OTUD1

OTU deubiquitinase 1, the group of OTU domain containing

Basic information

Region (hg38): 10:23439075-23442377

Previous symbols: [ "OTDC1" ]

Links

ENSG00000165312 ∙ NCBI:220213 ∙ OMIM:612022 ∙ HGNC:27346 ∙ Uniprot:Q5VV17 ∙ 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 OTUD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTUD1 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				7	3	10
missense			44	1	2	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	8	5

Variants in OTUD1

This is a list of pathogenic ClinVar variants found in the OTUD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-23439480-G-C		not specified	Uncertain significance (May 26, 2023)
10-23439487-C-G		not specified	Uncertain significance (Mar 28, 2024)
10-23439524-C-T		not specified	Uncertain significance (Nov 29, 2024)
10-23439533-C-T		not specified	Uncertain significance (Oct 12, 2024)
10-23439536-G-C		not specified	Uncertain significance (Sep 16, 2021)
10-23439541-C-T		OTUD1-related disorder	Benign (Apr 12, 2019)
10-23439542-G-C		not specified	Uncertain significance (Jun 02, 2024)
10-23439542-G-T		not specified	Uncertain significance (Dec 16, 2022)
10-23439548-C-G		not specified	Uncertain significance (Sep 25, 2024)
10-23439569-C-T		OTUD1-related disorder	Likely benign (Mar 21, 2022)
10-23439594-C-T		not specified	Uncertain significance (Feb 13, 2024)
10-23439597-A-C		not specified	Uncertain significance (Nov 30, 2022)
10-23439629-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-23439657-T-C		OTUD1-related disorder • not specified	Uncertain significance (Dec 16, 2023)
10-23439673-G-A		not specified	Uncertain significance (Aug 11, 2024)
10-23439689-T-A		not specified	Uncertain significance (May 04, 2022)
10-23439719-C-G		not specified	Uncertain significance (Mar 04, 2024)
10-23439761-C-G		not specified	Uncertain significance (Sep 16, 2021)
10-23439765-C-G		not specified	Uncertain significance (Dec 18, 2023)
10-23439766-G-A		OTUD1-related disorder	Likely benign (Jun 27, 2019)
10-23439767-C-T		OTUD1-related disorder	Likely benign (Jun 27, 2019)
10-23439791-G-A		not specified	Uncertain significance (Jun 27, 2023)
10-23439803-G-A		not specified	Uncertain significance (May 02, 2024)
10-23439823-C-G		not specified	Uncertain significance (Aug 19, 2023)
10-23439844-C-T			Likely benign (Feb 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTUD1	protein_coding	protein_coding	ENST00000376495	1	3111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.651	0.344	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	104	147	0.707	0.00000677	3005
Missense in Polyphen		26	57.008	0.45608		781
Synonymous	0.127	62	63.3	0.980	0.00000316	1027
Loss of Function	2.23	1	7.67	0.130	3.38e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinating enzyme that specifically hydrolyzes 'Lys-63'-linked polyubiquitin to monoubiquitin. {ECO:0000269|PubMed:23827681}.

Haploinsufficiency Scores

• pHI: 0.223
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.595

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otud1

Gene ontology

• Biological process: protein deubiquitination;protein K63-linked deubiquitination
• Molecular function: thiol-dependent ubiquitin-specific protease activity