UBXN4

gene
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Also known as KIAA0242

Summary

UBXN4 (UBX domain protein 4, HGNC:14860) is a protein-coding gene on chromosome 2q21.3, encoding UBX domain-containing protein 4 (Q92575). Involved in endoplasmic reticulum-associated protein degradation (ERAD).

UBXD2 is an integral membrane protein of the endoplasmic reticulum (ER) that binds valosin-containing protein (VCP; MIM 601023) and promotes ER-associated protein degradation (ERAD) (Liang et al., 2006 [PubMed 16968747]).

Source: NCBI Gene 23190 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 87 total
  • Druggable target: yes
  • MANE Select transcript: NM_014607

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14860
Approved symbolUBXN4
NameUBX domain protein 4
Location2q21.3
Locus typegene with protein product
StatusApproved
AliasesKIAA0242
Ensembl geneENSG00000144224
Ensembl biotypeprotein_coding
OMIM611216
Entrez23190

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 15 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000272638, ENST00000415164, ENST00000416538, ENST00000426921, ENST00000467065, ENST00000470687, ENST00000471246, ENST00000490163, ENST00000882676, ENST00000882677, ENST00000882678, ENST00000928823, ENST00000928824, ENST00000928825, ENST00000928826, ENST00000928827, ENST00000928828, ENST00000944515, ENST00000944516, ENST00000944517, ENST00000944518

RefSeq mRNA: 1 — MANE Select: NM_014607 NM_014607

CCDS: CCDS42761

Canonical transcript exons

ENST00000272638 — 13 exons

ExonStartEnd
ENSE00001269798135741855135742011
ENSE00003474674135753539135753567
ENSE00003521047135748267135748369
ENSE00003547148135770571135770735
ENSE00003550213135776249135776351
ENSE00003556279135778948135779079
ENSE00003583254135755517135755691
ENSE00003585360135772420135772547
ENSE00003588038135780183135780385
ENSE00003623067135782749135785056
ENSE00003670962135761818135761911
ENSE00003673641135769769135769823
ENSE00003683662135754159135754277

Expression profiles

Bgee: expression breadth ubiquitous, 303 present calls, max score 98.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 70.5819 / max 1385.2260, expressed in 1827 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
2265936.13811820
2265820.54951790
226559.37261712
226562.57751210
226571.2322736
226600.7119385

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001998.89gold quality
pylorusUBERON:000116698.56gold quality
cardia of stomachUBERON:000116298.26gold quality
secondary oocyteCL:000065598.18gold quality
cranial nerve IIUBERON:000094197.98gold quality
seminal vesicleUBERON:000099897.96gold quality
adrenal tissueUBERON:001830397.95gold quality
body of pancreasUBERON:000115097.78gold quality
nippleUBERON:000203097.58gold quality
endometriumUBERON:000129597.52gold quality
pancreasUBERON:000126497.48gold quality
corpus epididymisUBERON:000435997.47gold quality
renal medullaUBERON:000036297.39gold quality
male germ cellCL:000001597.38gold quality
islet of LangerhansUBERON:000000697.37gold quality
ventricular zoneUBERON:000305397.35gold quality
parietal pleuraUBERON:000240097.31gold quality
tendon of biceps brachiiUBERON:000818897.29gold quality
rectumUBERON:000105297.27gold quality
pancreatic ductal cellCL:000207997.22gold quality
oocyteCL:000002397.20gold quality
medial globus pallidusUBERON:000247797.18gold quality
caput epididymisUBERON:000435897.16gold quality
gall bladderUBERON:000211097.14gold quality
monocyteCL:000057697.13gold quality
cervix squamous epitheliumUBERON:000692297.04gold quality
mononuclear cellCL:000084297.02gold quality
visceral pleuraUBERON:000240197.00gold quality
pericardiumUBERON:000240796.94gold quality
pleuraUBERON:000097796.93gold 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

miRNA regulators (miRDB)

113 targeting UBXN4, 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-3925-3P100.0069.951237
HSA-MIR-4682100.0068.891258
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-453499.9966.581907
HSA-MIR-453199.9969.703181
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-1213699.9872.815713
HSA-MIR-548P99.9872.253784
HSA-MIR-807599.9767.20962
HSA-MIR-314899.9775.066478
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-365899.9673.874379
HSA-MIR-568899.9673.234504
HSA-MIR-391099.9571.132227
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358

Literature-anchored findings (GeneRIF, showing 2)

  • Erasin/UBXD2 may be involved in endoplasmic-reticulum-associated protein degradation and in Alzheimer’s disease. (PMID:16968747)
  • Knockdown of erasin, a platform for p97/VCP and ubiquilin binding, or knockdown of ubiquilin in human cells slowed degradation of two classical endoplasmic reticulum-associated protein degradation substrates. (PMID:19822669)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusUbxn4ENSMUSG00000026353
rattus_norvegicusUbxn4ENSRNOG00000003625
caenorhabditis_elegansWBGENE00022703

Paralogs (5): TNRC6C (ENSG00000078687), TNRC6A (ENSG00000090905), TNRC6B (ENSG00000100354), UBAC1 (ENSG00000130560), UBXN1 (ENSG00000162191)

Protein

Protein identifiers

UBX domain-containing protein 4Q92575 (reviewed: Q92575)

Alternative names: Erasin, UBX domain-containing protein 2

All UniProt accessions (4): Q92575, C9JLR4, F8WB86, Q6PJ80

UniProt curated annotations — full annotation on UniProt →

Function. Involved in endoplasmic reticulum-associated protein degradation (ERAD). Acts as a platform to recruit both UBQLN1 and VCP to the ER during ERAD.

Subunit / interactions. Directly interacts with VCP. Interacts with UBQLN1. Forms a complex with VCP and UBQLN1.

Subcellular location. Endoplasmic reticulum membrane. Nucleus envelope.

Tissue specificity. Expressed in many tissues, including heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Accumulates in Alzheimer disease-afflicted brains (at protein level).

Domain organisation. The UBX domain is required for interaction with VCP. The intramembrane domain also contains the signal for ER targeting.

Induction. By ER stress-inducing agents such as tunicamycin, thapsigargin, DTT and the calcium ionophore A23187 (at protein level).

RefSeq proteins (1): NP_055422* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001012UBX_domDomain
IPR029071Ubiquitin-like_domsfHomologous_superfamily
IPR036249Thioredoxin-like_sfHomologous_superfamily

Pfam: PF00789, PF23187

UniProt features (24 total): strand 6, compositionally biased region 5, helix 3, region of interest 3, topological domain 2, chain 1, modified residue 1, sequence variant 1, intramembrane region 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2KXJSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92575-F176.040.46

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): 489

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 189 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MORF_RAB5A, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MORF_PSMC2, OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP, ONKEN_UVEAL_MELANOMA_UP, MYOD_01, AMIT_EGF_RESPONSE_120_HELA, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, MORF_PPP6C, NRF2_Q4, STONER_ESOPHAGEAL_CARCINOGENESIS_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP

GO Biological Process (2): response to unfolded protein (GO:0006986), ERAD pathway (GO:0036503)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): nuclear envelope (GO:0005635), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), cytosol (GO:0005829), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
endomembrane system2
cytoplasm2
intracellular membrane-bounded organelle2
cellular anatomical structure2
response to topologically incorrect protein1
proteasomal protein catabolic process1
response to endoplasmic reticulum stress1
response to chemical1
binding1
nucleus1
organelle envelope1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1

Protein interactions and networks

STRING

1022 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UBXN4VCPP55072961
UBXN4FAF2Q96CS3825
UBXN4UBXN6Q9BZV1690
UBXN4UBQLN1Q9UMX0690
UBXN4CD3DP04234685
UBXN4UFD1Q92890657
UBXN4UBXN7O94888620
UBXN4UBE2G2P56554613
UBXN4SEL1LQ9UBV2597
UBXN4LRRC59Q96AG4579
UBXN4UBXN10Q96LJ8578
UBXN4FAF1Q9UNN5575
UBXN4UBXN8O00124553
UBXN4AMFRP26442553
UBXN4UBXN1Q04323549

IntAct

91 interactions, top by confidence:

