USP39

ubiquitin specific peptidase 39, the group of Ubiquitin specific peptidases|tri-snRP complex

Basic information

Region (hg38): 2:85602856-85649283

Links

ENSG00000168883 ∙ NCBI:10713 ∙ OMIM:611594 ∙ HGNC:20071 ∙ Uniprot:Q53GS9 ∙ 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 USP39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP39 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
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in USP39

This is a list of pathogenic ClinVar variants found in the USP39 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85611683-G-T		not specified	Uncertain significance (Jun 18, 2021)
2-85616202-G-A		not specified	Likely benign (Feb 05, 2024)
2-85616218-A-G		not specified	Uncertain significance (Nov 21, 2023)
2-85616226-G-A		not specified	Uncertain significance (Dec 27, 2023)
2-85616235-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-85616269-C-T		not specified	Uncertain significance (Sep 06, 2022)
2-85616305-A-T		not specified	Uncertain significance (Nov 24, 2024)
2-85616314-C-T		not specified	Uncertain significance (Nov 29, 2021)
2-85616319-A-C		not specified	Uncertain significance (Nov 17, 2023)
2-85616329-G-A		not specified	Uncertain significance (Oct 14, 2021)
2-85616332-G-C		not specified	Uncertain significance (Jul 22, 2024)
2-85616340-C-T		not specified	Uncertain significance (Mar 30, 2024)
2-85616344-T-C		not specified	Uncertain significance (Apr 17, 2024)
2-85616352-G-C		not specified	Uncertain significance (May 23, 2023)
2-85616368-G-T		not specified	Uncertain significance (Dec 01, 2022)
2-85616400-T-G		not specified	Uncertain significance (Oct 07, 2024)
2-85616421-C-T		not specified	Uncertain significance (Jul 30, 2024)
2-85616427-G-A		not specified	Uncertain significance (Jan 26, 2022)
2-85619251-G-C			Likely benign (Jun 01, 2022)
2-85619258-C-T		not specified	Uncertain significance (Jan 29, 2024)
2-85621578-A-T		not specified	Uncertain significance (Dec 26, 2023)
2-85623778-T-C		not specified	Uncertain significance (Oct 29, 2024)
2-85630752-A-G		not specified	Uncertain significance (Dec 10, 2024)
2-85630781-A-G		not specified	Uncertain significance (Sep 20, 2024)
2-85630785-A-G		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP39	protein_coding	protein_coding	ENST00000323701	13	46425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0104	0.990	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	227	312	0.728	0.0000166	3703
Missense in Polyphen		59	137.16	0.43016		1610
Synonymous	-0.479	129	122	1.06	0.00000656	1080
Loss of Function	3.45	9	29.0	0.310	0.00000148	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in pre-mRNA splicing as a component of the U4/U6-U5 tri-snRNP, one of the building blocks of the precatalytic spliceosome (PubMed:11350945, PubMed:26912367). Regulates AURKB mRNA levels, and thereby plays a role in cytokinesis and in the spindle checkpoint. Does not have ubiquitin-specific peptidase activity (PubMed:18728397). {ECO:0000269|PubMed:11350945, ECO:0000269|PubMed:18728397, ECO:0000269|PubMed:26912367}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.558
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.59

Haploinsufficiency Scores

• pHI: 0.337
• hipred: Y
• hipred_score: 0.639
• ghis: 0.599

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp39
• Phenotype: pigmentation 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: usp39
• Affected structure: proximal pars anterior
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: spliceosomal complex assembly;mRNA splicing, via spliceosome;mRNA processing;cell cycle;RNA splicing;protein deubiquitination;cell division
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U4/U6 x U5 tri-snRNP complex
• Molecular function: zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity