UBXN10

Summary

UBXN10 (UBX domain protein 10, HGNC:26354) is a protein-coding gene on chromosome 1p36.12, encoding UBX domain-containing protein 10 (Q96LJ8). VCP/p97-binding protein required for ciliogenesis.

Predicted to enable ubiquitin binding activity. Involved in cilium assembly. Located in cilium and intraciliary transport particle B.

Source: NCBI Gene 127733 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 50 total — 1 likely-pathogenic
• MANE Select transcript: NM_152376

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26354
Approved symbol	UBXN10
Name	UBX domain protein 10
Location	1p36.12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25429
Ensembl gene	ENSG00000162543
Ensembl biotype	protein_coding
OMIM	616783
Entrez	127733

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000375099, ENST00000866634, ENST00000866635, ENST00000866636, ENST00000957008, ENST00000957009

RefSeq mRNA: 1 — MANE Select: NM_152376 NM_152376

CCDS: CCDS205

Canonical transcript exons

ENST00000375099 — 2 exons

Exon	Start	End
ENSE00003994378	20190547	20196050
ENSE00003994379	20186096	20186153

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 96.74.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1258 / max 196.4363, expressed in 472 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1109	2.0616	464
1110	0.0311	9
1108	0.0181	5
1111	0.0150	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	96.74	gold quality
right uterine tube	UBERON:0001302	96.36	gold quality
bronchus	UBERON:0002185	95.46	gold quality
sperm	CL:0000019	95.44	gold quality
pancreatic ductal cell	CL:0002079	92.00	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.13	gold quality
oviduct epithelium	UBERON:0004804	89.89	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.34	gold quality
nasal cavity epithelium	UBERON:0005384	87.91	gold quality
epithelium of nasopharynx	UBERON:0001951	85.32	gold quality
fallopian tube	UBERON:0003889	84.98	gold quality
epithelial cell of pancreas	CL:0000083	83.61	silver quality
caput epididymis	UBERON:0004358	81.71	gold quality
endothelial cell	CL:0000115	81.12	silver quality
left ventricle myocardium	UBERON:0006566	79.72	gold quality
muscle layer of sigmoid colon	UBERON:0035805	79.45	gold quality
kidney epithelium	UBERON:0004819	79.34	gold quality
nasal cavity mucosa	UBERON:0001826	78.16	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.67	gold quality
lower esophagus	UBERON:0013473	77.56	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.00	gold quality
medial globus pallidus	UBERON:0002477	76.98	gold quality
tibialis anterior	UBERON:0001385	76.79	silver quality
left testis	UBERON:0004533	76.50	gold quality
testis	UBERON:0000473	76.26	gold quality
right testis	UBERON:0004534	76.09	gold quality
globus pallidus	UBERON:0001875	75.64	gold quality
germinal epithelium of ovary	UBERON:0001304	75.57	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	75.28	gold quality
rectum	UBERON:0001052	74.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

158 targeting UBXN10, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-4320	99.75	65.80	793
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741

Literature-anchored findings (GeneRIF, showing 1)

• Data show that UBXN10 localizes to cilia in a AAA-ATPase VCP-dependent manner and both VCP and UBXN10 are required for ciliogenesis. (PMID:26389662)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ubxn10	ENSDARG00000052535
mus_musculus	Ubxn10	ENSMUSG00000043621
rattus_norvegicus	Ubxn10	ENSRNOG00000027731

Paralogs (4): UBXN8 (ENSG00000104691), FAF2 (ENSG00000113194), UBXN7 (ENSG00000163960), FAF1 (ENSG00000185104)

Protein

Protein identifiers

UBX domain-containing protein 10 — Q96LJ8 (reviewed: Q96LJ8)

Alternative names: UBX domain-containing protein 3

All UniProt accessions (1): Q96LJ8

UniProt curated annotations — full annotation on UniProt →

Function. VCP/p97-binding protein required for ciliogenesis. Acts as a tethering factor that facilitates recruitment of VCP/p97 to the intraflagellar transport complex B (IFT-B) in cilia. UBX domain-containing proteins act as tethering factors for VCP/p97 and may specify substrate specificity of VCP/p97.

Subunit / interactions. Interacts with CLUAP1; the interaction is direct and mediates interaction with the intraflagellar transport complex B (IFT-B). Interacts with VCP; the interaction is direct.

Subcellular location. Cell projection. Cilium.

Similarity. Belongs to the UBXN10 family.

RefSeq proteins (1): NP_689589* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001012	UBX_dom	Domain
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily

Pfam: PF00789

UniProt features (9 total): mutagenesis site 5, chain 1, domain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96LJ8-F1	69.04	0.30

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): 87

Mutagenesis-validated functional residues (5):

Position	Phenotype
244	reduced interaction with vcp.
245	reduced interaction with vcp.
246	reduced interaction with vcp.
247	reduced interaction with vcp.
248	reduced interaction with vcp.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 156 (showing top): RNGTGGGC_UNKNOWN, RRAGTTGT_UNKNOWN, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, AP1_01, WANG_CLIM2_TARGETS_UP, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, NKX25_02, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, AREB6_01, TAL1ALPHAE47_01, AAAYRNCTG_UNKNOWN, USF_C, EVI1_05, MYOD_01

GO Biological Process (3): ERAD pathway (GO:0036503), cilium assembly (GO:0060271), cell projection organization (GO:0030030)

GO Molecular Function (2): ubiquitin binding (GO:0043130), protein binding (GO:0005515)

GO Cellular Component (4): endoplasmic reticulum (GO:0005783), cilium (GO:0005929), intraciliary transport particle B (GO:0030992), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intraciliary transport particle	2
proteasomal protein catabolic process	1
response to endoplasmic reticulum stress	1
response to chemical	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
cellular component organization	1
ubiquitin-like protein binding	1
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
protein-containing complex	1
cellular anatomical structure	1

Protein interactions and networks

STRING

464 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBXN10	UBXN2A	P68543	666
UBXN10	UBXN1	Q04323	662
UBXN10	UBXN7	O94888	648
UBXN10	UBXN6	Q9BZV1	645
UBXN10	UBXN11	Q5T124	643
UBXN10	UBXN2B	Q14CS0	625
UBXN10	UBXN8	O00124	624
UBXN10	IFT38	Q96AJ1	621
UBXN10	UBXN4	Q92575	578
UBXN10	FAF1	Q9UNN5	562
UBXN10	FAF2	Q96CS3	525
UBXN10	OR10G6	Q8NH81	517
UBXN10	NSFL1C	Q9UNZ2	489
UBXN10	ASPSCR1	Q9BZE9	480
UBXN10	VCP	P55072	435

IntAct

15 interactions, top by confidence:

A	B	Type	Score
UBXN10	VCP	psi-mi:“MI:0914”(association)	0.600
UBXN10	VCP	psi-mi:“MI:2364”(proximity)	0.600
VCP	UBXN10	psi-mi:“MI:2364”(proximity)	0.600
UBXN10	VCP	psi-mi:“MI:0915”(physical association)	0.600
UBXN10	UBXN6	psi-mi:“MI:0915”(physical association)	0.560
UBXN10	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
	UBXN10	psi-mi:“MI:0407”(direct interaction)	0.440
Ogn	UBXN10	psi-mi:“MI:0407”(direct interaction)	0.440
PRMT6	UBXN10	psi-mi:“MI:0915”(physical association)	0.370
UBXN10	UBXN6	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (64): UBXN10 (Affinity Capture-Western), UBXN10 (Affinity Capture-Western), UBXN10 (Affinity Capture-MS), UBXN10 (Affinity Capture-MS), UBXN10 (Affinity Capture-MS), WDR45B (Affinity Capture-Western), IFT81 (Affinity Capture-Western), UNC13B (Affinity Capture-Western), UBXN10 (Reconstituted Complex), UBXN10 (Reconstituted Complex), UBXN10 (Reconstituted Complex), UBXN10 (Reconstituted Complex), UBXN10 (Reconstituted Complex), UBXN10 (Reconstituted Complex), UBXN10 (Reconstituted Complex)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A2AGB2, A2ALV5, A3KMW7, A6NM62, A8MT70, A9JRX0, D3Z987, P15975, P56716, P70347, Q0P5X5, Q0VET5, Q28FY7, Q2M2Z5, Q3MHT3, Q3U0P1, Q3U3V8, Q3UXL4, Q3V089, Q5SXH7, Q5T1N1, Q5T4T6, Q5VXU9, Q68CR7, Q6NZK5, Q6P2D8, Q7M6U3, Q7Z4H7, Q7Z572, Q7ZYI3, Q7ZZH7, Q80VP2, Q86T90, Q86YC2, Q8BG34, Q8BL06, Q8CCC3, Q8MJ03

Diamond homologs: Q0P3Z8, Q8BG34, Q96LJ8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	41
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2685031	GRCh37/hg19 1p36.13-36.12(chr1:17291707-23016395)x4	Likely pathogenic

SpliceAI

338 predictions. Top by Δscore:

Variant	Effect	Δscore
1:20186149:GC:G	donor_gain	0.9900
1:20186150:C:G	donor_gain	0.9900
1:20186150:CTAG:C	donor_loss	0.9900
1:20186151:TAGGT:T	donor_loss	0.9900
1:20186152:AGG:A	donor_loss	0.9900
1:20186154:GTGAG:G	donor_loss	0.9900
1:20186155:T:A	donor_loss	0.9900
1:20186154:G:GG	donor_gain	0.9600
1:20186149:GCTAG:G	donor_gain	0.9500
1:20186379:C:G	donor_gain	0.9300
1:20186335:C:T	donor_gain	0.9200
1:20186479:G:GT	donor_gain	0.9200
1:20187261:GTT:G	donor_gain	0.9100
1:20187262:TTT:T	donor_gain	0.9100
1:20195193:A:AG	acceptor_gain	0.9000
1:20195194:G:GG	acceptor_gain	0.9000
1:20186303:C:T	donor_gain	0.8900
1:20186550:G:GT	donor_gain	0.8900
1:20191638:C:T	donor_gain	0.8800
1:20186206:G:GT	donor_gain	0.8600
1:20186403:GGACC:G	donor_gain	0.8600
1:20186468:G:GT	donor_gain	0.8600
1:20195194:GTTTA:G	acceptor_gain	0.8500
1:20186340:C:T	donor_gain	0.8400
1:20190545:AGG:A	acceptor_gain	0.8400
1:20190546:GGG:G	acceptor_gain	0.8400
1:20186156:G:GT	donor_loss	0.8200
1:20186369:AATAG:A	donor_gain	0.8100
1:20186378:A:AG	donor_gain	0.8100
1:20191651:T:TA	donor_gain	0.7900

AlphaMissense

1813 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:20191205:T:C	F215S	0.996
1:20191169:T:A	V203D	0.995
1:20191223:T:C	L221S	0.995
1:20191204:T:C	F215L	0.993
1:20191206:C:A	F215L	0.993
1:20191206:C:G	F215L	0.993
1:20191349:T:C	I263T	0.991
1:20191244:C:A	A228D	0.990
1:20191373:T:C	I271T	0.990
1:20191163:T:A	L201H	0.989
1:20191313:T:C	F251S	0.989
1:20191166:C:A	A202D	0.988
1:20191312:T:C	F251L	0.987
1:20191314:T:A	F251L	0.987
1:20191314:T:G	F251L	0.987
1:20191334:T:A	L258Q	0.987
1:20190902:A:G	Y114C	0.985
1:20190908:T:A	V116D	0.985
1:20191360:T:C	S267P	0.985
1:20190675:G:C	R38S	0.984
1:20190675:G:T	R38S	0.984
1:20190690:G:C	K43N	0.984
1:20190690:G:T	K43N	0.984
1:20190901:T:C	Y114H	0.984
1:20191243:G:C	A228P	0.984
1:20190902:A:C	Y114S	0.983
1:20191205:T:G	F215C	0.983
1:20191283:T:A	I241N	0.983
1:20190681:G:C	K40N	0.982
1:20190681:G:T	K40N	0.982

dbSNP variants (sampled 300 via entrez): RS1000058678 (1:20182799 A>G), RS1000301523 (1:20191765 G>A), RS1000417359 (1:20192157 G>A), RS1000616421 (1:20190012 C>T), RS1000644567 (1:20184118 G>A), RS1000653706 (1:20190265 C>T), RS1000750045 (1:20190472 G>A,T), RS1000876372 (1:20195115 G>A), RS1000931781 (1:20183667 G>C), RS1001717750 (1:20185977 C>G,T), RS1001765560 (1:20185655 C>G), RS1001775261 (1:20183906 T>C), RS1002152818 (1:20184362 A>G), RS1002196366 (1:20195833 A>G), RS1002228999 (1:20195618 A>G)

Disease associations

OMIM: gene MIM:616783 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008260_11	Group IIA secretory phospholipase A2 levels in individuals with elevated hsCRP	1.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
sodium arsenite	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
obeticholic acid	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Amiodarone	increases expression	1
Arsenic	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	increases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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