JOSD2

Josephin domain containing 2, the group of MJD deubiquinating enzymes

Basic information

Region (hg38): 19:50505998-50511220

Links

ENSG00000161677 ∙ NCBI:126119 ∙ OMIM:615324 ∙ HGNC:28853 ∙ Uniprot:Q8TAC2 ∙ 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 JOSD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JOSD2 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in JOSD2

This is a list of pathogenic ClinVar variants found in the JOSD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50506225-A-G		not specified	Uncertain significance (Oct 29, 2021)
19-50506406-C-T		not specified	Uncertain significance (Sep 20, 2023)
19-50506412-C-T		not specified	Uncertain significance (Aug 04, 2023)
19-50506415-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-50506472-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-50506477-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-50507581-T-C		not specified	Uncertain significance (Oct 03, 2022)
19-50507593-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-50507667-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-50507682-C-T		not specified	Uncertain significance (Jun 05, 2024)
19-50507683-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-50510343-T-C		not specified	Uncertain significance (Jan 09, 2024)
19-50510364-A-C		not specified	Uncertain significance (Dec 12, 2023)
19-50510380-G-C		not specified	Uncertain significance (Jan 26, 2022)
19-50510383-C-G		not specified	Uncertain significance (Nov 22, 2021)
19-50510383-C-T		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JOSD2	protein_coding	protein_coding	ENST00000598418	4	5356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000180	0.480	125298	0	8	125306	0.0000319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.834	95	121	0.786	0.00000810	1169
Missense in Polyphen		35	50.233	0.69675		512
Synonymous	0.416	57	61.1	0.932	0.00000422	436
Loss of Function	0.324	6	6.92	0.867	2.97e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000982	0.0000980
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves 'Lys-63'-linked poly-ubiquitin chains, and with lesser efficiency 'Lys-48'-linked poly-ubiquitin chains (in vitro). May act as a deubiquitinating enzyme. {ECO:0000269|PubMed:17696782, ECO:0000269|PubMed:21118805, ECO:0000269|PubMed:23625928}.
• Pathway: Josephin domain DUBs;Post-translational protein modification;Metabolism of proteins;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.279
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.434

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Josd2

Zebrafish Information Network

• Gene name: josd2
• Affected structure: pharyngeal arch cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

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