JOSD1

Josephin domain containing 1, the group of MJD deubiquinating enzymes

Basic information

Region (hg38): 22:38685543-38701556

Links

ENSG00000100221 ∙ NCBI:9929 ∙ OMIM:615323 ∙ HGNC:28953 ∙ Uniprot:Q15040 ∙ 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 JOSD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JOSD1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	5	0	0

Variants in JOSD1

This is a list of pathogenic ClinVar variants found in the JOSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38688948-C-T		not specified	Uncertain significance (Mar 28, 2024)
22-38688995-T-A		not specified	Uncertain significance (Feb 06, 2024)
22-38689086-T-C		not specified	Uncertain significance (Apr 20, 2024)
22-38689101-C-T		not specified	Uncertain significance (Jan 24, 2023)
22-38689323-T-C		not specified	Uncertain significance (Oct 30, 2023)
22-38689429-C-A			Benign (Oct 17, 2017)
22-38699840-C-T		not specified	Uncertain significance (Jan 22, 2024)
22-38699918-G-C		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JOSD1	protein_coding	protein_coding	ENST00000216039	4	16014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0446	0.932	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	63	119	0.531	0.00000629	1335
Missense in Polyphen		13	38.768	0.33533		506
Synonymous	-1.75	62	46.8	1.32	0.00000289	375
Loss of Function	1.97	4	11.1	0.362	6.21e-7	109

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)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinates monoubiquitinated probes (in vitro). When ubiquitinated, cleaves 'Lys-63'-linked and 'Lys-48'-linked poly-ubiquitin chains (in vitro), hence may act as a deubiquitinating enzyme. May increase macropinocytosis and suppress clathrin- and caveolae-mediated endocytosis. May enhance membrane dynamics and cell motility independently of its catalytic activity. {ECO:0000269|PubMed:21118805, ECO:0000269|PubMed:23625928}.
• Pathway: Josephin domain DUBs;Post-translational protein modification;Metabolism of proteins;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.245
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.547
• hipred: N
• hipred_score: 0.479
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.706

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Josd1

Zebrafish Information Network

• Gene name: josd1
• Affected structure: pharyngeal arch cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: protein deubiquitination
• Cellular component: cytosol;plasma membrane;membrane
• Molecular function: thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity