USP17L2

ubiquitin specific peptidase 17 like family member 2, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 8:12136435-12138849

Links

ENSG00000223443 ∙ NCBI:377630 ∙ OMIM:610186 ∙ HGNC:34434 ∙ Uniprot:Q6R6M4 ∙ 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 USP17L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP17L2 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				4		4
missense				6		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	10	0

Variants in USP17L2

This is a list of pathogenic ClinVar variants found in the USP17L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-12137263-C-T			Likely benign (Mar 01, 2023)
8-12137674-G-A			Likely benign (May 01, 2023)
8-12137874-T-A			Likely benign (Jan 01, 2024)
8-12137898-C-T			Likely benign (Sep 01, 2023)
8-12137975-C-T			Likely benign (Jul 13, 2017)
8-12138226-C-T			Likely benign (Jan 01, 2024)
8-12138295-C-A			Likely benign (Dec 01, 2022)
8-12138470-G-A			Likely benign (Jan 01, 2023)
8-12138613-C-T			Likely benign (Feb 01, 2023)
8-12138743-G-C			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP17L2	protein_coding	protein_coding	ENST00000333796	1	1910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-5.84	506	248	2.04	0.0000139	3352
Missense in Polyphen		134	62.831	2.1327		1048
Synonymous	-9.73	223	99.5	2.24	0.00000634	967
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate different cellular processes. Regulates cell proliferation by deubiquitinating and inhibiting RCE1 thereby controlling the small GTPases NRAS and HRAS localization and activation. In parallel, mediates deubiquitination of CDC25A, preventing CDC25A degradation by the proteasome during the G1/S and G2/M phases promoting cell-cycle progression. Also regulates cell proliferation and apoptosis through deubiquitination of SUDS3 a regulator of histone deacetylation. Through activation of the Rho family GTPases RAC1A, CDC42 and RHOA, regulates cell migration. Through the cleavage of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains of the cytoplasmic innate immune receptors DDX58 and IFIH1 stimulates the cellular response to viral infection. {ECO:0000269|PubMed:14699124, ECO:0000269|PubMed:17109758, ECO:0000269|PubMed:19188362, ECO:0000269|PubMed:20147298, ECO:0000269|PubMed:20228808, ECO:0000269|PubMed:20368735, ECO:0000269|PubMed:20388806, ECO:0000269|PubMed:21239494, ECO:0000269|PubMed:21448158}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Intolerance Scores

• loftool: 0.875
• rvis_EVS: 3.16
• rvis_percentile_EVS: 99.3

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;apoptotic process;mitotic cell cycle checkpoint;negative regulation of protein processing;protein deubiquitination;regulation of cell migration;negative regulation of histone deacetylation;negative regulation of GTPase activity;regulation of cell population proliferation;regulation of apoptotic process;positive regulation of GTPase activity;regulation of defense response to virus by host;protein K63-linked deubiquitination;protein K48-linked deubiquitination;CAAX-box protein processing;negative regulation of protein targeting to membrane;regulation of ruffle assembly;positive regulation of MDA-5 signaling pathway;positive regulation of RIG-I signaling pathway
• Cellular component: nucleus;endoplasmic reticulum membrane;cytosol
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity