (3):

PositionPhenotype
288no effect on interactions with cul2 and hif1a.
297severely reduces interaction with neddylated cul2.
459abolishes interaction with vcp/p97.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-8951664Neddylation
R-HSA-9755511KEAP1-NFE2L2 pathway

MSigDB gene sets: 119 (showing top): BORCZUK_MALIGNANT_MESOTHELIOMA_UP, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEIN_CATABOLIC_PROCESS, NUYTTEN_EZH2_TARGETS_DN, MORF_RFC1, GOCC_ATPASE_COMPLEX, GOCC_MEMBRANE_PROTEIN_COMPLEX, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOBP_PROTEOLYSIS

GO Biological Process (1): proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (4): ubiquitin protein ligase binding (GO:0031625), ubiquitin binding (GO:0043130), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), VCP-NPL4-UFD1 AAA ATPase complex (GO:0034098)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Post-translational protein modification1
Cellular response to chemical stress1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
ubiquitin-like protein ligase binding1
ubiquitin-like protein binding1
DNA-binding transcription factor binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cytoplasm1
endoplasmic reticulum membrane1
UFD1-NPL4 complex1
membrane protein complex1
endoplasmic reticulum protein-containing complex1

Protein interactions and networks

STRING

3271 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UBXN7UFD1Q92890827
UBXN7NPLOC4Q8TAT6812
UBXN7FAF2Q96CS3801
UBXN7UBXN1Q04323745
UBXN7UBXN6Q9BZV1744
UBXN7WDR53Q7Z5U6736
UBXN7VCPP55072722
UBXN7UBXN2AP68543710
UBXN7CUL2Q13617690
UBXN7SMCO1Q147U7690
UBXN7UBXN10Q96LJ8648
UBXN7UBXN8O00124646
UBXN7ASPSCR1Q9BZE9624
UBXN7UBXN4Q92575620
UBXN7UBXN2BQ14CS0605

IntAct

130 interactions, top by confidence:

ABTypeScore
UBXN7VCPpsi-mi:“MI:0915”(physical association)0.820
UBXN7VCPpsi-mi:“MI:0914”(association)0.820
VCPUBXN7psi-mi:“MI:0914”(association)0.820
UBXN7CUL2psi-mi:“MI:0914”(association)0.710
UBXN7CUL2psi-mi:“MI:0915”(physical association)0.710
CUL2UBXN7psi-mi:“MI:0914”(association)0.710
TGIF2LYPGPpsi-mi:“MI:0914”(association)0.640
NUAK2PPP1R12Apsi-mi:“MI:0914”(association)0.640
UBXN7CUL4Apsi-mi:“MI:0915”(physical association)0.620
UBXN7CUL3psi-mi:“MI:0915”(physical association)0.620
CUL4AUBXN7psi-mi:“MI:0914”(association)0.620
UBXN7psi-mi:“MI:0407”(direct interaction)0.590
UBXN7psi-mi:“MI:0914”(association)0.590

BioGRID (371): UBC (Affinity Capture-Western), UBC (Reconstituted Complex), VCP (Affinity Capture-Western), UBC (Affinity Capture-Western), CUL2 (Reconstituted Complex), UBXN7 (Biochemical Activity), UBXN7 (Affinity Capture-MS), UBXN7 (Affinity Capture-MS), UBXN7 (Affinity Capture-Western), UBXN7 (Affinity Capture-Western), UBXN7 (Affinity Capture-Western), ACAD11 (Affinity Capture-Western), ERCC3 (Affinity Capture-Western), CSNK1G3 (Affinity Capture-Western), UBXN7 (Affinity Capture-Western)

ESM2 similar proteins: A4FUF0, A4Q9F4, D2XV59, E1C1R4, O94888, O95267, P42694, P54198, P79987, Q15139, Q49A26, Q4R8V9, Q4SS66, Q562D5, Q5R372, Q5R5M3, Q5R7T2, Q5RDU9, Q5REY7, Q5RKH0, Q5RKN4, Q5T6S3, Q5ZIA0, Q5ZJ17, Q5ZLS2, Q5ZLS7, Q61666, Q62101, Q6DC64, Q6DFV5, Q6P5G6, Q6ZPY2, Q6ZWH5, Q70Z35, Q75Q39, Q80VL1, Q86W50, Q8BY87, Q8BYN5, Q8CIW5

Diamond homologs: O14048, O94888, P0DKI5, Q06682, Q55BU7, Q5REY7, Q6P5G6, P0DKI4, P54731, Q924K2, Q94HV8, Q94JZ8, Q9M0N1, Q9UNN5, Q9LUG7, O00124, F4JPR7, O74498, Q3TDN2, Q5BK32, Q6AZH6, Q6GQ69, Q9C5G7, Q4V3D3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 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
Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha524.0×2e-04
KEAP1-NFE2L2 pathway514.7×1e-03
Neddylation1213.9×9e-09
Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide513.0×2e-03
Cargo recognition for clathrin-mediated endocytosis512.8×2e-03
Antigen processing: Ubiquitination & Proteasome degradation109.1×2e-05
Ub-specific processing proteases67.8×4e-03

GO biological processes:

GO termPartnersFoldFDR
positive regulation of protein ubiquitination518.4×8e-04
G1/S transition of mitotic cell cycle517.3×9e-04
ubiquitin-dependent protein catabolic process911.5×2e-05
protein polyubiquitination59.9×5e-03
proteasome-mediated ubiquitin-dependent protein catabolic process119.9×6e-06
protein ubiquitination117.8×2e-05
positive regulation of canonical NF-kappaB signal transduction67.5×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance34
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2298 predictions. Top by Δscore:

VariantEffectΔscore
3:196351410:T:Adonor_gain1.0000
3:196356695:T:TAdonor_gain1.0000
3:196356771:T:Adonor_gain1.0000
3:196361836:GTACT:Gdonor_loss1.0000
3:196361837:TACTT:Tdonor_loss1.0000
3:196361838:ACT:Adonor_loss1.0000
3:196361839:CTTAC:Cdonor_loss1.0000
3:196361840:TTAC:Tdonor_loss1.0000
3:196361842:A:ACdonor_gain1.0000
3:196361842:ACTAG:Adonor_gain1.0000
3:196361843:C:Adonor_loss1.0000
3:196361843:C:CAdonor_gain1.0000
3:196361843:CT:Cdonor_gain1.0000
3:196361843:CTA:Cdonor_gain1.0000
3:196361843:CTAG:Cdonor_gain1.0000
3:196361843:CTAGC:Cdonor_gain1.0000
3:196361922:TC:Tacceptor_gain1.0000
3:196361923:CC:Cacceptor_gain1.0000
3:196361924:C:Aacceptor_loss1.0000
3:196361924:C:CCacceptor_gain1.0000
3:196361937:T:Cacceptor_gain1.0000
3:196361937:T:TCacceptor_gain1.0000
3:196362289:CTTA:Cdonor_loss1.0000
3:196362290:TTA:Tdonor_loss1.0000
3:196362291:TAC:Tdonor_loss1.0000
3:196362292:AC:Adonor_gain1.0000
3:196362293:CC:Cdonor_gain1.0000
3:196362683:CTCTC:Cacceptor_gain1.0000
3:196362685:CTC:Cacceptor_gain1.0000
3:196362695:A:ACacceptor_gain1.0000

AlphaMissense

3226 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:196356701:A:TV485E1.000
3:196356703:A:CF484L1.000
3:196356703:A:TF484L1.000
3:196356705:A:GF484L1.000
3:196356707:A:TV483D1.000
3:196356725:A:GL477P1.000
3:196356725:A:TL477H1.000
3:196356767:A:GL463S1.000
3:196356779:G:TP459H1.000
3:196356780:G:AP459S1.000
3:196356781:A:CF458L1.000
3:196356781:A:TF458L1.000
3:196356782:A:CF458C1.000
3:196356782:A:GF458S1.000
3:196356783:A:GF458L1.000
3:196361899:C:GR418P1.000
3:196362629:A:GL298S1.000
3:196362632:G:AS297F1.000
3:196362633:A:GS297P1.000
3:196362636:C:GA296P1.000
3:196362641:A:CI294S1.000
3:196362641:A:GI294T1.000
3:196362641:A:TI294N1.000
3:196362644:G:TA293D1.000
3:196362645:C:GA293P1.000
3:196362648:C:GA292P1.000
3:196362653:A:GL290P1.000
3:196362655:C:AQ289H1.000
3:196362655:C:GQ289H1.000
3:196362672:C:GA284P1.000

dbSNP variants (sampled 300 via entrez): RS1000057824 (3:196381977 A>G), RS1000087217 (3:196394631 A>C), RS1000118607 (3:196421942 T>C), RS1000146078 (3:196349055 G>A), RS1000169263 (3:196412790 C>T), RS1000184046 (3:196369075 C>T), RS1000187431 (3:196398279 T>C), RS1000195240 (3:196412440 G>C), RS1000204283 (3:196410099 C>A,T), RS1000214077 (3:196408017 G>A), RS1000255057 (3:196400095 A>G,T), RS1000268423 (3:196418242 A>G), RS1000299764 (3:196404001 T>C), RS1000317426 (3:196405941 T>A,C), RS1000328789 (3:196404338 C>T)

Disease associations

OMIM: gene MIM:616379 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001762_159Obesity-related traits7.000000e-06
GCST008575_9IgM levels2.000000e-12
GCST010241_246Apolipoprotein A1 levels4.000000e-09
GCST010242_385HDL cholesterol levels4.000000e-10
GCST010988_223Adult body size2.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004338body weight
EFO:0004614apolipoprotein A 1 measurement
EFO:0004612high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression2
GSK-J4increases expression1
FR900359increases phosphorylation1
bisphenol Faffects cotreatment, decreases expression1
bisphenol Aincreases methylation1
sodium arsenatedecreases expression1
butyraldehydedecreases expression1
coumarindecreases phosphorylation1
pentanaldecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrineincreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, increases expression1
Sunitinibincreases expression1
Arsenicincreases abundance, increases expression1
Cadmiumincreases abundance, increases expression1
Caffeineaffects phosphorylation1
Dexamethasoneaffects cotreatment, decreases expression1
Doxorubicinincreases expression1
Drugs, Chinese Herbalincreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Indomethacinaffects cotreatment, decreases expression1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases expression1
Naphthoquinonesincreases expression1
Quercetinincreases phosphorylation1
Urethaneincreases expression1

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.