USP35

ubiquitin specific peptidase 35, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 11:78188811-78215232

Links

ENSG00000118369 ∙ NCBI:57558 ∙ ∙ HGNC:20061 ∙ Uniprot:Q9P2H5 ∙ 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 USP35 gene.

• Inborn genetic diseases (56 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP35 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			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	4	1

Variants in USP35

This is a list of pathogenic ClinVar variants found in the USP35 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-78196265-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-78196294-G-T		not specified	Uncertain significance (Aug 28, 2023)
11-78196334-G-A		not specified	Uncertain significance (Aug 28, 2021)
11-78196340-C-T		not specified	Uncertain significance (Oct 02, 2023)
11-78196407-G-C		not specified	Likely benign (Apr 07, 2023)
11-78196467-C-A		not specified	Likely benign (Apr 07, 2023)
11-78196516-G-C		not specified	Uncertain significance (Jan 29, 2024)
11-78196720-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-78196727-G-T		not specified	Uncertain significance (Jun 02, 2023)
11-78196853-G-C		not specified	Uncertain significance (Jan 22, 2024)
11-78196856-G-T		not specified	Uncertain significance (Jun 22, 2021)
11-78196870-G-T		not specified	Uncertain significance (Jan 19, 2024)
11-78196894-C-G		not specified	Uncertain significance (Feb 02, 2024)
11-78198025-G-A		not specified	Uncertain significance (Dec 21, 2023)
11-78198032-G-C		not specified	Uncertain significance (Jul 08, 2022)
11-78199603-A-G		not specified	Uncertain significance (Nov 17, 2023)
11-78200163-C-T		not specified	Uncertain significance (Jul 08, 2022)
11-78200194-T-C		not specified	Uncertain significance (Dec 28, 2022)
11-78200217-C-T		not specified	Uncertain significance (Mar 20, 2023)
11-78200231-C-G		not specified	Uncertain significance (Dec 12, 2023)
11-78200678-C-T		not specified	Uncertain significance (Aug 05, 2021)
11-78200696-A-T		not specified	Uncertain significance (May 05, 2023)
11-78200705-C-T		not specified	Uncertain significance (Jan 30, 2024)
11-78200772-C-A		not specified	Uncertain significance (Aug 04, 2023)
11-78205914-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP35	protein_coding	protein_coding	ENST00000529308	10	25900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.49e-7	0.999	124853	0	66	124919	0.000264

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.294	589	569	1.03	0.0000376	6469
Missense in Polyphen		124	118.97	1.0423		1254
Synonymous	-1.36	280	253	1.11	0.0000173	2139
Loss of Function	2.81	16	33.6	0.477	0.00000143	429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000678	0.000676
Ashkenazi Jewish	0.00	0.00
East Asian	0.000281	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000316	0.000300
Middle Eastern	0.000281	0.000278
South Asian	0.000131	0.000131
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 2.05
• rvis_percentile_EVS: 97.78

Haploinsufficiency Scores

• pHI: 0.294
• hipred: Y
• hipred_score: 0.554
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp35

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity