UBAP2

Summary

UBAP2 (ubiquitin associated protein 2, HGNC:14185) is a protein-coding gene on chromosome 9p13.3, encoding Ubiquitin-associated protein 2 (Q5T6F2). Recruits the ubiquitination machinery to RNA polymerase II for polyubiquitination, removal and degradation, when the transcription-coupled nucleotide excision repair (TC-NER) machinery fails to resolve DNA damage.

The protein encoded by this gene contains a UBA (ubiquitin associated) domain, which is characteristic of proteins that function in the ubiquitination pathway. This gene may show increased expression in the adrenal gland and lymphatic tissues. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 55833 — RefSeq curated summary.

At a glance

• GWAS associations: 19
• Clinical variants (ClinVar): 214 total
• GTEx eGene: eQTL in 18 tissues, sQTL in 27 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.62 (unconstrained)
• MANE Select transcript: NM_001370062
• Interaction hub: 2,296 STRING partners (top 5% of genes corpus-wide)
• Notable: 214 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14185
Approved symbol	UBAP2
Name	ubiquitin associated protein 2
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1491, bA176F3.5, FLJ22435
Ensembl gene	ENSG00000137073
Ensembl biotype	protein_coding
Entrez	55833

Gene structure

Transcript identifiers

Ensembl transcripts: 76 — 43 protein_coding, 23 nonsense_mediated_decay, 9 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000379238

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 5, TSL 5: 6

ENST00000379238, ENST00000360802, ENST00000379225, ENST00000379235, ENST00000379239, ENST00000412543, ENST00000421278, ENST00000459988, ENST00000474372, ENST00000480885, ENST00000488443, ENST00000629575, ENST00000681980, ENST00000682209, ENST00000682239, ENST00000682538, ENST00000682914, ENST00000682949, ENST00000683084, ENST00000683140, ENST00000683252, ENST00000683659, ENST00000683717, ENST00000684158, ENST00000684245, ENST00000684298, ENST00000684754, ENST00000862362, ENST00000862365, ENST00000862367, ENST00000862370, ENST00000862372, ENST00000862374, ENST00000862375, ENST00000862376, ENST00000862377, ENST00000862378, ENST00000862379, ENST00000862380, ENST00000862381, ENST00000862382, ENST00000862383, ENST00000932759, ENST00000932760, ENST00000932761, ENST00000932762, ENST00000932763, ENST00000932764, ENST00000932765, ENST00000932766, ENST00000932767, ENST00000956118, ENST00000956119, ENST00000956120, ENST00000956121, ENST00000956122, ENST00000956123, ENST00000956124, ENST00000956125, ENST00000956126, ENST00000956127, ENST00000956128, ENST00000978770, ENST00000978771, ENST00000978772, ENST00001057146, ENST00001057147, ENST00001057148, ENST00001083831, ENST00001083832, ENST00001083833, ENST00001083834, ENST00001083835, ENST00001083836, ENST00001083837, ENST00001139554

RefSeq mRNA: 9 — MANE Select: NM_001370062 NM_001282530, NM_001370059, NM_001370062, NM_001370064, NM_001370066, NM_001370067, NM_001370068, NM_018449, NM_020867

CCDS: CCDS6547, CCDS6548

Canonical transcript exons

ENST00000379238 — 29 exons

Exon	Start	End
ENSE00001240220	33971651	33971754
ENSE00001240227	33973183	33973237
ENSE00001600863	33923795	33924000
ENSE00001608706	33923186	33923293
ENSE00001613981	33935839	33935878
ENSE00001649881	33923379	33923478
ENSE00001671251	33922687	33922878
ENSE00001678758	33941649	33941862
ENSE00001722731	33956079	33956146
ENSE00001762000	33943420	33943589
ENSE00001796921	33922966	33923033
ENSE00002323532	33944365	33944639
ENSE00003458372	33926617	33926664
ENSE00003469731	33996223	33996333
ENSE00003488113	33926989	33927080
ENSE00003522024	33988973	33989126
ENSE00003547890	33927797	33927992
ENSE00003551018	33963726	33963791
ENSE00003575552	33953285	33953474
ENSE00003580211	33960826	33960878
ENSE00003619077	34017050	34017189
ENSE00003626574	33924206	33924284
ENSE00003632689	33932562	33932628
ENSE00003665963	33933490	33933628
ENSE00003693809	33986760	33986837
ENSE00003745226	33998787	33998864
ENSE00003790695	33948374	33948587
ENSE00003901232	34048825	34048887
ENSE00003903606	33921693	33922599

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 98.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.5323 / max 531.0837, expressed in 1805 samples.

Highest expression (Bgee): sperm, pancreatic ductal cell, male germ cell, cervix squamous epithelium, vastus lateralis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

UBAP2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 18 tissues and its splicing (sQTL) in 27 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 45 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Nerve Tibial	sqtl	9.0e-28	+0.85	9:33836348:A:G
Skin Sun Exposed Lower leg	sqtl	1.7e-22	-0.71	9:33971742:A:G
Skin Not Sun Exposed Suprapubic	sqtl	1.9e-22	-0.78	9:33840683:C:T
Thyroid	sqtl	1.0e-19	-0.72	9:33971742:A:G
Esophagus Muscularis	sqtl	2.3e-18	-0.79	9:33982520:G:A
Artery Tibial	sqtl	2.3e-17	-0.73	9:33841829:C:A
Adipose Subcutaneous	sqtl	2.8e-16	-0.68	9:33841829:C:A
Testis	sqtl	1.9e-15	-0.75	9:34051167:CAA:C
Cells Cultured fibroblasts	sqtl	3.0e-13	-0.62	9:33957942:G:T
Lung	sqtl	9.0e-12	-0.57	9:33978494:C:T
Adipose Visceral Omentum	sqtl	5.7e-10	-0.59	9:33957942:G:T
Colon Transverse	sqtl	1.4e-08	-0.67	9:33841829:C:A
Esophagus Gastroesophageal Junction	sqtl	1.7e-07	-0.69	9:34006052:G:A
Breast Mammary Tissue	sqtl	2.7e-07	-0.57	9:33841829:C:A
Muscle Skeletal	eqtl	2.2e-05	+0.23	9:33928076:A:AC
Muscle Skeletal	sqtl	3.6e-05	-0.50	9:33974413:C:T
Thyroid	eqtl	4.3e-05	-0.14	9:34082970:C:T
Adipose Subcutaneous	eqtl	5.8e-05	+0.70	9:34048856:T:TGCC
Pituitary	sqtl	6.1e-05	-0.62	9:33957942:G:T
Colon Sigmoid	sqtl	9.0e-05	-0.56	9:33853527:C:T

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
100484	28.8629	1805
100485	1.6695	936

Top tissues by expression

showing 100 of 288 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.13	gold quality
pancreatic ductal cell	CL:0002079	97.29	gold quality
male germ cell	CL:0000015	96.74	gold quality
cervix squamous epithelium	UBERON:0006922	95.08	gold quality
vastus lateralis	UBERON:0001379	94.90	gold quality
quadriceps femoris	UBERON:0001377	94.87	gold quality
tongue squamous epithelium	UBERON:0006919	94.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.12	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.07	gold quality
secondary oocyte	CL:0000655	93.91	gold quality
calcaneal tendon	UBERON:0003701	93.86	gold quality
biceps brachii	UBERON:0001507	93.65	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.42	gold quality
skeletal muscle tissue	UBERON:0001134	93.39	gold quality
body of tongue	UBERON:0011876	93.20	gold quality
sural nerve	UBERON:0015488	93.12	gold quality
deltoid	UBERON:0001476	92.90	gold quality
adrenal tissue	UBERON:0018303	92.84	gold quality
colonic epithelium	UBERON:0000397	92.66	gold quality
pharyngeal mucosa	UBERON:0000355	92.63	gold quality
skin of hip	UBERON:0001554	92.40	gold quality
muscle organ	UBERON:0001630	92.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.39	gold quality
endothelial cell	CL:0000115	92.23	gold quality
tibialis anterior	UBERON:0001385	92.20	gold quality
nipple	UBERON:0002030	92.19	gold quality
gingival epithelium	UBERON:0001949	92.16	gold quality
adult organism	UBERON:0007023	92.14	gold quality
right testis	UBERON:0004534	92.12	gold quality
left testis	UBERON:0004533	92.10	gold quality
testis	UBERON:0000473	92.09	gold quality
squamous epithelium	UBERON:0006914	91.99	gold quality
mucosa of sigmoid colon	UBERON:0004993	91.90	gold quality
muscle of leg	UBERON:0001383	91.76	gold quality
renal glomerulus	UBERON:0000074	91.73	gold quality
muscle tissue	UBERON:0002385	91.73	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.73	gold quality
right adrenal gland cortex	UBERON:0035827	91.71	gold quality
metanephric glomerulus	UBERON:0004736	91.59	gold quality
tongue	UBERON:0001723	91.57	gold quality
gingiva	UBERON:0001828	91.52	gold quality
gastrocnemius	UBERON:0001388	91.42	gold quality
colonic mucosa	UBERON:0000317	91.40	gold quality
penis	UBERON:0000989	91.40	gold quality
mammalian vulva	UBERON:0000997	91.29	gold quality
right adrenal gland	UBERON:0001233	91.25	gold quality
gluteal muscle	UBERON:0002000	91.22	gold quality
triceps brachii	UBERON:0001509	91.07	gold quality
epithelium of esophagus	UBERON:0001976	91.01	gold quality
trabecular bone tissue	UBERON:0002483	90.92	gold quality
adrenal cortex	UBERON:0001235	90.85	gold quality
cardia of stomach	UBERON:0001162	90.79	gold quality
pylorus	UBERON:0001166	90.78	gold quality
visceral pleura	UBERON:0002401	90.68	gold quality
upper leg skin	UBERON:0004262	90.65	gold quality
adrenal gland	UBERON:0002369	90.61	gold quality
amniotic fluid	UBERON:0000173	90.55	gold quality
hair follicle	UBERON:0002073	90.55	gold quality
esophagus squamous epithelium	UBERON:0006920	90.53	gold quality
parotid gland	UBERON:0001831	90.36	gold quality
left adrenal gland	UBERON:0001234	90.30	gold quality
renal medulla	UBERON:0000362	90.28	gold quality
left adrenal gland cortex	UBERON:0035825	90.25	gold quality
nasal cavity epithelium	UBERON:0005384	90.24	gold quality
thymus	UBERON:0002370	90.21	gold quality
oral cavity	UBERON:0000167	90.19	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.16	gold quality
metanephros	UBERON:0000081	90.08	gold quality
cranial nerve II	UBERON:0000941	90.00	gold quality
bone marrow cell	CL:0002092	89.99	gold quality
superior surface of tongue	UBERON:0007371	89.95	gold quality
substantia nigra pars compacta	UBERON:0001965	89.94	gold quality
oocyte	CL:0000023	89.83	gold quality
trachea	UBERON:0003126	89.71	gold quality
dorsal root ganglion	UBERON:0000044	89.62	gold quality
tibia	UBERON:0000979	89.59	gold quality
placenta	UBERON:0001987	89.54	gold quality
lower esophagus mucosa	UBERON:0035834	89.51	gold quality
left ventricle myocardium	UBERON:0006566	89.50	gold quality
tonsil	UBERON:0002372	89.36	gold quality
cartilage tissue	UBERON:0002418	89.27	gold quality
palpebral conjunctiva	UBERON:0001812	89.10	gold quality
skin of leg	UBERON:0001511	89.05	gold quality
epithelium of mammary gland	UBERON:0003244	89.05	gold quality
zone of skin	UBERON:0000014	89.03	gold quality
choroid plexus epithelium	UBERON:0003911	88.87	gold quality
heart right ventricle	UBERON:0002080	88.82	gold quality
urethra	UBERON:0000057	88.65	gold quality
lower lobe of lung	UBERON:0008949	88.60	gold quality
mammary duct	UBERON:0001765	88.56	gold quality
pleura	UBERON:0000977	88.52	gold quality
trigeminal ganglion	UBERON:0001675	88.36	gold quality
kidney epithelium	UBERON:0004819	88.32	gold quality
skin of abdomen	UBERON:0001416	88.30	gold quality
saphenous vein	UBERON:0007318	88.26	gold quality
substantia nigra pars reticulata	UBERON:0001966	88.25	gold quality
uterine cervix	UBERON:0000002	88.24	gold quality
lateral nuclear group of thalamus	UBERON:0002736	88.14	gold quality
cauda epididymis	UBERON:0004360	88.14	gold quality
jejunum	UBERON:0002115	88.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Corpus callosum	tissue	37.0
Putamen	tissue	36.3
Spinal cord	tissue	32.3
Substantia nigra	tissue	31.6
Cerebral cortex	tissue	29.7	low
Motor cortex	tissue	29.7
Ventral forebrain	tissue	29.5
Prefrontal cortex	tissue	29.4
Skeletal muscle	tissue	29.4	medium
Insular cortex	tissue	28.3
Midbrain	tissue	27.6
Temporal cortex	tissue	27.6
Thalamus	tissue	27.4
Medulla oblongata	tissue	27.1
Pons	tissue	27.0
Hippocampal formation	tissue	27.0
Entorhinal cortex	tissue	26.5
Superior colliculi	tissue	26.4
Basal ganglia	tissue	26.3	low
Occipital cortex	tissue	26.3
Somatosensory cortex	tissue	25.5
Amygdala	tissue	25.4
Hypothalamus	tissue	24.7
Retrosplenial cortex	tissue	24.0
Retrosplenial and cingulate cortex	tissue	23.8
Septum	tissue	23.3
Postcentral gyrus	tissue	22.6
Periaqueductal gray	tissue	22.5
Cerebellum	tissue	20.9	low
Nucleus accumbens	tissue	20.7
Locus coeruleus	tissue	20.3
Frontal cortex	tissue	19.2
Choroid plexus	tissue	18.5
Hippocampus	tissue	18.3	low
Testis	tissue	17.2	low
Caudate putamen	tissue	16.4
Olfactory bulb	tissue	16.0
Tongue	tissue	15.6
Thymus	tissue	11.0
Adrenal gland	tissue	10.6	high
Skin 1	tissue	10.5	medium
Tonsil	tissue	10.3	high
Bone marrow	tissue	10.1	medium
Rectum	tissue	9.3	high
Placenta	tissue	9.3	medium
Ovary	tissue	8.9	low
Thyroid gland	tissue	8.6	low
Esophagus	tissue	8.5	medium
Colon	tissue	8.5	high
Heart muscle	tissue	8.1	medium
Parathyroid gland	tissue	8.0	low
Urinary bladder	tissue	7.9	medium
Smooth muscle	tissue	7.8	low
Duodenum	tissue	7.6	medium
Lung	tissue	7.5	low
Stomach 1	tissue	7.4	low
Lymph node	tissue	7.3	low
Pancreas	tissue	7.2	low
Breast	tissue	7.0	medium
Endometrium 1	tissue	7.0	medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — White matter (37.0), Orbitofrontal gyrus, anterior (34.0), Ventral spinal cord (32.3), Dorsal spinal cord (30.0), Cerebellar cortex (28.2).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting UBAP2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 36 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-549A-3P	99.54	68.17	825
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-548AO-5P	98.55	69.57	1362
HSA-MIR-548AX	98.55	69.58	1362
HSA-MIR-2117	98.48	67.97	1307
HSA-MIR-1910-3P	98.44	67.51	1695
HSA-MIR-6511A-5P	98.13	67.47	1770
HSA-MIR-4257	97.86	68.05	1190
HSA-MIR-4676-5P	97.54	65.29	715
HSA-MIR-575	97.54	65.18	718
HSA-MIR-4433B-3P	97.22	63.62	663
HSA-MIR-3192-5P	96.98	65.76	1926
HSA-MIR-3184-3P	96.96	66.91	845
HSA-MIR-1270	96.94	66.65	931
HSA-MIR-620	96.94	66.79	888
HSA-MIR-591	96.29	68.16	611

Functional genomics

gnomAD constraint: pLI 8.51e-08, LOEUF 0.625, missense Z 0.575 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000379238 — one region, missense o/e 1.00.

Literature-anchored findings (GeneRIF, showing 13)

• UBAP2 serves as a host gene for snoRNAs (PMID:19446021)
• By incorporating the information from bioinformatics and RNA expression analyses, we identified at least two of the most promising risk genes for alcohol dependence: APOER2 and UBAP2 (PMID:23739027)
• We found that the 9p13.3 amplification harbors several genes that are able to affect the growth of PC cells when downregulated using siRNA. Of these, UBAP2 was the most prominently upregulated gene in the clinical prostate tumor samples (PMID:27074291)
• UBAP2 formed a complex with Annexin A2 and promoted the degradation of Annexin A2 protein by ubiquitination, and then inhibited HCC progression. (PMID:27121050)
• Effect of Circular RNA UBAP2 Silencing on Proliferation and Invasion of Human Lung Cancer A549 Cells (PMID:29277177)
• The circ-UBAP2 plays a vital regulatory role in triple-negative breast cancer (TNBC) via the miR-661/MTA1 axis and may serve as a promising therapeutic target for TNBC patients. (PMID:30314706)
• circRNA-UBAP2 promotes the proliferation and inhibits apoptosis of ovarian cancer though miR-382-5p/PRPF8 axis. (PMID:32690086)
• Ubiquitin-binding associated protein 2 regulates KRAS activation and macropinocytosis in pancreatic cancer. (PMID:32692445)
• Circ-UBAP2 functions as sponges of miR-1205 and miR-382 to promote glioma progression by modulating STC1 expression. (PMID:33543830)
• Emerging roles of circUBAP2 targeting miR-370-3p in proliferation, apoptosis, and invasion of papillary thyroid cancer cells. (PMID:34346032)
• UBAP2/UBAP2L regulate UV-induced ubiquitylation of RNA polymerase II and are the human orthologues of yeast Def1. (PMID:35633597)
• PAICS ubiquitination recruits UBAP2 to trigger phase separation for purinosome assembly. (PMID:37848033)
• Novel Circular RNA CircUBAP2 Drives Tumor Progression by Regulating the miR-143/TFAP2B Axis in Prostate Cancer. (PMID:37962045)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	ubap2b	ENSDARG00000060065
danio_rerio	ubap2a	ENSDARG00000088318
mus_musculus	Ubap2	ENSMUSG00000028433
rattus_norvegicus	Ubap2	ENSRNOG00000052087
drosophila_melanogaster	lig	FBGN0020279
caenorhabditis_elegans	pqn-59	WBGENE00004143

Paralogs (1): UBAP2L (ENSG00000143569)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1916176) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 2 distinct phenotype terms.

Mouse phenotype (MP)	Records
hyperactivity	1
decreased blood urea nitrogen level	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Drosophila pseudoobscura pseudoobscura	Q290X3	67.4%	Diamond
Anopheles gambiae	Q7PMS9	63.7%	Diamond
Aedes aegypti	Q16VD3	55.1%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
SNORD121B	snoRNA	101340252
UBE2R2	protein-coding	54926
SNORD121A	snoRNA	100113379
DCAF12	protein-coding	25853
UBAP1	protein-coding	51271
UBE2R2-AS1	ncRNA	101929688
PRSS3	protein-coding	5646

Protein

Protein identifiers

Ubiquitin-associated protein 2 — Q5T6F2 (reviewed: Q5T6F2)

Alternative names: RNA polymerase II degradation factor UBAP2

All UniProt accessions (12): A0A0D9SFI5, A0A804HIK1, A0A804HIV8, A0A804HJY7, A0A804HLD2, A0A804HLJ4, A0A8C8KGQ8, A0A8C8MQ70, A2A305, Q5T6F2, H0YDN2, Q5JV08

UniProt curated annotations — full annotation on UniProt →

Function. Recruits the ubiquitination machinery to RNA polymerase II for polyubiquitination, removal and degradation, when the transcription-coupled nucleotide excision repair (TC-NER) machinery fails to resolve DNA damage. May promote the degradation of ANXA2.

Subunit / interactions. May interact with ANXA2.

Subcellular location. Nucleus. Chromosome. Cytoplasm.

Disease relevance. Reduced expression of UBAP2 correlates with hepatocellular carcinoma tumor progression.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5T6F2-1	1	yes
Q5T6F2-2	2

RefSeq proteins (9): NP_001269459, NP_001356988, NP_001356991, NP_001356993, NP_001356995, NP_001356996, NP_001356997, NP_060919, NP_065918 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009060	UBA-like_sf	Homologous_superfamily
IPR015940	UBA	Domain
IPR022166	UBAP2/Lig	Family
IPR051833	TC-DDR_regulator	Family
IPR060532	UBA_UBAP2	Domain

Pfam: PF12478, PF28540

UniProt features (35 total): compositionally biased region 13, region of interest 8, modified residue 5, sequence variant 5, chain 1, domain 1, coiled-coil region 1, splice variant 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T6F2-F1	43.47	0.03

Human Protein Atlas

Protein class: Predicted intracellular proteins, Disease related genes

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol

Antibody reliability (HPA): IH approved · IF approved

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 (5)

Type	Positions
Omega-n-methylarginine	166
Phosphoserine	432, 439, 473, 630

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 118 (showing top): CACCAGC_MIR138, GTGCCTT_MIR506, CAGCAGG_MIR370, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, BLALOCK_ALZHEIMERS_DISEASE_UP, chr9p13, LIAO_METASTASIS, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, TTGGAGA_MIR5155P_MIR519E, TCCAGAT_MIR5165P, CAIRO_HEPATOBLASTOMA_UP, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, LIAO_HAVE_SOX4_BINDING_SITES, AGTCAGC_MIR345, AGCGCAG_MIR191

GO Biological Process (2): regulation of gene expression (GO:0010468), hematopoietic stem cell homeostasis (GO:0061484)

GO Molecular Function (3): RNA binding (GO:0003723), cadherin binding (GO:0045296), protein binding (GO:0005515)

GO Cellular Component (4): P-body (GO:0000932), nucleus (GO:0005634), chromosome (GO:0005694), cytoplasm (GO:0005737)

GO top-level categories

11 GO namespaces:

Category	Terms
gene expression	1
regulation of macromolecule biosynthetic process	1
homeostasis of number of cells	1
nucleic acid binding	1
cell adhesion molecule binding	1
binding	1
cytoplasmic ribonucleoprotein granule	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 9 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO term	NS	Evidence
RNA binding	MF	high-throughput assay
cadherin binding	MF	high-throughput assay

Protein interactions and networks

STRING

showing 16 of 2,296 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBAP2	UBAP1	Q9NZ09	591
UBAP2	KCMF1	Q9P0J7	491
UBAP2	G3BP1	Q13283	484
UBAP2	BLTP3A	Q6BDS2	462
UBAP2	DCAF12	Q5T6F0	434
UBAP2	DPH6	Q7L8W6	429
UBAP2	RNF17	Q9BXT8	399
UBAP2	LARP1B	Q659C4	395
UBAP2	LSMEM2	Q8N112	373
UBAP2	HIPK3	Q9H422	369
UBAP2	KGD4	P82909	366
UBAP2	SHQ1	Q6PI26	366
UBAP2	DIP2C	Q9Y2E4	363
UBAP2	FAM240B	A0A1B0GVZ2	361
UBAP2	ITCH	Q96J02	361
UBAP2	ISCA1	Q9BUE6	361

IntAct

Human interaction partners of UBAP2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 45 partners by confidence:

Partner	Interaction type	MIscore	Records
ASB13	physical association	0.560	3
ATPAF2	physical association	0.560	3
BANP	physical association	0.560	3
C10orf55	physical association	0.560	3
CREM	physical association	0.560	3
DAZAP2	physical association	0.560	3
EFHC1	physical association	0.560	3
FAM168B	physical association	0.560	3
FNDC3B	physical association	0.560	3
FOXH1	physical association	0.560	3
HGS	physical association	0.560	3
IGFN1	physical association	0.560	3
ISX	physical association	0.560	3
JMJD7	physical association	0.560	3
KANK2	physical association	0.560	3
KRTAP15-1	physical association	0.560	3
LCK	physical association	0.560	3
NOXA1	physical association	0.560	3
NPAS2	physical association	0.560	3
NUTF2	physical association	0.560	3
OTX1	physical association	0.560	3
PLEKHB2	physical association	0.560	3
PPP2CA	physical association	0.560	3
PRSS53	physical association	0.560	3
PSMB8	physical association	0.560	3
RBPMS	physical association	0.560	3
RHOXF2	physical association	0.560	3
SHC3	physical association	0.560	3
SPAG8	physical association	0.560	3
SPMIP9	physical association	0.560	3

BioGRID (218 interactions; top human partners by supporting records): PAICS (Proximity Label-MS; 4 records), FXR1 (Proximity Label-MS; 3 records), BAG2 (Affinity Capture-MS; 2 records), G3BP1 (Affinity Capture-MS; 2 records), HAO2 (Affinity Capture-MS; 2 records), HSPA1A (Affinity Capture-MS; 2 records), PARK2 (Proximity Label-MS; 2 records), UBAP2L (Proximity Label-MS; 2 records), WWP2 (Affinity Capture-MS; 2 records), ZC3H7A (Proximity Label-MS; 2 records), ZC3HAV1 (Proximity Label-MS; 2 records), ADSL (Co-localization), AES (Two-hybrid), ANKRD17 (Proximity Label-MS), ASB13 (Two-hybrid)

SIGNOR signaling

1 signaling interactions:

A	Effect	B	Mechanism
UBAP2	“down-regulates quantity”	ANXA2	ubiquitination

Disease & clinical

Genetic variants

Variant evidence for UBAP2: 214 ClinVar records (0 pathogenic / likely pathogenic); 19 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	164
Likely benign	15
Benign	3

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 39 predictions of 2,895):

Position(s)	Effect	Δscore	Sites
9:33922879–33922880	acceptor_loss	1.0000	3
9:33922888	acceptor_gain	1.0000
9:33923294–33923295	acceptor_loss	1.0000	5
9:33923377–33923378	donor_loss	1.0000	5
9:33923479–33923480	acceptor_loss	1.0000	5
9:33924204–33924205	donor_loss	1.0000	5
9:33924285–33924286	acceptor_loss	1.0000	6
9:33941647–33941648	donor_loss	1.0000	5
9:33941863–33941864	acceptor_loss	1.0000	2
9:33948589–33948590	acceptor_gain	1.0000	2

AlphaMissense

1,234 missense substitutions predicted likely pathogenic (of 7,235 scored), across 373 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M523	9	0.904	0.994
F273	8	0.963	0.997
D77	8	0.962	0.988
F536	8	0.943	0.990
F925	8	0.883	0.977
F541	8	0.882	0.980
D69	8	0.864	0.973
D838	8	0.810	0.964
W99	7	0.992	0.999
F325	7	0.949	0.989
H76	7	0.943	0.997
W263	7	0.938	0.990
E91	7	0.920	0.975
D81	7	0.914	0.980
F932	7	0.907	0.980
F53	7	0.904	0.976
F869	7	0.896	0.982
W258	7	0.882	0.983
W1117	7	0.881	0.971
F1031	7	0.867	0.977

HPA cancer prognostics

RNA cancer specificity: Cancer enhanced (Testicular Germ Cell Tumor)

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	3.23e-10
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	3.59e-05
Lung Adenocarcinoma (validation)	unfavorable	3.89e-05
Liver Hepatocellular Carcinoma (validation)	unfavorable	0.000166

Disease associations

OMIM: gene `` | disease phenotypes:

GWAS associations

19 associations:

Study	Trait	p-value
GCST90002386_125	High light scatter reticulocyte percentage of red cells	3e-40
GCST90002385_10	High light scatter reticulocyte count	2e-37
GCST90002406_404	Reticulocyte fraction of red cells	6e-24
GCST90002405_321	Reticulocyte count	3e-20
GCST008058_142	Estimated glomerular filtration rate	9e-15
GCST90011900_189	Serum alkaline phosphatase levels	3e-14
GCST010002_296	Refractive error	4e-13
GCST006979_211	Heel bone mineral density	9e-13
GCST011320_27	Type 2 diabetes or prostate cancer (pleiotropy)	1e-12
GCST90002397_314	Mean spheric corpuscular volume	8e-12
GCST90002388_506	Lymphocyte count	1e-11
GCST008059_177	Estimated glomerular filtration rate	2e-11
GCST009379_111	Type 2 diabetes	3e-10
GCST011494_69	Daytime nap	3e-10
GCST010988_61	Adult body size	9e-10
GCST006867_91	Type 2 diabetes	1e-9
GCST009325_50	Parkinson’s disease or first degree relation to individual with Parkinson’s disease	7e-9
GCST004863_1	Mosquito bite size	2e-6
GCST006865_17	Bipolar disorder	5e-6

EFO canonical traits (from GWAS)

6 canonical traits:

EFO ID	Trait name
EFO:0008378	mosquito bite reaction size measurement
EFO:0009270	heel bone mineral density
EFO:0007828	daytime rest measurement
EFO:0007986	reticulocyte count
EFO:0004587	lymphocyte count
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067203 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (2 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL5653589	KD	1440 nM

ChEMBL bioactivities

2 potent at pChembl≥5 of 3 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.35	Kd	4502	nM	CHEMBL5653589
5.35	ED50	4502	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 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.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149704: Binding affinity to human UBAP2 incubated for 45 mins by Kinobead based pull down assay	kd	4.5017	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, decreases methylation	3
Acetaminophen	increases expression	2
Benzo(a)pyrene	decreases methylation, increases expression	2
Lead	affects methylation, decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
cobaltous chloride	affects expression, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1
LDN 193189	affects cotreatment, decreases expression	1
Atrazine	decreases expression	1
Cadmium	decreases expression, increases abundance	1
Caffeine	affects phosphorylation	1
Dactinomycin	affects cotreatment, increases secretion	1
Dimethyl Sulfoxide	increases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Ribonucleotides	affects binding	1
Selenium	decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
Vincristine	decreases expression	1
Vitamin E	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652746	Binding	Binding affinity to human UBAP2 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — *ChemMedChem*

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for UBAP2 across ~30M SureChEMBL compounds — explore on Sugi Predict.