UBE2K

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

Basic information

Region (hg38): 4:39698109-39782792

Previous symbols: [ "HIP2" ]

Links

ENSG00000078140

∙ NCBI:3093 ∙ OMIM:602846 ∙ HGNC:4914 ∙ Uniprot:P61086 ∙ 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 UBE2K gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2K 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				1 clinvar		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in UBE2K

This is a list of pathogenic ClinVar variants found in the UBE2K region.

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

Position	Type	Phenotype	Significance	ClinVar
4-39737450-G-A			Likely benign (May 24, 2018)	717387

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2K	protein_coding	protein_coding	ENST00000261427	7	84749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0138	121023	0	1	121024	0.00000413

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.23	12	105	0.114	0.00000516	1298
Missense in Polyphen		1	34.764	0.028765		412
Synonymous	1.09	28	36.4	0.770	0.00000174	378
Loss of Function	3.34	0	13.0	0.00	6.15e-7	152

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)	0.00000899	0.00000899
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro, in the presence or in the absence of BRCA1-BARD1 E3 ubiquitin-protein ligase complex, catalyzes the synthesis of 'Lys-48'-linked polyubiquitin chains. Does not transfer ubiquitin directly to but elongates monoubiquitinated substrate protein. Mediates the selective degradation of short-lived and abnormal proteins, such as the endoplasmic reticulum-associated degradation (ERAD) of misfolded lumenal proteins. Ubiquitinates huntingtin. May mediate foam cell formation by the suppression of apoptosis of lipid-bearing macrophages through ubiquitination and subsequence degradation of p53/TP53. Proposed to be involved in ubiquitination and proteolytic processing of NF-kappa-B; in vitro supports ubiquitination of NFKB1. In case of infection by cytomegaloviruses may be involved in the US11-dependent degradation of MHC class I heavy chains following their export from the ER to the cytosol. In case of viral infections may be involved in the HPV E7 protein- dependent degradation of RB1. {ECO:0000269|PubMed:10634809, ECO:0000269|PubMed:10675012, ECO:0000269|PubMed:16714285, ECO:0000269|PubMed:16868077, ECO:0000269|PubMed:17873885, ECO:0000269|PubMed:19906396, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:8702625}.;
Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Protein ubiquitination (Consensus)

Recessive Scores

pRec: 0.124

Intolerance Scores

loftool
rvis_EVS: 0.06
rvis_percentile_EVS: 58

Haploinsufficiency Scores

pHI: 0.749
hipred: Y
hipred_score: 0.738
ghis: 0.645

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ube2k
Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype;

Gene ontology

Biological process: ubiquitin-dependent protein catabolic process;positive regulation of peptidyl-threonine phosphorylation;free ubiquitin chain polymerization;protein ubiquitination;regulation of proteasomal ubiquitin-dependent protein catabolic process;cellular response to interferon-beta;positive regulation of type I interferon-mediated signaling pathway;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;protein K48-linked ubiquitination
Cellular component: nucleus;cytosol;filopodium tip
Molecular function: ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin-ubiquitin ligase activity;ubiquitin conjugating enzyme activity