USP42

ubiquitin specific peptidase 42, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 7:6104949-6161564

Links

ENSG00000106346 ∙ NCBI:84132 ∙ ∙ HGNC:20068 ∙ Uniprot:Q9H9J4 ∙ 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 USP42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP42 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				3	1	4
missense			174	17		191
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	174	20	1

Variants in USP42

This is a list of pathogenic ClinVar variants found in the USP42 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-6111155-T-G		not specified	Uncertain significance (Oct 12, 2024)
7-6111162-C-A		not specified	Uncertain significance (Aug 07, 2024)
7-6111198-G-A		not specified	Uncertain significance (Jul 20, 2021)
7-6111203-G-C		not specified	Uncertain significance (Oct 24, 2024)
7-6111207-C-G		not specified	Uncertain significance (Sep 25, 2024)
7-6111257-T-C		not specified	Uncertain significance (Mar 07, 2025)
7-6111286-A-G			Likely benign (Mar 01, 2023)
7-6111356-T-C		not specified	Uncertain significance (Jan 18, 2025)
7-6115340-G-A		not specified	Uncertain significance (Dec 27, 2023)
7-6115380-G-A		not specified	Uncertain significance (Mar 01, 2023)
7-6115407-T-C		not specified	Uncertain significance (Jan 27, 2022)
7-6115454-G-A		not specified	Uncertain significance (Jan 24, 2025)
7-6135927-A-G		not specified	Uncertain significance (Feb 15, 2023)
7-6135932-T-G		not specified	Uncertain significance (Oct 26, 2022)
7-6135940-A-G		not specified	Uncertain significance (Oct 13, 2023)
7-6139104-A-T		not specified	Uncertain significance (Jan 17, 2024)
7-6139109-C-T		not specified	Uncertain significance (Dec 10, 2024)
7-6139110-G-A		not specified	Uncertain significance (Jun 18, 2021)
7-6144115-G-T		not specified	Uncertain significance (Jan 24, 2025)
7-6145535-A-G		not specified	Uncertain significance (Nov 20, 2024)
7-6145543-A-G		not specified	Uncertain significance (Jan 10, 2022)
7-6146160-C-T		not specified	Uncertain significance (Dec 26, 2023)
7-6146202-A-G		not specified	Uncertain significance (May 16, 2023)
7-6147768-T-A		not specified	Uncertain significance (Mar 10, 2025)
7-6147783-A-G		not specified	Uncertain significance (Jun 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP42	protein_coding	protein_coding	ENST00000306177	16	56681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000103	124547	0	108	124655	0.000433

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.63	916	787	1.16	0.0000508	8497
Missense in Polyphen		217	297.6	0.72916		3669
Synonymous	-3.62	414	330	1.25	0.0000246	2550
Loss of Function	6.10	2	47.2	0.0423	0.00000233	619

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000205	0.000205
Ashkenazi Jewish	0.00	0.00
East Asian	0.00497	0.00491
Finnish	0.00	0.00
European (Non-Finnish)	0.000119	0.0000973
Middle Eastern	0.00497	0.00491
South Asian	0.0000657	0.0000654
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinating enzyme which may play an important role during spermatogenesis. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.284
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.4

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.360
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp42
• Phenotype: vision/eye phenotype; skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; hematopoietic system phenotype; reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: usp42
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: bent

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;spermatogenesis;protein deubiquitination;cell differentiation;regulation of apoptotic process
• Cellular component: nucleoplasm
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity