UBL4B

Summary

UBL4B (ubiquitin like 4B, HGNC:32309) is a protein-coding gene on chromosome 1p13.3, encoding Ubiquitin-like protein 4B (Q8N7F7).

Involved in positive regulation of protein targeting to mitochondrion. Predicted to be located in cytoplasm.

Source: NCBI Gene 164153 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 30 total
• MANE Select transcript: NM_203412

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32309
Approved symbol	UBL4B
Name	ubiquitin like 4B
Location	1p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25690
Ensembl gene	ENSG00000186150
Ensembl biotype	protein_coding
OMIM	611127
Entrez	164153

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000334179

RefSeq mRNA: 1 — MANE Select: NM_203412 NM_203412

CCDS: CCDS820

Canonical transcript exons

ENST00000334179 — 1 exons

Exon	Start	End
ENSE00001331233	110112443	110113947

Expression profiles

Bgee: expression breadth ubiquitous, 106 present calls, max score 95.71.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1632 / max 169.1569, expressed in 5 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4512	0.1422	5
4514	0.0094	3
4513	0.0082	3
4511	0.0034	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	95.71	gold quality
right testis	UBERON:0004534	95.44	gold quality
testis	UBERON:0000473	91.54	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.38	gold quality
cerebellar vermis	UBERON:0004720	68.77	gold quality
saphenous vein	UBERON:0007318	61.93	gold quality
subthalamic nucleus	UBERON:0001906	61.65	gold quality
inferior vagus X ganglion	UBERON:0005363	61.40	gold quality
ventral tegmental area	UBERON:0002691	61.39	gold quality
pericardium	UBERON:0002407	61.23	gold quality
dorsal plus ventral thalamus	UBERON:0001897	61.10	gold quality
nipple	UBERON:0002030	61.04	gold quality
thymus	UBERON:0002370	60.96	gold quality
pharyngeal mucosa	UBERON:0000355	60.76	gold quality
trachea	UBERON:0003126	60.70	gold quality
cardia of stomach	UBERON:0001162	60.67	gold quality
superior surface of tongue	UBERON:0007371	60.65	gold quality
synovial joint	UBERON:0002217	60.63	gold quality
trigeminal ganglion	UBERON:0001675	60.62	gold quality
pons	UBERON:0000988	60.58	gold quality
tongue	UBERON:0001723	60.57	gold quality
pylorus	UBERON:0001166	60.56	gold quality
substantia nigra pars reticulata	UBERON:0001966	60.56	gold quality
dorsal root ganglion	UBERON:0000044	60.54	gold quality
medulla oblongata	UBERON:0001896	60.54	gold quality
epithelium of nasopharynx	UBERON:0001951	60.50	gold quality
substantia nigra pars compacta	UBERON:0001965	60.50	gold quality
lateral globus pallidus	UBERON:0002476	60.41	gold quality
superior vestibular nucleus	UBERON:0007227	60.40	gold quality
body of tongue	UBERON:0011876	60.30	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	32.70
E-ANND-3	no	0.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting UBL4B, 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-10401-5P	99.99	65.79	948
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-622	98.99	66.48	1050
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-6827-5P	98.46	64.88	1256
HSA-MIR-5589-5P	98.34	64.82	1148
HSA-MIR-4736	97.96	65.89	1287
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-6783-5P	97.67	67.21	1528
HSA-MIR-2467-5P	97.36	67.71	991
HSA-MIR-939-5P	97.10	65.80	1579
HSA-MIR-500B-3P	96.49	65.40	1087
HSA-MIR-1343-5P	96.48	66.06	1506
HSA-MIR-6089	89.72	61.35	324

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ubl4b	ENSMUSG00000055891
rattus_norvegicus	Ubl4b	ENSRNOG00000070136

Paralogs (10): UBL4A (ENSG00000102178), NEDD8 (ENSG00000129559), RPS27A (ENSG00000143947), UBC (ENSG00000150991), UBB (ENSG00000170315), ZFAND4 (ENSG00000172671), ISG15 (ENSG00000187608), ANKUB1 (ENSG00000206199), UBD (ENSG00000213886), UBA52 (ENSG00000221983)

Protein

Protein identifiers

Ubiquitin-like protein 4B — Q8N7F7 (reviewed: Q8N7F7)

All UniProt accessions (1): Q8N7F7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Miscellaneous. May have arisen from retrotransposition of the X-linked UBL4A gene during mammalian evolution.

RefSeq proteins (1): NP_981957* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000626	Ubiquitin-like_dom	Domain
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR041421	Ubl4_C_TUGS	Domain
IPR043317	UBL4B	Family

Pfam: PF00240, PF17840

UniProt features (5 total): compositionally biased region 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7F7-F1	75.74	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 41 (showing top): GOBP_PROTEIN_TARGETING, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, EFC_Q6, WCTCNATGGY_UNKNOWN, GOBP_REGULATION_OF_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MITOCHONDRION, GOBP_PROTEIN_TARGETING_TO_MITOCHONDRION, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_POSITIVE_REGULATION_OF_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION, GOBP_REGULATION_OF_PROTEIN_TARGETING, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, GOBP_POSITIVE_REGULATION_OF_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MITOCHONDRION, MIR5003_3P, MIR3619_5P, MIR214_3P, MIR761

GO Biological Process (1): obsolete positive regulation of protein targeting to mitochondrion (GO:1903955)

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

2582 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBL4B	TEX15	Q9BXT5	927
UBL4B	SLC6A17	Q9H1V8	922
UBL4B	ALX3	O95076	825
UBL4B	ZFAND4	Q86XD8	548
UBL4B	RPL10L	Q96L21	500
UBL4B	DIRAS1	O95057	481
UBL4B	LRCH1	Q9Y2L9	477
UBL4B	SGTA	O43765	451
UBL4B	TMEM167B	Q9NRX6	448
UBL4B	LDLRAD2	Q5SZI1	447
UBL4B	MACO1	Q8N5G2	412
UBL4B	SGTB	Q96EQ0	411
UBL4B	DISP3	Q9P2K9	407
UBL4B	UTP14C	Q5TAP6	398
UBL4B	OR6C3	Q9NZP0	395

IntAct

25 interactions, top by confidence:

A	B	Type	Score
UBL4B	TRAF4	psi-mi:“MI:0915”(physical association)	0.780
TRAF4	UBL4B	psi-mi:“MI:0915”(physical association)	0.780
MEOX2	UBL4B	psi-mi:“MI:0915”(physical association)	0.560
BAG6	UBL4B	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	UBL4B	psi-mi:“MI:0915”(physical association)	0.560
UBL4B	IL36RN	psi-mi:“MI:0915”(physical association)	0.560
P		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
UBL4B	FECH	psi-mi:“MI:0914”(association)	0.350
UBL4B	UBL4A	psi-mi:“MI:0914”(association)	0.350
HRAS	IGKV2D-24	psi-mi:“MI:0914”(association)	0.350
UBL4B	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
IL36RN	UBL4B	psi-mi:“MI:0915”(physical association)	0.000
TRAF4	UBL4B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): UBL4B (Two-hybrid), UBL4B (Two-hybrid), UBL4B (Two-hybrid), UBL4B (Two-hybrid), GOLGA6L9 (Two-hybrid), BAG6 (Two-hybrid), AARSD1 (Affinity Capture-MS), ANKZF1 (Affinity Capture-MS), RNF126 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), GOLGA2 (Affinity Capture-MS), BAG6 (Affinity Capture-MS), GET4 (Affinity Capture-MS), FECH (Affinity Capture-MS), CLMN (Affinity Capture-MS)

ESM2 similar proteins: A0JNQ6, A6NC42, A6NGQ2, A6NGR9, A6QP75, A7E3N7, A9X185, E1BDF2, E9PGG2, F6SZT2, P0C7A0, P85965, Q06VW1, Q0ZFW8, Q14DK4, Q3UK37, Q3UV16, Q3ZBN4, Q400G9, Q4VXA5, Q587J8, Q5JSQ8, Q60953, Q60I26, Q60I27, Q6NUI2, Q6ZUX3, Q810I0, Q8BH06, Q8C0R7, Q8IWB1, Q8IWY9, Q8IYX4, Q8K4C2, Q8N6L0, Q8N7F7, Q8NCV1, Q8TE82, Q91WA6, Q95JV3

Diamond homologs: A4QND0, B0KWT6, B1MTV8, B2GV38, B2KIK3, B5X9S9, B5XFI8, B7NZQ9, B9DHA6, C1BGZ8, C1BHN7, C1BXU5, C3KHF2, P05759, P0C030, P0C031, P0C032, P0C073, P0C224, P0C273, P0CG68, P0CG70, P0CG73, P0CG83, P0CG84, P0CG85, P0CG86, P0CG87, P0CH04, P0CH05, P0CH06, P0CH07, P0CH08, P0CH09, P0CH10, P0CH11, P0CH27, P0CH28, P0CH32, P0CH33

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

171 predictions. Top by Δscore:

Variant	Effect	Δscore
1:110112775:G:GT	donor_gain	0.9500
1:110113056:G:GG	donor_gain	0.6700
1:110112907:A:G	donor_gain	0.5500
1:110112688:G:GT	donor_gain	0.5400
1:110113039:G:GT	donor_gain	0.5200
1:110113036:G:GT	donor_gain	0.4700
1:110113055:A:AG	donor_gain	0.4600
1:110113472:A:AG	acceptor_gain	0.4500
1:110113473:G:GG	acceptor_gain	0.4500
1:110113108:T:G	donor_gain	0.4400
1:110113193:A:T	donor_gain	0.4400
1:110112880:C:T	donor_gain	0.4300
1:110113108:T:TG	donor_gain	0.4100
1:110113120:T:A	donor_gain	0.4100
1:110113192:G:GT	donor_gain	0.4100
1:110113473:GACC:G	acceptor_gain	0.4100
1:110112984:G:GT	donor_gain	0.4000
1:110113051:GATCA:G	donor_gain	0.3900
1:110113085:C:G	donor_gain	0.3900
1:110113195:GGTT:G	donor_gain	0.3900
1:110113248:GA:G	donor_gain	0.3800
1:110113126:C:G	donor_gain	0.3700
1:110113153:G:GT	donor_gain	0.3700
1:110113280:TAGA:T	acceptor_gain	0.3700
1:110113281:AGAA:A	acceptor_gain	0.3700
1:110113282:GAAG:G	acceptor_gain	0.3700
1:110112640:GTGCC:G	donor_gain	0.3600
1:110112641:TGCCT:T	donor_gain	0.3600
1:110112642:GCCTG:G	donor_gain	0.3600
1:110113052:A:G	donor_gain	0.3600

AlphaMissense

1129 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:110112615:G:C	K27N	0.980
1:110112615:G:T	K27N	0.980
1:110112667:T:C	F45L	0.967
1:110112669:C:A	F45L	0.967
1:110112669:C:G	F45L	0.967
1:110112614:A:C	K27T	0.938
1:110112740:T:A	V69D	0.911
1:110112657:G:C	Q41H	0.910
1:110112657:G:T	Q41H	0.910
1:110112613:A:G	K27E	0.902
1:110112548:T:A	V5D	0.901
1:110112614:A:T	K27M	0.892
1:110112838:T:C	F102L	0.891
1:110112840:T:A	F102L	0.891
1:110112840:T:G	F102L	0.891
1:110112668:T:C	F45S	0.886
1:110112734:T:C	I67T	0.883
1:110112734:T:A	I67N	0.881
1:110112623:T:A	V30E	0.878
1:110112734:T:G	I67S	0.874
1:110112662:T:A	L43Q	0.868
1:110112716:T:A	I61N	0.860
1:110112701:T:A	L56H	0.855
1:110112602:T:A	V23E	0.853
1:110112805:T:A	W91R	0.840
1:110112805:T:C	W91R	0.840
1:110112807:G:C	W91C	0.833
1:110112807:G:T	W91C	0.833
1:110112875:T:C	L114P	0.832
1:110112662:T:C	L43P	0.814

dbSNP variants (sampled 300 via entrez): RS1000714329 (1:110110650 C>T), RS1001989186 (1:110112194 C>T), RS1002359466 (1:110111755 A>C,T), RS1002522023 (1:110111201 A>C), RS1002664868 (1:110110951 A>T), RS1003035220 (1:110114436 A>C), RS1003629321 (1:110113149 T>A), RS1004071817 (1:110112259 C>T), RS1004805325 (1:110111173 T>G), RS1005178090 (1:110110845 G>A,T), RS1005769739 (1:110112224 T>C), RS1005984703 (1:110111901 C>A,G), RS1006528220 (1:110113208 C>T), RS1007183056 (1:110113390 C>T), RS1007534414 (1:110114378 G>A)

Disease associations

OMIM: gene MIM:611127 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001524_21	Visceral adipose tissue/subcutaneous adipose tissue ratio	2.000000e-06
GCST006479_143	Diverticular disease	4.000000e-08
GCST010397_103	Gut microbiota (bacterial taxa, rank normal transformation method)	1.000000e-07
GCST010397_71	Gut microbiota (bacterial taxa, rank normal transformation method)	5.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004767	visceral:subcutaneous adipose tissue ratio
EFO:0009959	diverticular disease
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tebuconazole	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Diethylhexyl Phthalate	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Toluene	decreases methylation, increases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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