UBE2F

ubiquitin conjugating enzyme E2 F (putative), the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 2:237966827-238042782

Links

ENSG00000184182 ∙ NCBI:140739 ∙ OMIM:617700 ∙ HGNC:12480 ∙ Uniprot:Q969M7 ∙ 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 UBE2F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2F 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in UBE2F

This is a list of pathogenic ClinVar variants found in the UBE2F region.

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

Position	Type	Phenotype	Significance	ClinVar
2-237973135-C-T		not specified	Uncertain significance (Oct 26, 2022)
2-237973180-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-237973184-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-238016619-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-238025360-C-G		not specified	Uncertain significance (Mar 11, 2022)
2-238032252-A-G		not specified	Uncertain significance (Dec 02, 2022)
2-238041324-C-T		not specified	Uncertain significance (Sep 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2F	protein_coding	protein_coding	ENST00000272930	9	75768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.923	0.0772	125235	0	1	125236	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	69	108	0.639	0.00000628	1204
Missense in Polyphen		14	33.93	0.41261		462
Synonymous	1.48	28	39.9	0.703	0.00000244	341
Loss of Function	3.03	1	12.6	0.0794	5.30e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accepts the ubiquitin-like protein NEDD8 from the UBA3- NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The specific interaction with the E3 ubiquitin ligase RBX2, but not RBX1, suggests that the RBX2-UBE2F complex neddylates specific target proteins, such as CUL5. {ECO:0000269|PubMed:19250909}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Cell Cycle;Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.188
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.260
• hipred: Y
• hipred_score: 0.594
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2f

Gene ontology

• Biological process: post-translational protein modification;protein neddylation
• Cellular component: cytosol
• Molecular function: protein binding;ATP binding;NEDD8 transferase activity;NEDD8 conjugating enzyme activity