USP17L5

ubiquitin specific peptidase 17 like family member 5

Basic information

Region (hg38): 4:9339403-9340995

Links

ENSG00000227140 ∙ NCBI:728386 ∙ ∙ HGNC:37177 ∙ Uniprot:A8MUK1 ∙ 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 USP17L5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP17L5 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						0
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in USP17L5

This is a list of pathogenic ClinVar variants found in the USP17L5 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-9340007-G-T		not specified	Uncertain significance (Sep 10, 2024)
4-9340163-G-C		not specified	Uncertain significance (Jun 24, 2022)
4-9340171-T-G		not specified	Uncertain significance (Nov 29, 2023)
4-9340187-C-T		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP17L5	protein_coding	protein_coding	ENST00000507227	1	1593

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	-0.0205	1	0.944	1.06	5.43e-8	3438
Missense in Polyphen		0	0.36084	0		1110
Synonymous	-0.342	1	0.649	1.54	4.76e-8	1026
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 that may include cell proliferation, progression through the cell cycle, apoptosis, cell migration, and the cellular response to viral infection. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Haploinsufficiency Scores

• ghis: 0.395

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;apoptotic process;protein deubiquitination;regulation of apoptotic process
• Cellular component: nucleus;endoplasmic reticulum
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity