UBTD2

Summary

UBTD2 (ubiquitin domain containing 2, HGNC:24463) is a protein-coding gene on chromosome 5q35.1, encoding Ubiquitin domain-containing protein 2 (Q8WUN7).

Predicted to be located in cytoplasm.

Source: NCBI Gene 92181 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_152277

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24463
Approved symbol	UBTD2
Name	ubiquitin domain containing 2
Location	5q35.1
Locus type	gene with protein product
Status	Approved
Aliases	DC-UbP, MGC30022
Ensembl gene	ENSG00000168246
Ensembl biotype	protein_coding
OMIM	610174
Entrez	92181

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000393792, ENST00000901619, ENST00000901620, ENST00000901621, ENST00000931717, ENST00000931718

RefSeq mRNA: 1 — MANE Select: NM_152277 NM_152277

CCDS: CCDS4379

Canonical transcript exons

ENST00000393792 — 3 exons

Exon	Start	End
ENSE00001226299	172209646	172212227
ENSE00001653344	172234122	172234358
ENSE00001728104	172283596	172283764

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 97.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.7195 / max 440.4307, expressed in 1746 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64860	10.3983	1714
64862	4.8345	1571
64861	0.4867	235

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.17	gold quality
tibia	UBERON:0000979	96.79	gold quality
cortical plate	UBERON:0005343	96.45	gold quality
visceral pleura	UBERON:0002401	96.10	gold quality
ganglionic eminence	UBERON:0004023	96.09	gold quality
parietal pleura	UBERON:0002400	96.02	gold quality
cardiac muscle of right atrium	UBERON:0003379	95.90	silver quality
cartilage tissue	UBERON:0002418	95.84	gold quality
germinal epithelium of ovary	UBERON:0001304	95.20	gold quality
ileal mucosa	UBERON:0000331	95.08	gold quality
amniotic fluid	UBERON:0000173	94.94	gold quality
oviduct epithelium	UBERON:0004804	94.82	gold quality
left ventricle myocardium	UBERON:0006566	94.74	silver quality
ventricular zone	UBERON:0003053	94.24	gold quality
cerebellar vermis	UBERON:0004720	94.07	gold quality
tibialis anterior	UBERON:0001385	93.35	silver quality
right testis	UBERON:0004534	93.34	gold quality
palpebral conjunctiva	UBERON:0001812	93.24	gold quality
left testis	UBERON:0004533	93.00	gold quality
epithelial cell of pancreas	CL:0000083	92.71	gold quality
endometrium	UBERON:0001295	92.11	gold quality
synovial joint	UBERON:0002217	92.11	gold quality
testis	UBERON:0000473	92.04	gold quality
jejunal mucosa	UBERON:0000399	91.97	gold quality
tendon of biceps brachii	UBERON:0008188	91.96	gold quality
cerebellum	UBERON:0002037	90.98	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.83	gold quality
oocyte	CL:0000023	90.60	gold quality
cerebellar cortex	UBERON:0002129	90.60	gold quality
gingival epithelium	UBERON:0001949	90.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

170 targeting UBTD2, 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-4795-3P	100.00	74.62	4024
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-12136	99.98	72.81	5713
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-1297	99.91	73.41	3162

Literature-anchored findings (GeneRIF, showing 4)

• cloning and identification; DC-UbP might be downregulated during cellular differentiation and apoptosis (PMID:12507522)
• Solution NMR structure of the ubiquitin-like domain of DC-UbP is very similar to that of ubiquitin despite low similarity (<30%) in amino-acid sequence. (PMID:15987890)
• The results show that DC-UbP_N holds a novel structural fold and acts as a Ub-binding domain (UBD) but with low affinity. (PMID:20440844)
• A ubiquitin shuttle DC-UbP reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes. (PMID:25207809)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ubtd2	ENSDARG00000069184
mus_musculus	Ubtd2	ENSMUSG00000044949
rattus_norvegicus	Ubtd2	ENSRNOG00000004137
drosophila_melanogaster	CG1172	FBGN0264712

Paralogs (1): UBTD1 (ENSG00000165886)

Protein

Protein identifiers

Ubiquitin domain-containing protein 2 — Q8WUN7 (reviewed: Q8WUN7)

Alternative names: Dendritic cell-derived ubiquitin-like protein, Ubiquitin-like protein SB72

All UniProt accessions (1): Q8WUN7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Detected in dendritic cells. Highly expressed in tumor cell lines, but not detectable in most tissues.

RefSeq proteins (1): NP_689490* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000626	Ubiquitin-like_dom	Domain
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR032752	DC-UbP/UBTD2_N	Domain
IPR038169	DC-UbP/UBTD2_N_sf	Homologous_superfamily
IPR039869	UBTD1/2	Family

Pfam: PF00240, PF16455

UniProt features (24 total): strand 8, helix 6, turn 4, compositionally biased region 2, chain 1, domain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
1TTN	SOLUTION NMR
2KSN	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WUN7-F1	71.30	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): GCACCTT_MIR18A_MIR18B, TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP, KIM_GERMINAL_CENTER_T_HELPER_UP, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, CHEN_METABOLIC_SYNDROM_NETWORK, GAGCCAG_MIR149, JOHNSTONE_PARVB_TARGETS_2_DN, CAMP_UP.V1_DN, DACH1_TARGET_GENES, KLF7_TARGET_GENES, PITX1_TARGET_GENES, ZNF512_TARGET_GENES, MIR607, MIR6835_3P, MIR545_3P

GO Biological Process (0):

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

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

282 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBTD2	C5orf58	C9J3I9	520
UBTD2	FBXW11	Q9UKB1	483
UBTD2	TM2D1	Q9BX74	460
UBTD2	SLC66A1LP	A1A4F0	447
UBTD2	C2CD2	Q9Y426	416
UBTD2	EFCAB9	A8MZ26	398
UBTD2	GPR52	Q9Y2T5	397
UBTD2	OGFRL1	Q5TC84	396
UBTD2	SVIP	Q8NHG7	395
UBTD2	CIBAR1	A1XBS5	391
UBTD2	DENND11	A4D1U4	387
UBTD2	ENDOD1	O94919	381
UBTD2	SH3PXD2B	A1X283	376
UBTD2	ELP2	Q6IA86	370
UBTD2	PABPC5	Q96DU9	351

IntAct

53 interactions, top by confidence:

A	B	Type	Score
GALT	UBTD2	psi-mi:“MI:0915”(physical association)	0.770
UBTD2	GALT	psi-mi:“MI:0915”(physical association)	0.770
UBTD2	MVP	psi-mi:“MI:0915”(physical association)	0.560
AQP6	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
ARID5A	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
GPS2	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
KLHL35	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
UBTD2	TRIB3	psi-mi:“MI:0915”(physical association)	0.560
RNF4	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
INCA1	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
UBTD2	MRPL17	psi-mi:“MI:0915”(physical association)	0.560
UBTD2	UBE2D4	psi-mi:“MI:0915”(physical association)	0.560
MVP	UBTD2	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	VPS37C	psi-mi:“MI:0914”(association)	0.530
GJB7	PALM3	psi-mi:“MI:0914”(association)	0.530
TMEM185A	TSPAN6	psi-mi:“MI:0914”(association)	0.530
UBTD2	CST4	psi-mi:“MI:0914”(association)	0.530
TRIM39	UBTD2	psi-mi:“MI:0915”(physical association)	0.370
ECE1	UBTD2	psi-mi:“MI:0915”(physical association)	0.370
UBTD2	ECE1	psi-mi:“MI:0915”(physical association)	0.370
DUSP22	POTEF	psi-mi:“MI:0914”(association)	0.350
PCDHGC3	HRAS	psi-mi:“MI:0914”(association)	0.350
ZDHHC23	VPS37C	psi-mi:“MI:0914”(association)	0.350

BioGRID (51): UBA1 (Affinity Capture-MS), USP5 (Affinity Capture-MS), UBC (Affinity Capture-MS), UBA1 (Affinity Capture-Western), USP5 (Affinity Capture-Western), UBA1 (Co-crystal Structure), USP5 (Co-crystal Structure), UBA1 (Reconstituted Complex), USP5 (Reconstituted Complex), UBTD2 (Affinity Capture-Western), UBTD2 (Two-hybrid), UBC (Affinity Capture-Western), GALT (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST4 (Affinity Capture-MS)

ESM2 similar proteins: A0JN39, A0MT11, A1Z3X3, A4GWN3, A4QNE0, A5PK00, D2SW95, F1LNJ2, O35841, O60763, O75643, P0C0A2, P23514, P41541, P49754, P53618, Q0JNK5, Q2YDI2, Q53PC7, Q5EAE3, Q5KU39, Q5R922, Q5RJU0, Q5RK19, Q5U3V9, Q5ZIA5, Q5ZKG8, Q640W6, Q66HV4, Q6DDF4, Q6GLK9, Q6NRL4, Q6P4T2, Q7ZVK4, Q80UM3, Q86VN1, Q8BHL5, Q8K2G4, Q8RWF0, Q8WUN7

Diamond homologs: P0C032, Q05120, Q3ZBQ1, Q4V8W7, Q54XV3, Q5EAE3, Q640W6, Q68FV8, Q6DG43, Q6GL38, Q6PGH0, Q8WUN7, Q91WB7, Q9HAC8, Q9HDW4, Q03919, Q8RUC6, P29595, Q15843, Q54L35, Q71UE8, Q93725

