USP38

ubiquitin specific peptidase 38, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 4:143184917-143225212

Links

ENSG00000170185NCBI:84640OMIM:618322HGNC:20067Uniprot:Q8NB14AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
3
clinvar
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)2493347
4-143185514-G-T not specified Uncertain significance (Jan 08, 2024)3187554
4-143185540-G-C not specified Uncertain significance (Mar 26, 2024)3331523
4-143185555-G-C not specified Uncertain significance (Oct 25, 2023)3187538
4-143185601-G-C not specified Uncertain significance (Oct 28, 2024)3467043
4-143185715-C-T not specified Uncertain significance (May 29, 2024)3331528
4-143185744-G-C not specified Uncertain significance (Feb 06, 2024)3187549
4-143185786-G-T not specified Uncertain significance (Jun 26, 2024)3467036
4-143185817-C-G not specified Uncertain significance (May 24, 2024)3331527
4-143185826-C-G not specified Uncertain significance (Nov 09, 2021)2260322
4-143185826-C-T not specified Uncertain significance (Dec 16, 2023)3187552
4-143185878-T-A not specified Uncertain significance (May 30, 2023)2567820
4-143185931-G-A not specified Uncertain significance (Nov 18, 2022)2327399
4-143185968-G-A not specified Uncertain significance (Jan 17, 2024)3187553
4-143186094-C-T not specified Uncertain significance (Apr 18, 2023)2538132
4-143187894-G-C not specified Uncertain significance (Jul 17, 2024)3467037
4-143187940-G-A not specified Uncertain significance (Oct 13, 2023)3187555
4-143195753-G-A not specified Uncertain significance (Nov 07, 2022)2360684
4-143197871-G-C not specified Uncertain significance (Sep 26, 2023)3187556
4-143203448-A-C not specified Uncertain significance (Oct 21, 2024)3467042
4-143203519-T-C not specified Uncertain significance (Mar 20, 2023)2527166
4-143203520-A-G not specified Uncertain significance (Aug 14, 2024)3467038
4-143206079-A-G not specified Uncertain significance (Apr 15, 2024)3331525
4-143206081-A-G not specified Uncertain significance (Aug 01, 2024)3467030
4-143206109-T-C not specified Uncertain significance (May 31, 2023)2554395

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
USP38protein_codingprotein_codingENST00000307017 1038914
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.85e-71.001256900581257480.000231
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.044715390.8740.00002536795
Missense in Polyphen100170.710.585792208
Synonymous0.08352082100.9930.00001022093
Loss of Function3.371841.40.4350.00000200517

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001860.000186
Ashkenazi Jewish0.002310.00209
East Asian0.0001100.000109
Finnish0.0001390.0000924
European (Non-Finnish)0.0001790.000176
Middle Eastern0.0001100.000109
South Asian0.0002060.000196
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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
Cellular component
Molecular function
cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity