USP38

ubiquitin specific peptidase 38, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 4:143184917-143225212

Links

ENSG00000170185 ∙ NCBI:84640 ∙ OMIM:618322 ∙ HGNC:20067 ∙ Uniprot:Q8NB14 ∙ 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 USP38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP38 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						0
missense			67	3		70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	3	0

Variants in USP38

This is a list of pathogenic ClinVar variants found in the USP38 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-143185457-A-G		not specified	Uncertain significance (Mar 02, 2023)
4-143185514-G-T		not specified	Uncertain significance (Jan 08, 2024)
4-143185540-G-C		not specified	Uncertain significance (Mar 26, 2024)
4-143185555-G-C		not specified	Uncertain significance (Oct 25, 2023)
4-143185601-G-C		not specified	Uncertain significance (Oct 28, 2024)
4-143185715-C-T		not specified	Uncertain significance (May 29, 2024)
4-143185744-G-C		not specified	Uncertain significance (Feb 06, 2024)
4-143185786-G-T		not specified	Uncertain significance (Jun 26, 2024)
4-143185817-C-G		not specified	Uncertain significance (May 24, 2024)
4-143185826-C-G		not specified	Uncertain significance (Nov 09, 2021)
4-143185826-C-T		not specified	Uncertain significance (Dec 16, 2023)
4-143185878-T-A		not specified	Uncertain significance (May 30, 2023)
4-143185931-G-A		not specified	Uncertain significance (Nov 18, 2022)
4-143185968-G-A		not specified	Uncertain significance (Jan 17, 2024)
4-143186094-C-T		not specified	Uncertain significance (Apr 18, 2023)
4-143187894-G-C		not specified	Uncertain significance (Jul 17, 2024)
4-143187940-G-A		not specified	Uncertain significance (Oct 13, 2023)
4-143195753-G-A		not specified	Uncertain significance (Nov 07, 2022)
4-143197871-G-C		not specified	Uncertain significance (Sep 26, 2023)
4-143203448-A-C		not specified	Uncertain significance (Oct 21, 2024)
4-143203519-T-C		not specified	Uncertain significance (Mar 20, 2023)
4-143203520-A-G		not specified	Uncertain significance (Aug 14, 2024)
4-143206079-A-G		not specified	Uncertain significance (Apr 15, 2024)
4-143206081-A-G		not specified	Uncertain significance (Aug 01, 2024)
4-143206109-T-C		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP38	protein_coding	protein_coding	ENST00000307017	10	38914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.85e-7	1.00	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	471	539	0.874	0.0000253	6795
Missense in Polyphen		100	170.71	0.58579		2208
Synonymous	0.0835	208	210	0.993	0.0000102	2093
Loss of Function	3.37	18	41.4	0.435	0.00000200	517

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000186
Ashkenazi Jewish	0.00231	0.00209
East Asian	0.000110	0.000109
Finnish	0.000139	0.0000924
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.000110	0.000109
South Asian	0.000206	0.000196
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinating enzyme exhibiting a preference towards 'Lys-63'-linked ubiquitin chains. {ECO:0000269|PubMed:22689415}.
• Pathway: Integrated Breast Cancer Pathway (Consensus)

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.685
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.28

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.492
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.716

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp38
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); skeleton phenotype; hematopoietic system phenotype

Gene ontology

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