USPL1

ubiquitin specific peptidase like 1, the group of Ubiquitin specific peptidase like |Ubiquitin specific peptidases

Basic information

Region (hg38): 13:30617692-30660770

Previous symbols: [ "C13orf22" ]

Links

ENSG00000132952 ∙ NCBI:10208 ∙ OMIM:617470 ∙ HGNC:20294 ∙ Uniprot:Q5W0Q7 ∙ 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 USPL1 gene.

• Inborn genetic diseases (55 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USPL1 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			44	11		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	11	0

Variants in USPL1

This is a list of pathogenic ClinVar variants found in the USPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-30621148-A-T		not specified	Uncertain significance (Mar 07, 2024)
13-30621216-C-T		not specified	Uncertain significance (Jun 09, 2022)
13-30621237-A-G		not specified	Uncertain significance (Mar 01, 2023)
13-30621849-G-A		not specified	Uncertain significance (Nov 10, 2021)
13-30630845-C-G		not specified	Uncertain significance (Dec 16, 2023)
13-30630863-T-G		not specified	Uncertain significance (Nov 21, 2022)
13-30630867-T-A		not specified	Uncertain significance (Apr 13, 2022)
13-30630870-C-A		not specified	Uncertain significance (Dec 07, 2021)
13-30630880-C-G		not specified	Uncertain significance (Mar 01, 2023)
13-30630894-A-C		not specified	Likely benign (Feb 22, 2023)
13-30630997-A-G		not specified	Uncertain significance (Dec 19, 2022)
13-30631019-A-G		not specified	Uncertain significance (Aug 02, 2022)
13-30631034-G-A		not specified	Uncertain significance (Nov 07, 2022)
13-30631117-C-T		not specified	Uncertain significance (Feb 21, 2024)
13-30631199-G-A		not specified	Uncertain significance (Nov 09, 2022)
13-30631201-C-A		not specified	Likely benign (Apr 13, 2023)
13-30631267-T-C		not specified	Uncertain significance (Sep 01, 2021)
13-30631307-C-T		not specified	Uncertain significance (May 04, 2023)
13-30631349-C-T		not specified	Likely benign (Mar 21, 2023)
13-30631376-G-A		not specified	Likely benign (Mar 24, 2023)
13-30631399-A-C		not specified	Uncertain significance (Oct 06, 2021)
13-30631399-A-G		not specified	Likely benign (May 30, 2023)
13-30637753-G-C		not specified	Uncertain significance (Apr 12, 2022)
13-30637765-C-G		not specified	Uncertain significance (Jul 11, 2023)
13-30642743-C-A		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USPL1	protein_coding	protein_coding	ENST00000255304	8	41857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0218	0.978	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.427	528	556	0.949	0.0000269	7142
Missense in Polyphen		115	139.76	0.82284		1985
Synonymous	0.0532	209	210	0.995	0.0000108	2121
Loss of Function	4.24	11	39.9	0.276	0.00000191	570

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SUMO-specific isopeptidase involved in protein desumoylation. Specifically binds SUMO proteins with a higher affinity for SUMO2 and SUMO3 which it cleaves more efficiently. Also able to process full-length SUMO proteins to their mature forms (PubMed:22878415). Plays a key role in RNA polymerase-II- mediated snRNA transcription in the Cajal bodies (PubMed:24413172). Is a component of complexes that can bind to U snRNA genes (PubMed:24413172). {ECO:0000269|PubMed:22878415, ECO:0000269|PubMed:24413172}.

Recessive Scores

• pRec: 0.0852

Intolerance Scores

• loftool: 0.724
• rvis_EVS: 0.45
• rvis_percentile_EVS: 78.05

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.233
• ghis: 0.498

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uspl1

Zebrafish Information Network

• Gene name: uspl1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved dorsal

Gene ontology

• Biological process: cell population proliferation;snRNA transcription;protein desumoylation;Cajal body organization
• Cellular component: extracellular space;Cajal body
• Molecular function: protein binding;SUMO binding;ubiquitin binding;SUMO-specific isopeptidase activity