USP40

ubiquitin specific peptidase 40, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 2:233475526-233566782

Links

ENSG00000085982 ∙ NCBI:55230 ∙ OMIM:610570 ∙ HGNC:20069 ∙ Uniprot:Q9NVE5 ∙ 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 USP40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP40 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	2	3
missense			74	5		79
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	6	2

Variants in USP40

This is a list of pathogenic ClinVar variants found in the USP40 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-233477415-T-A		not specified	Uncertain significance (Jan 04, 2022)
2-233477417-G-C		not specified	Uncertain significance (Jul 11, 2023)
2-233477423-G-C		not specified	Uncertain significance (Jan 23, 2023)
2-233477432-G-C		not specified	Uncertain significance (Dec 15, 2022)
2-233477438-C-T		not specified	Uncertain significance (Jan 29, 2024)
2-233477445-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-233477453-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-233477455-C-G		not specified	Uncertain significance (Nov 10, 2024)
2-233477478-T-A		not specified	Uncertain significance (Jan 17, 2023)
2-233481225-G-A		not specified	Uncertain significance (Mar 07, 2023)
2-233481245-C-T		not specified	Uncertain significance (Feb 01, 2023)
2-233481282-C-T		not specified	Uncertain significance (Nov 06, 2023)
2-233485551-C-T		not specified	Uncertain significance (Aug 12, 2024)
2-233485618-T-G		not specified	Uncertain significance (Jul 14, 2024)
2-233485768-C-G		not specified	Uncertain significance (Apr 15, 2024)
2-233485775-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-233485780-G-A		not specified	Uncertain significance (Jul 30, 2024)
2-233485808-A-T		not specified	Uncertain significance (Dec 07, 2022)
2-233485819-T-A		not specified	Uncertain significance (Nov 30, 2024)
2-233485822-A-G		not specified	Uncertain significance (Feb 23, 2023)
2-233485832-C-T		not specified	Uncertain significance (Nov 24, 2024)
2-233485840-C-T		not specified	Uncertain significance (Apr 22, 2024)
2-233485850-C-A		not specified	Uncertain significance (Apr 22, 2022)
2-233485895-C-T		not specified	Likely benign (Dec 04, 2023)
2-233485919-G-A		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP40	protein_coding	protein_coding	ENST00000450966	31	91263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-25	0.308	124400	0	239	124639	0.000959

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.241	611	628	0.973	0.0000332	8145
Missense in Polyphen		195	201.11	0.9696		2719
Synonymous	0.325	223	229	0.973	0.0000130	2263
Loss of Function	2.06	49	67.2	0.729	0.00000324	880

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00625	0.00619
Ashkenazi Jewish	0.000100	0.0000994
East Asian	0.00119	0.00117
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000754	0.000690
Middle Eastern	0.00119	0.00117
South Asian	0.000683	0.000654
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be catalytically inactive.

Recessive Scores

• pRec: 0.0910

Intolerance Scores

• loftool: 0.986
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.68

Haploinsufficiency Scores

• pHI: 0.0605
• hipred: N
• hipred_score: 0.176
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp40

Zebrafish Information Network

• Gene name: usp40
• Affected structure: pronephric glomerular basement membrane
• Phenotype tag: abnormal
• Phenotype quality: decreased functionality

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;regulation of protein stability
• Cellular component: cytosol
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity