YOD1

YOD1 deubiquitinase, the group of OTU domain containing

Basic information

Region (hg38): 1:207043849-207052980

Links

ENSG00000180667 ∙ NCBI:55432 ∙ OMIM:612023 ∙ HGNC:25035 ∙ Uniprot:Q5VVQ6 ∙ 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 YOD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YOD1 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		1
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in YOD1

This is a list of pathogenic ClinVar variants found in the YOD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-207049036-T-C		not specified	Uncertain significance (Mar 01, 2023)
1-207049306-C-G		not specified	Uncertain significance (Feb 23, 2023)
1-207049427-T-C		not specified	Uncertain significance (Mar 11, 2022)
1-207049453-G-T		not specified	Uncertain significance (Feb 22, 2023)
1-207049469-C-T		not specified	Uncertain significance (Oct 05, 2021)
1-207049477-T-C		not specified	Uncertain significance (Jul 14, 2023)
1-207049518-T-G		not specified	Uncertain significance (Nov 30, 2022)
1-207049526-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-207049528-G-C		not specified	Uncertain significance (Aug 02, 2021)
1-207049614-T-A		not specified	Uncertain significance (Aug 17, 2021)
1-207049643-C-G		not specified	Uncertain significance (Apr 15, 2024)
1-207050741-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-207050778-C-A		not specified	Uncertain significance (Nov 19, 2022)
1-207050846-C-T		not specified	Uncertain significance (Jun 20, 2024)
1-207050907-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-207050940-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-207050943-T-C		not specified	Uncertain significance (Feb 27, 2024)
1-207050950-G-A		not specified	Likely benign (Nov 21, 2023)
1-207050957-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-207050961-G-T		not specified	Uncertain significance (Aug 02, 2022)
1-207050973-C-G		not specified	Uncertain significance (Sep 26, 2022)
1-207050975-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-207050976-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-207050988-C-A		not specified	Uncertain significance (Oct 10, 2023)
1-207050994-G-A		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YOD1	protein_coding	protein_coding	ENST00000315927	2	9132

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.135	0.846	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.524	174	195	0.894	0.00000994	2247
Missense in Polyphen		43	70.28	0.61184		885
Synonymous	-1.03	86	74.6	1.15	0.00000378	725
Loss of Function	2.03	3	9.87	0.304	4.24e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000170	0.000163
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000170	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCP's axial channel. Mediates deubiquitination of 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitin chains. Also able to hydrolyze 'Lys-11'-linked ubiquitin chains. Cleaves both polyubiquitin and di-ubiquitin. May play a role in macroautophagy, regulating for instance the clearance of damaged lysosomes. May recruit PLAA, UBXN6 and VCP to damaged lysosome membranes decorated with K48-linked ubiquitin chains and remove these chains allowing autophagosome formation (PubMed:27753622). {ECO:0000269|PubMed:19818707, ECO:0000269|PubMed:23827681, ECO:0000269|PubMed:27753622}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Ovarian tumor domain proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.0740

Intolerance Scores

• loftool: 0.106
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.754
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yod1

Zebrafish Information Network

• Gene name: yod1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curled

Gene ontology

• Biological process: macroautophagy;protein deubiquitination;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;protein K29-linked deubiquitination;protein K11-linked deubiquitination;protein K63-linked deubiquitination;protein K48-linked deubiquitination;negative regulation of retrograde protein transport, ER to cytosol;protein K27-linked deubiquitination;protein K33-linked deubiquitination
• Cellular component: cytoplasm;cytosol
• Molecular function: nucleic acid binding;thiol-dependent ubiquitin-specific protease activity;protein binding;ubiquitin protein ligase binding;metal ion binding;Lys63-specific deubiquitinase activity;ubiquitin-specific protease activity involved in negative regulation of retrograde protein transport, ER to cytosol;Lys48-specific deubiquitinase activity