ABTypeScore
UBXN4VCPpsi-mi:“MI:0915”(physical association)0.740
VCPUBXN4psi-mi:“MI:0914”(association)0.740
UBXN4VCPpsi-mi:“MI:2364”(proximity)0.740
VCPUBXN4psi-mi:“MI:2364”(proximity)0.740
UBXN4UBQLN1psi-mi:“MI:0915”(physical association)0.720
UBQLN1UBXN4psi-mi:“MI:0915”(physical association)0.720
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
VCPUBXN8psi-mi:“MI:0914”(association)0.690
UBXN4UBE4Apsi-mi:“MI:0914”(association)0.620
UBXN4UBE4Apsi-mi:“MI:0915”(physical association)0.620
IGF1RPIK3R2psi-mi:“MI:2364”(proximity)0.590
INSRPIK3R2psi-mi:“MI:2364”(proximity)0.570
UBQLN1UBXN4psi-mi:“MI:0915”(physical association)0.560
UBXN4UBQLN1psi-mi:“MI:0915”(physical association)0.560
GNGT1UBXN4psi-mi:“MI:0915”(physical association)0.560
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
ESR1ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (288): UBQLN1 (Two-hybrid), UBXN4 (Affinity Capture-MS), UBE4A (Affinity Capture-MS), UBXN4 (Affinity Capture-Western), UBXN4 (Affinity Capture-Western), PSMA6 (Affinity Capture-Western), ACTA2 (Affinity Capture-MS), VPS13A (Affinity Capture-MS), VPS13C (Affinity Capture-MS), IP6K1 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), UBE4A (Affinity Capture-MS), BCL11A (Affinity Capture-MS), DPP8 (Affinity Capture-MS), UBXN4 (Two-hybrid)

ESM2 similar proteins: E9PSK7, O12940, O35815, O43815, O48726, O55106, O60271, P04973, P09496, P35521, P54105, P54106, P54252, P54731, P70483, Q04753, Q05B58, Q15650, Q28678, Q3ZBU9, Q58A65, Q5EAE3, Q5R4I3, Q5R719, Q5RGJ6, Q5XIJ6, Q5ZKG8, Q61189, Q640W6, Q68FJ8, Q6DG43, Q6DKA1, Q6PGH0, Q8CFK2, Q8UVK2, Q924K2, Q92575, Q92994, Q96MW1, Q9CR27

Diamond homologs: E1BMF7, E1BY77, F1QFS9, P34631, P38237, P45974, P54201, P56399, P57075, Q04323, Q11119, Q28DG7, Q32KW2, Q3V3E1, Q3ZBU9, Q499N6, Q5BKP2, Q5HZY0, Q5R407, Q5R4I3, Q5XIR9, Q5ZJI9, Q6GL77, Q6GLV4, Q6IP50, Q6NXA9, Q7YTB0, Q8BGG7, Q8L6Y1, Q8TF42, Q8VCH8, Q8VDI7, Q922Y1, Q92575, Q92995, Q9BSL1, Q9BZV1, Q9TXH9, Q9VCE9, Q8H0T4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 82 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
Signaling by BRAF and RAF1 fusions514.2×6e-04
Autophagy512.4×9e-04
Macroautophagy59.6×2e-03

GO biological processes:

GO termPartnersFoldFDR
ERAD pathway1025.2×4e-09
macroautophagy516.7×3e-03
insulin receptor signaling pathway515.4×3e-03
axonogenesis511.2×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2627 predictions. Top by Δscore:

VariantEffectΔscore
2:135748261:TTACA:Tacceptor_loss1.0000
2:135748262:TACA:Tacceptor_loss1.0000
2:135748264:CA:Cacceptor_loss1.0000
2:135748265:A:AGacceptor_gain1.0000
2:135748265:A:Tacceptor_loss1.0000
2:135748266:G:GGacceptor_gain1.0000
2:135748365:AAAAG:Adonor_loss1.0000
2:135748366:AAAG:Adonor_loss1.0000
2:135748367:AAGG:Adonor_loss1.0000
2:135748368:AG:Adonor_loss1.0000
2:135748369:GGTT:Gdonor_loss1.0000
2:135748370:G:Cdonor_loss1.0000
2:135748371:T:Adonor_loss1.0000
2:135754129:T:Gacceptor_gain1.0000
2:135755511:GCCTA:Gacceptor_loss1.0000
2:135755512:CCTA:Cacceptor_loss1.0000
2:135755513:CTAG:Cacceptor_loss1.0000
2:135755514:TA:Tacceptor_loss1.0000
2:135755515:AGATG:Aacceptor_loss1.0000
2:135755516:G:Aacceptor_loss1.0000
2:135755687:AACAG:Adonor_loss1.0000
2:135755688:ACAG:Adonor_loss1.0000
2:135755689:CAG:Cdonor_loss1.0000
2:135755690:AG:Adonor_loss1.0000
2:135755691:GG:Gdonor_loss1.0000
2:135755692:G:GCdonor_loss1.0000
2:135755693:T:Adonor_loss1.0000
2:135761804:A:AGacceptor_gain1.0000
2:135761805:T:Gacceptor_gain1.0000
2:135761808:A:AGacceptor_gain1.0000

