UBE2L6

ubiquitin conjugating enzyme E2 L6, the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 11:57551656-57568284

Links

ENSG00000156587

∙ NCBI:9246 ∙ OMIM:603890 ∙ HGNC:12490 ∙ Uniprot:O14933 ∙ 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 UBE2L6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2L6 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			10 clinvar	1 clinvar		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in UBE2L6

This is a list of pathogenic ClinVar variants found in the UBE2L6 region.

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

Position	Phenotype	Significance	ClinVar
11-57552456-G-A	not specified	Uncertain significance (Jan 03, 2024)	3185531
11-57552476-G-A	not specified	Uncertain significance (May 24, 2024)	3330561
11-57552494-T-C	not specified	Likely benign (Apr 07, 2022)	3185530
11-57552495-T-G	not specified	Uncertain significance (Sep 27, 2022)	2386188
11-57554447-C-A	not specified	Uncertain significance (May 27, 2022)	2292977
11-57554506-C-T	not specified	Uncertain significance (Jun 16, 2023)	2601786
11-57554507-G-T	not specified	Uncertain significance (Sep 16, 2021)	2249727
11-57554512-C-T	not specified	Uncertain significance (Oct 26, 2022)	2378107
11-57554571-G-A	not specified	Uncertain significance (Oct 12, 2024)	3465078
11-57554594-G-T	not specified	Uncertain significance (Jun 18, 2021)	2407248
11-57560352-G-T	not specified	Uncertain significance (Jul 13, 2022)	2301520
11-57560366-C-T	not specified	Uncertain significance (May 24, 2024)	3330562
11-57560368-T-C	not specified	Uncertain significance (Oct 02, 2023)	3185532
11-57567586-T-G	not specified	Uncertain significance (Jul 26, 2021)	2239380

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2L6	protein_coding	protein_coding	ENST00000287156	4	16629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00770	0.795	125733	0	13	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.545	82	97.1	0.844	0.00000598	1007
Missense in Polyphen		28	36.096	0.77572		364
Synonymous	0.232	41	42.9	0.955	0.00000302	302
Loss of Function	0.993	4	6.79	0.589	3.88e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000791	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the covalent attachment of ubiquitin or ISG15 to other proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Promotes ubiquitination and subsequent proteasomal degradation of FLT3. {ECO:0000269|PubMed:15131269, ECO:0000269|PubMed:16428300, ECO:0000269|PubMed:20508617}.;
Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Parkin-Ubiquitin Proteasomal System pathway;Parkinsons Disease Pathway;DNA Repair;role of parkin in ubiquitin-proteasomal pathway;Cytokine Signaling in Immune system;DDX58/IFIH1-mediated induction of interferon-alpha/beta;protein ubiquitylation;Metabolism of proteins;Innate Immune System;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Amyloid fiber formation;Class I MHC mediated antigen processing & presentation;Negative regulators of DDX58/IFIH1 signaling;Termination of translesion DNA synthesis;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling (Consensus)

Recessive Scores

pRec: 0.0809

Intolerance Scores

loftool: 0.498
rvis_EVS: -0.08
rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

pHI: 0.0529
hipred: N
hipred_score: 0.457
ghis: 0.564

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ube2l6
Phenotype

Gene ontology

Biological process: cellular protein modification process;ubiquitin-dependent protein catabolic process;protein ubiquitination;translesion synthesis;ISG15-protein conjugation;negative regulation of type I interferon production;cellular protein metabolic process
Cellular component: ubiquitin ligase complex;nucleoplasm;cytosol
Molecular function: ubiquitin-protein transferase activity;protein binding;ubiquitin protein ligase binding;ISG15 transferase activity;ubiquitin binding;ubiquitin conjugating enzyme activity