USP47

Summary

USP47 (ubiquitin specific peptidase 47, HGNC:20076) is a protein-coding gene on chromosome 11p15.3, encoding Ubiquitin carboxyl-terminal hydrolase 47 (Q96K76). Ubiquitin-specific protease that specifically deubiquitinates monoubiquitinated DNA polymerase beta (POLB), stabilizing POLB thereby playing a role in base-excision repair (BER).

Enables WD40-repeat domain binding activity and cysteine-type deubiquitinase activity. Involved in base-excision repair; monoubiquitinated protein deubiquitination; and positive regulation of canonical Wnt signaling pathway. Located in cytoplasm. Part of SCF ubiquitin ligase complex. Is active in nucleus.

Source: NCBI Gene 55031 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 160 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_001282659

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20076
Approved symbol	USP47
Name	ubiquitin specific peptidase 47
Location	11p15.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000170242
Ensembl biotype	protein_coding
OMIM	614460
Entrez	55031

Gene structure

Transcript identifiers

Ensembl transcripts: 33 — 25 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000305481, ENST00000339865, ENST00000399455, ENST00000525078, ENST00000525257, ENST00000525367, ENST00000527733, ENST00000529813, ENST00000530041, ENST00000530369, ENST00000531513, ENST00000856814, ENST00000856815, ENST00000856816, ENST00000856817, ENST00000856818, ENST00000856819, ENST00000856820, ENST00000914135, ENST00000914136, ENST00000914137, ENST00000948454, ENST00000948455, ENST00000948456, ENST00000948457, ENST00000948458, ENST00000948459, ENST00000948460, ENST00000948461, ENST00000948462, ENST00000948463, ENST00000948464, ENST00000948465

RefSeq mRNA: 16 — MANE Select: NM_001282659 NM_001282659, NM_001330208, NM_001372091, NM_001372092, NM_001372093, NM_001372094, NM_001372095, NM_001372096, NM_001372097, NM_001372098, NM_001372099, NM_001372100, NM_001372101, NM_001372102, NM_001372103, NM_017944

CCDS: CCDS41619, CCDS60725, CCDS81554

Canonical transcript exons

ENST00000527733 — 28 exons

Exon	Start	End
ENSE00002187969	11956001	11961887
ENSE00003464205	11950364	11950482
ENSE00003480921	11938257	11938372
ENSE00003499807	11933004	11933116
ENSE00003532853	11841972	11842224
ENSE00003544901	11920156	11920251
ENSE00003545644	11949889	11950004
ENSE00003546654	11954897	11954944
ENSE00003554259	11933831	11933935
ENSE00003555737	11955034	11955164
ENSE00003569376	11942335	11943112
ENSE00003595673	11948478	11948558
ENSE00003597487	11929434	11929565
ENSE00003605269	11891968	11892106
ENSE00003611142	11952741	11952871
ENSE00003614589	11922724	11922891
ENSE00003622504	11905399	11905548
ENSE00003624760	11936303	11936510
ENSE00003626413	11930696	11930751
ENSE00003634726	11880177	11880380
ENSE00003637890	11902715	11902860
ENSE00003646847	11930044	11930120
ENSE00003651946	11920342	11920494
ENSE00003654835	11903263	11903342
ENSE00003658388	11940429	11940548
ENSE00003679387	11947945	11948120
ENSE00003682421	11884467	11884580
ENSE00003690957	11897597	11897693

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.3041 / max 550.3680, expressed in 1817 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113097	28.2768	1816
113098	4.0273	1378

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	99.61	gold quality
medial globus pallidus	UBERON:0002477	98.86	gold quality
endothelial cell	CL:0000115	98.51	gold quality
globus pallidus	UBERON:0001875	98.07	gold quality
gluteal muscle	UBERON:0002000	97.86	gold quality
secondary oocyte	CL:0000655	97.71	gold quality
seminal vesicle	UBERON:0000998	97.67	gold quality
vena cava	UBERON:0004087	97.63	gold quality
cervix squamous epithelium	UBERON:0006922	97.45	gold quality
tendon	UBERON:0000043	97.41	gold quality
corpus callosum	UBERON:0002336	97.04	gold quality
biceps brachii	UBERON:0001507	96.95	gold quality
periodontal ligament	UBERON:0008266	96.89	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.87	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.81	gold quality
inferior olivary complex	UBERON:0002127	96.63	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.51	gold quality
tongue squamous epithelium	UBERON:0006919	96.38	gold quality
calcaneal tendon	UBERON:0003701	96.37	gold quality
ventricular zone	UBERON:0003053	96.33	gold quality
triceps brachii	UBERON:0001509	96.32	gold quality
deltoid	UBERON:0001476	96.30	gold quality
pons	UBERON:0000988	96.28	gold quality
adrenal tissue	UBERON:0018303	96.03	gold quality
gastrocnemius	UBERON:0001388	95.98	gold quality
cardia of stomach	UBERON:0001162	95.95	gold quality
skeletal muscle tissue	UBERON:0001134	95.92	gold quality
inferior vagus X ganglion	UBERON:0005363	95.88	gold quality
substantia nigra pars reticulata	UBERON:0001966	95.80	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	95.80	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.34
E-CURD-135	no	958.03
E-CURD-112	no	2.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

140 targeting USP47, 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-4668-3P	100.00	68.74	2635
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4500	99.99	72.72	2367
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-557	99.96	70.01	1640
HSA-LET-7D-5P	99.96	71.76	1632
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-9983-3P	99.94	71.48	3631

Literature-anchored findings (GeneRIF, showing 22)

• USP47, a novel beta-Trcp interactor, regulates cell growth and survival, potentially providing a novel target for anticancer therapies. (PMID:19966869)
• USP47 has a role in regulating DNA repair and maintaining genome integrity (PMID:21362556)
• The results of this study indicated that USP47 plays a crucial role in the control of axonal growth during neuronal development by antagonizing CHIP-mediated katanin-p60 degradation. (PMID:23904609)
• Data indicate that E-cadherin ubiquitination consistently increases after depletion of kinesin-like protein KIFC3 or ubiquitin-specific protease USP47. (PMID:25253721)
• miR-204-5p acts as a tumor suppressor in gastric cancer through inhibiting USP47 and RAB22A. (PMID:25429829)
• these results suggest that USP47 may play distinct roles in ubiquitin-mediated cellular processes via de-ubiquitinating enzymes activity. (PMID:26115687)
• USP47 is a deubiquitinase that prevents beta-catenin ubiquitination. (PMID:26169834)
• These results demonstrate, for the first time, the role for USP47, as a novel target of Sox9, in the regulation of epithelial-mesenchymal transition and metastasis of colorectal cancer cells. (PMID:29162839)
• these data reveal a new post-transcriptional role for USP47 and USP7 in inflammation by regulating inflammasome activation and the release of the pro-inflammatory cytokines IL-1beta and IL-18, and implicate dual USP7 and USP47 inhibitors as potential therapeutic agents for inflammatory disease. (PMID:30206189)
• lncRNA LINC00668 acted as an oncogenic role in CRC cells by sponging miR-188-5p and upregulating USP47 (PMID:31233752)
• USP47-mediated deubiquitination and stabilization of YAP contributes to the progression of colorectal cancer. (PMID:31748975)
• Spatial transcriptomics identifies spatially dysregulated expression of GRM3 and USP47 in amyotrophic lateral sclerosis. (PMID:31925813)
• Proteomics analysis reveals the role of ubiquitin specific protease (USP47) in Epithelial to Mesenchymal Transition (EMT) induced by TGFbeta2 in breast cells. (PMID:32201364)
• Long non-coding RNA DSCAM-AS1 upregulates USP47 expression through sponging miR-101-3p to accelerate osteosarcoma progression. (PMID:32379981)
• Targeting USP47 overcomes tyrosine kinase inhibitor resistance and eradicates leukemia stem/progenitor cells in chronic myelogenous leukemia. (PMID:33397955)
• USP47 maintains the stemness of colorectal cancer cells and is inhibited by parthenolide. (PMID:34030041)
• Ubiquitin specific peptidase 47 promotes proliferation of lung squamous cell carcinoma. (PMID:35254655)
• USP47 deubiquitylates Groucho/TLE to promote Wnt-beta-catenin signaling. (PMID:36749823)
• Deubiquitinase USP47 attenuates virus-induced type I interferon signaling. (PMID:37001379)
• Structural and functional characterization of USP47 reveals a hot spot for inhibitor design. (PMID:37740002)
• USP47 inhibits m6A-dependent c-Myc translation to maintain regulatory T cell metabolic and functional homeostasis. (PMID:37788092)
• USP47 stabilizes YBX1 to promote the progression of acute myeloid leukemia. (PMID:38104157)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	usp47	ENSDARG00000102645
mus_musculus	Usp47	ENSMUSG00000059263
rattus_norvegicus	Usp47	ENSRNOG00000026754
drosophila_melanogaster	Usp47	FBGN0016756
caenorhabditis_elegans		WBGENE00011507

Paralogs (71): USP2 (ENSG00000036672), USP28 (ENSG00000048028), USP36 (ENSG00000055483), USP13 (ENSG00000058056), USP33 (ENSG00000077254), USP40 (ENSG00000085982), USP48 (ENSG00000090686), USP14 (ENSG00000101557), USP11 (ENSG00000102226), USP10 (ENSG00000103194), USP31 (ENSG00000103404), USP42 (ENSG00000106346), USP5 (ENSG00000111667), USP4 (ENSG00000114316), USP9Y (ENSG00000114374), USP34 (ENSG00000115464), USP35 (ENSG00000118369), USP45 (ENSG00000123552), USP22 (ENSG00000124422), USP9X (ENSG00000124486), USP6 (ENSG00000129204), USP29 (ENSG00000131864), USP26 (ENSG00000134588), USP30 (ENSG00000135093), USP15 (ENSG00000135655), USP37 (ENSG00000135913), USP44 (ENSG00000136014), USP20 (ENSG00000136878), USP8 (ENSG00000138592), USP3 (ENSG00000140455), USP21 (ENSG00000143258), USP43 (ENSG00000154914), USP25 (ENSG00000155313), USP16 (ENSG00000156256), USP24 (ENSG00000162402), USP1 (ENSG00000162607), USP49 (ENSG00000164663), USP38 (ENSG00000170185), USP50 (ENSG00000170236), USP32 (ENSG00000170832)

Protein

Protein identifiers

Ubiquitin carboxyl-terminal hydrolase 47 — Q96K76 (reviewed: Q96K76)

Alternative names: Deubiquitinating enzyme 47, Ubiquitin thioesterase 47, Ubiquitin-specific-processing protease 47

All UniProt accessions (1): Q96K76

UniProt curated annotations — full annotation on UniProt →

Function. Ubiquitin-specific protease that specifically deubiquitinates monoubiquitinated DNA polymerase beta (POLB), stabilizing POLB thereby playing a role in base-excision repair (BER). Acts as a regulator of cell growth and genome integrity. May also indirectly regulate CDC25A expression at a transcriptional level.

Subunit / interactions. Interacts with BTRC and FBXW11. Interacts with POLB.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in skeletal muscle, heart and testis.

Similarity. Belongs to the peptidase C19 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q96K76-1	1	yes
Q96K76-2	2
Q96K76-3	3
Q96K76-4	4

RefSeq proteins (16): NP_001269588, NP_001317137, NP_001359020, NP_001359021, NP_001359022, NP_001359023, NP_001359024, NP_001359025, NP_001359026, NP_001359027, NP_001359028, NP_001359029, NP_001359030, NP_001359031, NP_001359032, NP_060414 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001394	Peptidase_C19_UCH	Domain
IPR018200	USP_CS	Conserved_site
IPR028889	USP	Domain
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR038765	Papain-like_cys_pep_sf	Homologous_superfamily
IPR045578	USP47_C	Domain
IPR050164	Peptidase_C19	Family

Pfam: PF00443, PF19718, PF25985

UniProt features (36 total): sequence conflict 9, compositionally biased region 8, modified residue 7, region of interest 4, splice variant 3, active site 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96K76-F1	72.63	0.31

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 197 (nucleophile); 503 (proton acceptor)

Post-translational modifications (7): 122, 832, 910, 933, 1013, 1015, 1017

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5689880	Ub-specific processing proteases

MSigDB gene sets: 206 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, CACCAGC_MIR138, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE, GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_REMOVAL, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GTGCCTT_MIR506, SMITH_TERT_TARGETS_DN, ACCAATC_MIR509, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN

GO Biological Process (10): base-excision repair (GO:0006284), proteolysis (GO:0006508), DNA damage response (GO:0006974), intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630), protein deubiquitination (GO:0016579), regulation of protein stability (GO:0031647), monoubiquitinated protein deubiquitination (GO:0035520), positive regulation of canonical Wnt signaling pathway (GO:0090263), negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230), DNA repair (GO:0006281)

GO Molecular Function (7): cysteine-type deubiquitinase activity (GO:0004843), WD40-repeat domain binding (GO:0071987), deubiquitinase activity (GO:0101005), protein binding (GO:0005515), peptidase activity (GO:0008233), cysteine-type peptidase activity (GO:0008234), hydrolase activity (GO:0016787)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), SCF ubiquitin ligase complex (GO:0019005)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Deubiquitination	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
DNA damage response	2
DNA repair	1
protein metabolic process	1
cellular response to stress	1
intrinsic apoptotic signaling pathway	1
cysteine-type deubiquitinase activity	1
protein modification by small protein removal	1
regulation of biological quality	1
protein deubiquitination	1
positive regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
intrinsic apoptotic signaling pathway in response to DNA damage	1
regulation of intrinsic apoptotic signaling pathway in response to DNA damage	1
negative regulation of intrinsic apoptotic signaling pathway	1
DNA metabolic process	1
cysteine-type peptidase activity	1
deubiquitinase activity	1
protein domain specific binding	1
ubiquitin-like protein peptidase activity	1
binding	1
hydrolase activity	1
catalytic activity, acting on a protein	1
peptidase activity	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1
cullin-RING ubiquitin ligase complex	1

Protein interactions and networks

STRING

1546 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
USP47	USP50	Q70EL3	700
USP47	ZUP1	Q96AP4	613
USP47	WDR48	Q8TAF3	591
USP47	OTUD5	Q96G74	573
USP47	UCHL5	Q9Y5K5	536
USP47	ERAP1	Q9NZ08	511
USP47	JOSD2	Q8TAC2	504
USP47	UCHL3	P15374	503
USP47	RPS2	P15880	497
USP47	HDAC6	Q9UBN7	495
USP47	USP30	Q70CQ3	490
USP47	TRIP12	Q14669	476
USP47	HDAC11	Q96DB2	467
USP47	JOSD1	Q15040	464
USP47	OTUB1	Q96FW1	461

IntAct

101 interactions, top by confidence:

A	B	Type	Score
PHF1	EED	psi-mi:“MI:0914”(association)	0.790
KIF22	KPNA3	psi-mi:“MI:0914”(association)	0.730
RHPN1	PODXL	psi-mi:“MI:0914”(association)	0.690
FBXW11	EEF2K	psi-mi:“MI:0914”(association)	0.640
FOXK2	DVL2	psi-mi:“MI:0914”(association)	0.640
HOGA1	USP47	psi-mi:“MI:0915”(physical association)	0.640
INPP5K	GART	psi-mi:“MI:0914”(association)	0.640
RND2	USP47	psi-mi:“MI:0915”(physical association)	0.590
USP47	AP4M1	psi-mi:“MI:0915”(physical association)	0.560
AP4M1	USP47	psi-mi:“MI:0915”(physical association)	0.560
STN1	SMCO3	psi-mi:“MI:0914”(association)	0.530
USP47	DENR	psi-mi:“MI:0914”(association)	0.530
ASTE1	USP47	psi-mi:“MI:0914”(association)	0.530
AURKA	WDR62	psi-mi:“MI:0914”(association)	0.530
FBXW11	AHCYL1	psi-mi:“MI:0914”(association)	0.530
NCF2	BPGM	psi-mi:“MI:0914”(association)	0.530
DPYSL4	PLCG1	psi-mi:“MI:0914”(association)	0.530
PHF1	EPOP	psi-mi:“MI:0914”(association)	0.530
AVIL	VIL1	psi-mi:“MI:0914”(association)	0.530

BioGRID (290): USP47 (Affinity Capture-Western), USP47 (Affinity Capture-MS), PLA2G2A (Biochemical Activity), USP47 (Affinity Capture-Western), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS), USP47 (Two-hybrid), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS), USP47 (Affinity Capture-MS)

ESM2 similar proteins: A1A5G2, A2AFR3, A7MBL8, B9EJ86, E1C1R4, E1C3P4, F1LXF1, O94806, O94967, P0C6S7, P0CAX5, P11274, P22682, Q0V9G5, Q14161, Q14CM0, Q15139, Q16513, Q1RMU2, Q3KR37, Q3LAC4, Q3UGM2, Q5RED8, Q5T6S3, Q5U252, Q62101, Q66H62, Q6DFZ1, Q6P5G6, Q6PAJ1, Q70Z35, Q7Z6G8, Q80TI0, Q80TQ2, Q80YA9, Q8BIZ1, Q8BWW9, Q8BY87, Q8K1Y2, Q8NEL9

Diamond homologs: A1A5G2, E1C1R4, P38187, P50101, Q09879, Q0E2F9, Q24574, Q4VSI4, Q5U252, Q60MK8, Q6A4J8, Q6U7I1, Q7JKC3, Q84WU2, Q8BWR4, Q8BY87, Q8W4N3, Q93009, Q96K76, Q9FPS9, Q9FPT1, Q9NVE5, Q9UTT1, Q9VYQ8, P39538, Q08DA3, Q2KJ09, Q4R6X7, Q99LG0, Q9FPT5, Q9P2H5, Q9SCJ9, Q9Y5T5, A2XDG4, A3AF13, E9QG68, O60079, P39967, Q09931, Q13107

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 112 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:

Pathway	Partners	Fold	FDR
Regulation of PLK1 Activity at G2/M Transition	7	11.4×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	124
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

4787 predictions. Top by Δscore:

Variant	Effect	Δscore
11:11880318:G:GG	donor_gain	1.0000
11:11884457:AT:A	acceptor_gain	1.0000
11:11884458:T:G	acceptor_gain	1.0000
11:11884458:T:TA	acceptor_gain	1.0000
11:11884463:A:AG	acceptor_gain	1.0000
11:11884463:ATAG:A	acceptor_gain	1.0000
11:11884464:T:G	acceptor_gain	1.0000
11:11884464:TA:T	acceptor_loss	1.0000
11:11884465:A:AG	acceptor_gain	1.0000
11:11884465:AG:A	acceptor_gain	1.0000
11:11884466:G:GT	acceptor_gain	1.0000
11:11884466:GG:G	acceptor_gain	1.0000
11:11884466:GGC:G	acceptor_gain	1.0000
11:11884466:GGCA:G	acceptor_gain	1.0000
11:11884466:GGCAC:G	acceptor_gain	1.0000
11:11884577:GCTG:G	donor_gain	1.0000
11:11884581:G:GA	donor_loss	1.0000
11:11884581:G:GG	donor_gain	1.0000
11:11884582:T:A	donor_loss	1.0000
11:11897694:G:GG	donor_gain	1.0000
11:11902835:G:GT	donor_gain	1.0000
11:11902852:GTA:G	donor_gain	1.0000
11:11902855:G:GG	donor_gain	1.0000
11:11902860:GGTAC:G	donor_gain	1.0000
11:11903260:CA:C	acceptor_loss	1.0000
11:11903261:A:AG	acceptor_gain	1.0000
11:11903261:A:AT	acceptor_loss	1.0000
11:11903261:AGCTT:A	acceptor_gain	1.0000
11:11903262:G:GG	acceptor_gain	1.0000
11:11903262:GC:G	acceptor_gain	1.0000

AlphaMissense

9047 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:11897605:G:A	G189R	1.000
11:11897605:G:C	G189R	1.000
11:11897606:G:A	G189E	1.000
11:11897606:G:T	G189V	1.000
11:11897609:T:A	L190Q	1.000
11:11897609:T:C	L190P	1.000
11:11897614:A:G	N192D	1.000
11:11897615:A:T	N192I	1.000
11:11897616:C:A	N192K	1.000
11:11897616:C:G	N192K	1.000
11:11897619:A:C	Q193H	1.000
11:11897619:A:T	Q193H	1.000
11:11897625:G:A	M195I	1.000
11:11897625:G:C	M195I	1.000
11:11897625:G:T	M195I	1.000
11:11897627:C:T	T196I	1.000
11:11897629:T:C	C197R	1.000
11:11897630:G:A	C197Y	1.000
11:11897630:G:T	C197F	1.000
11:11897631:C:G	C197W	1.000
11:11897632:T:C	Y198H	1.000
11:11897632:T:G	Y198D	1.000
11:11897633:A:G	Y198C	1.000
11:11897636:T:C	L199S	1.000
11:11897636:T:G	L199W	1.000
11:11897640:T:A	N200K	1.000
11:11897640:T:G	N200K	1.000
11:11897641:A:C	S201R	1.000
11:11897643:C:A	S201R	1.000
11:11897643:C:G	S201R	1.000

dbSNP variants (sampled 300 via entrez): RS1000018090 (11:11852323 G>T), RS1000049426 (11:11942389 C>T), RS1000087237 (11:11854763 T>C), RS1000091329 (11:11919642 T>G), RS1000123376 (11:11895664 T>A,C), RS1000144232 (11:11932146 T>C), RS1000180483 (11:11867420 C>T), RS1000191527 (11:11956414 A>G,T), RS1000201407 (11:11956152 A>T), RS1000261045 (11:11861334 G>A), RS1000276223 (11:11953406 TAAAA>T,TA,TAAA,TAAAAA), RS1000286245 (11:11845507 G>T), RS1000291314 (11:11903675 G>A,T), RS1000305233 (11:11888480 C>T), RS1000311259 (11:11916648 G>A,T)

Disease associations

OMIM: gene MIM:614460 | 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
GCST008161_31	Waist circumference adjusted for body mass index	1.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2157851 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 20,825 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL169	URSOLIC ACID	2	20,825

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

ChEMBL bioactivities

48 potent at pChembl≥5 of 53 total, top 37 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.70	EC50	200	nM	CHEMBL5290347
6.46	IC50	350	nM	CHEMBL2159507
6.44	EC50	360	nM	CHEMBL4125810
6.44	EC50	360	nM	CHEMBL4127188
6.40	IC50	400	nM	CHEMBL2398212
6.35	EC50	450	nM	CHEMBL5275791
6.30	IC50	500	nM	CHEMBL2159505
6.28	IC50	530	nM	CHEMBL2159503
6.06	IC50	870	nM	CHEMBL2159504
6.06	EC50	870	nM	CHEMBL2159504
6.03	EC50	940	nM	CHEMBL5288615
6.00	IC50	1000	nM	CHEMBL2159508
5.96	EC50	1100	nM	CHEMBL5273899
5.92	IC50	1200	nM	CHEMBL2159500
5.89	IC50	1300	nM	CHEMBL2159501
5.89	EC50	1280	nM	CHEMBL5287756
5.89	EC50	1300	nM	CHEMBL2159501
5.88	EC50	1330	nM	CHEMBL4129261
5.85	EC50	1400	nM	CHEMBL5279110
5.82	EC50	1500	nM	CHEMBL5277692
5.80	EC50	1590	nM	CHEMBL5289526
5.80	EC50	1600	nM	CHEMBL5282678
5.70	EC50	2000	nM	CHEMBL5269773
5.69	EC50	2030	nM	CHEMBL4125949
5.66	IC50	2200	nM	CHEMBL2159499
5.66	EC50	2200	nM	CHEMBL5271884
5.46	IC50	3500	nM	CHEMBL4569978
5.46	EC50	3500	nM	CHEMBL5276074
5.43	IC50	3700	nM	CHEMBL2159497
5.39	EC50	4100	nM	CHEMBL5285749
5.37	IC50	4300	nM	CHEMBL2159495
5.37	IC50	4300	nM	CHEMBL5281075
5.29	EC50	5100	nM	CHEMBL5268148
5.26	IC50	5500	nM	CHEMBL2159502
5.19	EC50	6400	nM	CHEMBL5275562
5.06	IC50	8700	nM	CHEMBL2159498
5.03	EC50	9300	nM	CHEMBL5272070

PubChem BioAssay actives

48 with measured affinity, of 99 total; 35 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
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-[3-[2-(dimethylamino)ethylamino]-1,1-dioxo-2,3-dihydro-1-benzothiophen-6-yl]-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	0.2000	uM
4-cyano-5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-[4-[3-(dimethylamino)propoxy]phenyl]thiophene-2-carboxamide	1930789: Inhibition of USP47 (unknown origin)	ic50	0.3500	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(3-methyl-1,1-dioxo-2,3-dihydro-1-benzothiophen-6-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	0.3600	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(3-methyl-1,1-dioxo-1-benzothiophen-6-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	0.3600	uM
7-chloro-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930789: Inhibition of USP47 (unknown origin)	ic50	0.4000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-[4-[2-(dimethylamino)ethoxy]phenyl]-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	0.4500	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(4-methylsulfonylphenyl)-4-nitrothiophene-2-carboxamide	1930789: Inhibition of USP47 (unknown origin)	ic50	0.5000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-[4-[3-(dimethylamino)propoxy]phenyl]-4-nitrothiophene-2-carboxamide	1930789: Inhibition of USP47 (unknown origin)	ic50	0.5300	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(4-methoxyphenyl)-4-nitrothiophene-2-carboxamide	1930789: Inhibition of USP47 (unknown origin)	ic50	0.8700	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(3-ethylsulfonylphenyl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	0.9400	uM
4-cyano-5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(4-methylsulfonylphenyl)thiophene-2-carboxamide	1930790: Inhibition of human recombinant USP47 expressed in Escherichia coli sf9 cells	ic50	1.0000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1-imino-3-methyl-1-oxo-2,3-dihydro-1-benzothiophen-6-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	1.1000	uM
1-[5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-4-nitrothiophen-2-yl]ethanone	1930789: Inhibition of USP47 (unknown origin)	ic50	1.2000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-[3-(methanesulfonamido)phenyl]-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	1.2800	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1-methylpiperidin-4-yl)-4-nitrothiophene-2-carboxamide	1930789: Inhibition of USP47 (unknown origin)	ic50	1.3000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1,1-dioxo-1-benzothiophen-6-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	1.3300	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(3-methylsulfonylphenyl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	1.4000	uM
N-[3-(cyclopropylmethylsulfonyl)phenyl]-5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	1.5000	uM
N-(3-cyclopropylsulfonylphenyl)-5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	1.5900	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1,1-dioxo-3,4-dihydro-2H-thiochromen-4-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	1.6000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-[3-(2-methoxyethylamino)-1,1-dioxo-2,3-dihydro-1-benzothiophen-6-yl]-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	2.0000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1,1-dioxo-2,3-dihydro-1-benzothiophen-6-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	2.0300	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-[3-(methylsulfonimidoyl)phenyl]-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	2.2000	uM
1-[5-(2,6-dichlorophenyl)sulfanyl-4-nitrothiophen-2-yl]ethanone	1930789: Inhibition of USP47 (unknown origin)	ic50	2.2000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1,1-dioxothian-4-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	3.5000	uM
9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930789: Inhibition of USP47 (unknown origin)	ic50	3.5000	uM
1-[5-(2,4-dichlorophenyl)sulfanyl-4-nitrothiophen-2-yl]ethanone	694816: Inhibition of USP47 by Ub-CHOP reporter assay	ic50	3.7000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1,1-dioxo-2,3,4,4a,5,6,8,8a-octahydrothiopyrano[2,3-c]pyran-4-yl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	4.1000	uM
7-fluoro-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930789: Inhibition of USP47 (unknown origin)	ic50	4.3000	uM
1-[5-(2,3-dichlorophenyl)sulfanyl-4-nitrothiophen-2-yl]ethanone	1930790: Inhibition of human recombinant USP47 expressed in Escherichia coli sf9 cells	ic50	4.3000	uM
4-cyano-5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(1,1-dioxo-1-benzothiophen-6-yl)thiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	5.1000	uM
5-(2,6-dichlorophenyl)sulfanyl-N-(1-methylpiperidin-4-yl)-4-nitrothiophene-2-carboxamide	1930789: Inhibition of USP47 (unknown origin)	ic50	5.5000	uM
[5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-4-nitrothiophen-2-yl]-(1,1-dioxo-1,4-thiazinan-4-yl)methanone	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	6.4000	uM
1-[5-(2,4-difluorophenyl)sulfanyl-4-nitrothiophen-2-yl]ethanone	1930790: Inhibition of human recombinant USP47 expressed in Escherichia coli sf9 cells	ic50	8.7000	uM
5-[(3,5-dichloro-4-pyridinyl)sulfanyl]-N-(2-methylsulfonylphenyl)-4-nitrothiophene-2-carboxamide	1930814: Inhibition of human USP47 using Ub-EKL as substrate by SDS-PAGE assay	ec50	9.3000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	8
Benzo(a)pyrene	affects methylation, decreases expression	4
sodium arsenite	decreases expression, increases expression	2
entinostat	decreases expression, affects cotreatment	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, decreases expression, affects cotreatment	2
Endosulfan	decreases expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Cyclosporine	increases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
FR900359	affects phosphorylation	1
dicrotophos	decreases expression	1
2,4,6-tribromophenol	increases expression	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
decabromobiphenyl ether	increases expression	1
trichostatin A	decreases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
cobaltous chloride	increases expression	1
butyraldehyde	decreases expression	1
tetrabromobisphenol A	increases expression	1
coumarin	increases phosphorylation	1
perfluorooctane sulfonic acid	decreases expression	1
K 7174	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
pentabrominated diphenyl ether 100	increases expression	1

ChEMBL screening assays

12 unique, capped per target: 12 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL2162865	Binding	Inhibition of USP47 by Ub-CHOP reporter assay	Selective Dual Inhibitors of the Cancer-Related Deubiquitylating Proteases USP7 and USP47. — ACS Med Chem Lett

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TX02	HAP1 USP47 (-) 1	Cancer cell line	Male
CVCL_TX03	HAP1 USP47 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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