UBE2J1

ubiquitin conjugating enzyme E2 J1, the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 6:89326625-89352722

Links

ENSG00000198833 ∙ NCBI:51465 ∙ OMIM:616175 ∙ HGNC:17598 ∙ Uniprot:Q9Y385 ∙ 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 UBE2J1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2J1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in UBE2J1

This is a list of pathogenic ClinVar variants found in the UBE2J1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-89329692-T-C		not specified	Uncertain significance (Jan 03, 2024)
6-89329728-A-G		not specified	Uncertain significance (Nov 21, 2024)
6-89329759-T-C		not specified	Uncertain significance (Feb 06, 2023)
6-89329785-T-C		not specified	Uncertain significance (Dec 05, 2022)
6-89329806-G-A		not specified	Uncertain significance (Jan 23, 2023)
6-89329818-T-C		not specified	Uncertain significance (Aug 17, 2022)
6-89329820-G-C		not specified	Uncertain significance (Jun 27, 2023)
6-89329837-T-C		not specified	Uncertain significance (Nov 30, 2021)
6-89329860-T-A		not specified	Uncertain significance (Jul 20, 2021)
6-89329867-C-T		not specified	Uncertain significance (Dec 04, 2021)
6-89329870-G-A		not specified	Uncertain significance (Dec 11, 2023)
6-89329882-G-A		not specified	Uncertain significance (Jul 17, 2024)
6-89333087-G-A		not specified	Uncertain significance (Nov 13, 2024)
6-89333099-G-A		not specified	Uncertain significance (Sep 20, 2024)
6-89333133-G-T		not specified	Uncertain significance (Oct 03, 2022)
6-89333148-A-G		not specified	Uncertain significance (Nov 24, 2024)
6-89333162-A-G		not specified	Uncertain significance (Mar 05, 2024)
6-89335377-C-A		not specified	Uncertain significance (Apr 09, 2024)
6-89338286-A-G		not specified	Uncertain significance (Jul 11, 2023)
6-89338467-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-89338515-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-89342430-G-A		not specified	Uncertain significance (Dec 17, 2023)
6-89343696-G-A		not specified	Uncertain significance (Jun 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2J1	protein_coding	protein_coding	ENST00000435041	8	26224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.437	0.563	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	137	175	0.781	0.00000940	2056
Missense in Polyphen		32	65.182	0.49093		737
Synonymous	0.213	60	62.1	0.966	0.00000337	614
Loss of Function	3.12	4	18.5	0.216	0.00000103	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000594	0.0000594
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in the selective degradation of misfolded membrane proteins from the endoplasmic reticulum (ERAD). {ECO:0000255|PROSITE-ProRule:PRU00388, ECO:0000269|PubMed:12082160, ECO:0000269|PubMed:22607976}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Parkin-Ubiquitin Proteasomal System pathway;Parkinsons Disease Pathway;protein ubiquitylation;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.448
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.172
• hipred: Y
• hipred_score: 0.644
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2j1
• Phenotype: cellular phenotype; growth/size/body region phenotype; skeleton phenotype; limbs/digits/tail phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: spermatid development;protein ubiquitination;protein N-linked glycosylation via asparagine;ubiquitin-dependent ERAD pathway;regulation of tumor necrosis factor biosynthetic process;negative regulation of retrograde protein transport, ER to cytosol
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity