OTUD6A

OTU deubiquitinase 6A, the group of OTU domain containing

Basic information

Region (hg38): X:70062457-70064179

Links

ENSG00000189401 ∙ NCBI:139562 ∙ OMIM:300714 ∙ HGNC:32312 ∙ Uniprot:Q7L8S5 ∙ 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 OTUD6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTUD6A 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					2	2
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	2

Variants in OTUD6A

This is a list of pathogenic ClinVar variants found in the OTUD6A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-70062769-T-C		not specified	Uncertain significance (Jan 04, 2024)
X-70062786-C-G		not specified	Uncertain significance (Jun 07, 2023)
X-70062841-G-A		not specified	Uncertain significance (Feb 07, 2023)
X-70062846-C-G		not specified	Uncertain significance (Dec 27, 2023)
X-70062924-G-A		not specified	Uncertain significance (Sep 16, 2021)
X-70063047-G-T		not specified	Uncertain significance (Oct 29, 2021)
X-70063118-C-T			Benign (May 17, 2018)
X-70063126-A-C		not specified	Uncertain significance (Nov 09, 2021)
X-70063203-C-A		not specified	Uncertain significance (Jan 26, 2022)
X-70063386-C-T			Benign (May 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTUD6A	protein_coding	protein_coding	ENST00000338352	1	1689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.285	0.501	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	91	155	0.588	0.0000153	1896
Missense in Polyphen		15	42.828	0.35024		579
Synonymous	0.819	65	74.0	0.879	0.00000814	556
Loss of Function	0.190	0	0.0419	0.00	2.60e-9	1

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 hydrolyzes 'Lys-27'-, 'Lys- 29'- and 'Lys-33'-linked polyubiquitin chains. Also able to hydrolyze 'Lys-11'-linked ubiquitin chains. {ECO:0000269|PubMed:23827681}.

Recessive Scores

• pRec: 0.0934

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.0517
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otud6a
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein deubiquitination;protein K29-linked deubiquitination;protein K11-linked deubiquitination;protein K27-linked deubiquitination;protein K33-linked deubiquitination
• Molecular function: thiol-dependent ubiquitin-specific protease activity