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1321 predictions. Top by Δscore:

Variant	Effect	Δscore
5:172212232:A:T	acceptor_gain	1.0000
5:172234355:GCAA:G	acceptor_gain	1.0000
5:172234356:CAA:C	acceptor_gain	1.0000
5:172234356:CAAC:C	acceptor_gain	1.0000
5:172234357:AA:A	acceptor_gain	1.0000
5:172234359:C:CC	acceptor_gain	1.0000
5:172212224:GCAC:G	acceptor_gain	0.9900
5:172212225:CAC:C	acceptor_gain	0.9900
5:172212225:CACC:C	acceptor_gain	0.9900
5:172212228:C:CC	acceptor_gain	0.9900
5:172212231:C:CT	acceptor_gain	0.9900
5:172234115:AACCT:A	donor_loss	0.9900
5:172234116:ACCT:A	donor_loss	0.9900
5:172234117:CCTAC:C	donor_loss	0.9900
5:172234118:CTA:C	donor_loss	0.9900
5:172234119:TAC:T	donor_loss	0.9900
5:172234120:ACCA:A	donor_loss	0.9900
5:172234121:C:G	donor_loss	0.9900
5:172234354:AGCAA:A	acceptor_gain	0.9900
5:172272348:C:CT	donor_gain	0.9900
5:172272349:T:TT	donor_gain	0.9900
5:172283595:C:CA	donor_loss	0.9900
5:172212226:AC:A	acceptor_gain	0.9800
5:172212227:CC:C	acceptor_gain	0.9800
5:172234227:T:A	donor_gain	0.9800
5:172283339:C:A	donor_gain	0.9800
5:172212223:TGCAC:T	acceptor_gain	0.9700
5:172212228:C:T	acceptor_gain	0.9700
5:172234120:A:AC	donor_gain	0.9700
5:172234121:C:CC	donor_gain	0.9700

AlphaMissense

1551 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:172211955:A:G	W194R	1.000
5:172211955:A:T	W194R	1.000
5:172212158:G:T	P126Q	1.000
5:172212189:A:C	Y116D	1.000
5:172212189:A:G	Y116H	1.000
5:172212197:C:A	G113V	1.000
5:172212197:C:T	G113E	1.000
5:172212198:C:A	G113W	1.000
5:172212198:C:G	G113R	1.000
5:172212198:C:T	G113R	1.000
5:172212206:T:A	D110V	1.000
5:172212206:T:G	D110A	1.000
5:172212207:C:G	D110H	1.000
5:172234136:A:C	I98R	1.000
5:172234136:A:T	I98K	1.000
5:172234154:A:C	I92S	1.000
5:172234154:A:T	I92N	1.000
5:172234158:C:G	A91P	1.000
5:172234199:G:T	A77D	1.000
5:172234208:A:C	L74W	1.000
5:172234208:A:G	L74S	1.000
5:172234211:G:T	A73D	1.000
5:172234216:C:A	W71C	1.000
5:172234216:C:G	W71C	1.000
5:172234217:C:G	W71S	1.000
5:172234218:A:G	W71R	1.000
5:172234218:A:T	W71R	1.000
5:172234232:C:A	G66V	1.000
5:172234232:C:T	G66D	1.000
5:172234233:C:G	G66R	1.000

dbSNP variants (sampled 300 via entrez): RS1000014923 (5:172285171 G>A), RS1000044577 (5:172217452 G>A), RS1000044931 (5:172247002 C>T), RS1000090845 (5:172257631 C>G,T), RS1000123292 (5:172210020 A>G), RS1000128927 (5:172266913 G>A,C), RS1000158422 (5:172256623 A>G), RS1000238792 (5:172270392 T>C), RS1000367752 (5:172217548 A>T), RS1000398528 (5:172246697 G>T), RS1000399910 (5:172224960 A>C), RS1000415507 (5:172240492 A>C,G), RS1000441650 (5:172257346 A>G), RS1000463971 (5:172263519 G>A), RS1000500488 (5:172281127 T>C)

Disease associations

OMIM: gene MIM:610174 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Tobacco Smoke Pollution	affects expression, decreases expression	2
Valproic Acid	affects expression, decreases methylation	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
monomethylarsonous acid	decreases expression	1
jinfukang	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	increases abundance, increases methylation	1
Estradiol	affects expression	1
Formaldehyde	decreases expression	1
Lead	affects expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Tretinoin	decreases expression	1
Cyclosporine	decreases expression	1
Asbestos, Serpentine	affects expression	1
Asbestos, Crocidolite	affects expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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