AlphaMissense

3326 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:135753556:T:CF68S1.000
2:135754182:A:CS80R1.000
2:135754184:T:AS80R1.000
2:135754184:T:GS80R1.000
2:135772424:G:CR276P1.000
2:135782858:T:AW500R1.000
2:135782858:T:CW500R1.000
2:135782860:G:CW500C1.000
2:135782860:G:TW500C1.000
2:135782863:T:AN501K1.000
2:135782863:T:GN501K1.000
2:135782864:G:AG502R1.000
2:135782864:G:CG502R1.000
2:135782865:G:AG502E1.000
2:135782865:G:TG502V1.000
2:135741936:T:AW3R0.999
2:135741936:T:CW3R0.999
2:135741961:C:AA11D0.999
2:135741964:T:AI12N0.999
2:135741973:C:AA15D0.999
2:135748302:T:AW40R0.999
2:135748302:T:CW40R0.999
2:135753555:T:CF68L0.999
2:135753556:T:GF68C0.999
2:135753557:T:AF68L0.999
2:135753557:T:GF68L0.999
2:135754177:C:AP78Q0.999
2:135754185:T:CF81L0.999
2:135754187:C:AF81L0.999
2:135754187:C:GF81L0.999

dbSNP variants (sampled 300 via entrez): RS1000004143 (2:135778746 C>T), RS1000059371 (2:135748734 A>T), RS1000096397 (2:135748019 G>A,T), RS1000213057 (2:135775116 T>A), RS1000262679 (2:135759281 T>A,G), RS1000267044 (2:135759592 C>A), RS1000392589 (2:135765904 G>C,T), RS1000464306 (2:135783933 G>A), RS1000464365 (2:135750453 C>G), RS1000495560 (2:135750146 A>T), RS1000516104 (2:135784283 A>G), RS1000569486 (2:135741062 A>G), RS1000620002 (2:135743297 T>C), RS1000695474 (2:135746679 G>A,C), RS1000793076 (2:135753815 A>C)

Disease associations

OMIM: gene MIM:611216 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST001261_4Corneal structure1.000000e-06
GCST005951_44Body mass index1.000000e-09
GCST007576_42Chronotype5.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008328chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066308 (SINGLE PROTEIN)

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

ChEMBL bioactivities

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

pChemblTypeValueUnitMolecule
5.28Kd5251nMCHEMBL5653589
5.28ED505251nMCHEMBL5653589

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]benzamide2149720: Binding affinity to human UBXN4 incubated for 45 mins by Kinobead based pull down assaykd5.2510uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Sdecreases methylation, increases expression2
Valproic Acidaffects expression, decreases expression2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
dicrotophosdecreases expression1
lasiocarpinedecreases expression1
propionaldehydeincreases methylation1
bisphenol Aincreases expression1
nonanalincreases methylation1
n-hexanalincreases methylation1
trichostatin Aaffects expression1
beta-lapachoneincreases expression1
sodium arseniteincreases expression1
butyraldehydeincreases methylation1
caprylic aldehydeincreases methylation1
pentanalincreases methylation1
heptanalincreases methylation1
di-n-butylphosphoric acidaffects expression1
torcetrapibincreases expression1
bisphenol Bincreases expression1
ON 01910increases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-olincreases expression1
bisphenol AFincreases expression1
Bortezomibincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Vorinostatdecreases expression1
Acetaminophenincreases expression1
Benzo(a)pyreneincreases methylation1
Caffeineincreases phosphorylation1
Endosulfandecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652762BindingBinding affinity to human UBXN4 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

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2KCAbcam HeLa UBXN4 KOCancer cell lineFemale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): keratoconus