USP36

ubiquitin specific peptidase 36, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 17:78787381-78841441

Links

ENSG00000055483 ∙ NCBI:57602 ∙ OMIM:612543 ∙ HGNC:20062 ∙ Uniprot:Q9P275 ∙ 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 USP36 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP36 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				6	6	12
missense			74	10	4	88
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	74	16	10

Variants in USP36

This is a list of pathogenic ClinVar variants found in the USP36 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-78798428-G-A		not specified	Uncertain significance (Dec 07, 2023)
17-78798455-G-C		not specified	Uncertain significance (Jan 04, 2022)
17-78798498-G-C		not specified	Uncertain significance (Mar 25, 2024)
17-78798504-G-A			Benign (May 09, 2018)
17-78798546-C-A		not specified	Uncertain significance (Jan 23, 2024)
17-78798958-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-78799711-T-A		not specified	Uncertain significance (Mar 07, 2024)
17-78799729-C-T		not specified	Uncertain significance (Jul 15, 2021)
17-78802329-C-T		not specified	Likely benign (Mar 07, 2024)
17-78802363-C-T		not specified	Likely benign (Feb 14, 2023)
17-78802376-C-G		not specified	Uncertain significance (Jul 30, 2023)
17-78802419-T-C		not specified	Uncertain significance (Jun 30, 2022)
17-78802423-G-A		not specified	Uncertain significance (Oct 05, 2022)
17-78802441-C-A		not specified	Uncertain significance (Jun 26, 2023)
17-78803401-C-T		not specified	Uncertain significance (Nov 08, 2022)
17-78803416-C-T		not specified	Uncertain significance (Mar 16, 2022)
17-78803431-C-A		not specified	Uncertain significance (Oct 17, 2023)
17-78803494-C-G		not specified	Uncertain significance (Dec 14, 2022)
17-78803535-C-G			Benign (Jul 31, 2018)
17-78803622-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-78803644-G-A		not specified	Uncertain significance (Dec 13, 2023)
17-78803647-T-G		not specified	Uncertain significance (Jan 03, 2024)
17-78803655-T-C		not specified	Likely benign (Dec 16, 2023)
17-78803684-A-G			Likely benign (Apr 01, 2022)
17-78803748-A-G		not specified	Uncertain significance (Mar 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP36	protein_coding	protein_coding	ENST00000542802	18	54061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000188	1.00	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.398	720	691	1.04	0.0000425	7306
Missense in Polyphen		204	248.31	0.82155		2720
Synonymous	-1.40	316	286	1.11	0.0000193	2238
Loss of Function	4.35	18	51.8	0.347	0.00000278	576

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000217	0.000217
South Asian	0.0000656	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinase essential for the regulation of nucleolar structure and function. Required for cell and organism viability. Plays an important role in ribosomal RNA processing and protein synthesis, which is mediated, at least in part, through deubiquitination of DHX33, NPM1 and FBL, regulating their protein stability (PubMed:29273634, PubMed:19208757, PubMed:22902402). Function as a transcriptional repressor by deubiquiting histone H2B at the promoters of genes critical for cellular differentiation, such as CDKN1A, thereby preventing histone H3 'Lys-4' trimethylation (H3K4) (PubMed:29274341). Specifically deubiquitinates MYC in the nucleolus, leading to prevent MYC degradation by the proteasome: acts by specifically interacting with isoform 3 of FBXW7 (FBW7gamma) in the nucleolus and counteracting ubiquitination of MYC by the SCF(FBW7) complex. In contrast, it does not interact with isoform 1 of FBXW7 (FBW7alpha) in the nucleoplasm (PubMed:25775507). Interacts to and regulates the actions of E3 ubiquitin-protein ligase NEDD4L over substrates such as NTRK1, KCNQ2 and KCNQ3, affecting their expression an functions (PubMed:27445338). Deubiquitinates SOD2, regulates SOD2 protein stability (PubMed:21268071). Deubiquitinase activity is required to control selective autophagy activation by ubiquitinated proteins (PubMed:22622177). {ECO:0000269|PubMed:19208757, ECO:0000269|PubMed:21268071, ECO:0000269|PubMed:22622177, ECO:0000269|PubMed:22902402, ECO:0000269|PubMed:25775507, ECO:0000269|PubMed:27445338, ECO:0000269|PubMed:29273634, ECO:0000269|PubMed:29274341}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.637
• rvis_EVS: 2.11
• rvis_percentile_EVS: 97.9

Haploinsufficiency Scores

• pHI: 0.0950
• hipred: Y
• hipred_score: 0.553
• ghis: 0.415

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp36
• Phenotype: cellular 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); embryo phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: usp36
• Affected structure: pharyngeal arch cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;nucleolus organization;negative regulation of macroautophagy;histone deubiquitination;protein deubiquitination;regulation of protein stability;regulation of apoptotic process;protein stabilization;regulation of autophagy of mitochondrion;positive regulation of protein targeting to mitochondrion;regulation of rRNA processing
• Cellular component: nucleolus;cytoplasm;nuclear speck
• Molecular function: RNA binding;cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding