USP5

ubiquitin specific peptidase 5, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 12:6852148-6866632

Links

ENSG00000111667

∙ ∙ OMIM:601447 ∙ HGNC:12628 ∙ Uniprot:P45974 ∙ 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 USP5 gene.

not_specified (63 variants)
not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001098536.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	5 clinvar	6
missense			62 clinvar	1 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	2	5

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP5	protein_coding	protein_coding	ENST00000229268	20	14505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.964	0.0360	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.36	310	527	0.588	0.0000315	5621
Missense in Polyphen		83	184.75	0.44927		2024
Synonymous	-0.470	219	210	1.04	0.0000130	1661
Loss of Function	5.16	8	45.6	0.175	0.00000236	522

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000114	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys- 63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition. {ECO:0000269|PubMed:19098288}.;
Pathway: Post-translational protein modification;Metabolism of proteins;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Ub-specific processing proteases;Deubiquitination;Protein ubiquitination (Consensus)

Recessive Scores

pRec: 0.128

Intolerance Scores

loftool: 0.358
rvis_EVS: -1.68
rvis_percentile_EVS: 2.63

Haploinsufficiency Scores

pHI: 0.690
hipred: Y
hipred_score: 0.800
ghis: 0.534

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Usp5
Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype;

Zebrafish Information Network

Gene name: usp5
Affected structure: caudal fin upper lobe
Phenotype tag: abnormal
Phenotype quality: fused with

Gene ontology

Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;protein K48-linked deubiquitination
Cellular component: lysosome;cytosol
Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity;ubiquitin binding