USP47

ubiquitin specific peptidase 47, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 11:11841422-11961887

Links

ENSG00000170242 ∙ NCBI:55031 ∙ OMIM:614460 ∙ HGNC:20076 ∙ Uniprot:Q96K76 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USP47 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP47 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	52	2	1

Variants in USP47

This is a list of pathogenic ClinVar variants found in the USP47 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-11884506-G-A		not specified	Uncertain significance (Aug 08, 2023)
11-11884509-A-C		not specified	Uncertain significance (Dec 20, 2023)
11-11884532-C-T			Likely benign (May 01, 2022)
11-11892004-A-G		not specified	Uncertain significance (Dec 05, 2022)
11-11892049-A-G		not specified	Uncertain significance (Aug 02, 2022)
11-11892058-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-11902812-A-G		not specified	Uncertain significance (Jul 25, 2023)
11-11902833-A-G		not specified	Uncertain significance (Aug 28, 2023)
11-11920247-G-A		not specified	Uncertain significance (Apr 25, 2022)
11-11920415-T-C		not specified	Uncertain significance (Oct 14, 2023)
11-11920462-G-C		not specified	Uncertain significance (Jan 23, 2024)
11-11920465-A-C		not specified	Uncertain significance (Jun 24, 2022)
11-11922760-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-11922796-A-G		not specified	Uncertain significance (Nov 17, 2022)
11-11929489-G-C		not specified	Uncertain significance (Feb 10, 2023)
11-11930090-G-A		not specified	Uncertain significance (Mar 16, 2022)
11-11933103-G-A		not specified	Uncertain significance (May 05, 2023)
11-11933853-C-G		not specified	Uncertain significance (Jan 04, 2024)
11-11933916-C-T		not specified	Uncertain significance (Nov 17, 2022)
11-11933925-T-G		not specified	Uncertain significance (Jan 10, 2022)
11-11936393-G-A		not specified	Uncertain significance (May 21, 2024)
11-11936456-C-A		not specified	Uncertain significance (Aug 02, 2021)
11-11938313-A-G		not specified	Likely benign (Dec 27, 2023)
11-11938329-A-G		not specified	Uncertain significance (Jul 19, 2022)
11-11938343-G-A		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP47	protein_coding	protein_coding	ENST00000339865	27	117901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.56e-9	124776	0	13	124789	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	489	666	0.734	0.0000334	8568
Missense in Polyphen		138	273.65	0.50429		3569
Synonymous	0.586	221	232	0.951	0.0000117	2267
Loss of Function	7.34	4	70.5	0.0567	0.00000364	894

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000109	0.0000993
East Asian	0.00	0.00
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.0000535	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.000135	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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. {ECO:0000269|PubMed:19966869, ECO:0000269|PubMed:21362556}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.171
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.45

Haploinsufficiency Scores

• pHI: 0.190
• hipred: Y
• hipred_score: 0.816
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.637

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Usp47
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: base-excision repair;ubiquitin-dependent protein catabolic process;cellular response to DNA damage stimulus;negative regulation of G2/M transition of mitotic cell cycle;protein deubiquitination;positive regulation of cell growth;regulation of protein stability;cellular response to UV;monoubiquitinated protein deubiquitination;response to drug;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of transcription, DNA-templated;positive regulation of canonical Wnt signaling pathway;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
• Cellular component: nucleoplasm;cytoplasm;cytosol;SCF ubiquitin ligase complex
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity;WD40-repeat domain binding;ubiquitinyl hydrolase activity