UBE2S

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

Basic information

Region (hg38): 19:55399745-55407788

Links

ENSG00000108106 ∙ NCBI:27338 ∙ OMIM:610309 ∙ HGNC:17895 ∙ Uniprot:Q16763 ∙ 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 UBE2S gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2S 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				2	3	5
missense			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	19	3	4

Variants in UBE2S

This is a list of pathogenic ClinVar variants found in the UBE2S region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55401446-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-55401453-C-A		not specified	Uncertain significance (Jun 03, 2022)
19-55401467-G-A		not specified	Uncertain significance (May 10, 2024)
19-55401481-C-T		not specified	Likely benign (Jan 04, 2024)
19-55401541-C-T			Benign (Jul 20, 2018)
19-55401545-C-A		not specified	Uncertain significance (Jun 03, 2022)
19-55401545-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-55401564-C-T		not specified	Uncertain significance (May 03, 2023)
19-55401578-T-G			Benign (Dec 31, 2019)
19-55401601-A-C			Likely benign (Jul 02, 2018)
19-55401603-C-T		not specified	Uncertain significance (Apr 25, 2022)
19-55401610-G-A			Benign (Jun 14, 2018)
19-55401618-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-55401633-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-55401660-G-T		not specified	Uncertain significance (Jul 05, 2023)
19-55401729-C-T		not specified	Uncertain significance (Dec 28, 2023)
19-55404338-C-T		not specified	Uncertain significance (Mar 04, 2024)
19-55404340-T-C		not specified	Uncertain significance (Oct 12, 2022)
19-55404345-G-A			Benign (Jun 19, 2018)
19-55404442-T-G		not specified	Uncertain significance (Apr 04, 2023)
19-55404476-C-A		not specified	Uncertain significance (Dec 06, 2021)
19-55404483-A-T			Benign (Dec 04, 2017)
19-55406848-G-C		not specified	Uncertain significance (Mar 31, 2024)
19-55406850-T-A		not specified	Uncertain significance (Aug 12, 2021)
19-55406851-C-G		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2S	protein_coding	protein_coding	ENST00000264552	4	6494

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.632	0.362	125525	0	2	125527	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.959	121	155	0.783	0.0000105	1410
Missense in Polyphen		27	60.342	0.44745		605
Synonymous	-1.18	88	75.0	1.17	0.00000579	492
Loss of Function	2.19	1	7.45	0.134	4.01e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
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	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins (PubMed:22496338). Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle- regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit (PubMed:19820702, PubMed:19822757, PubMed:27259151). Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as an E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A (PubMed:16819549). In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination (PubMed:20061386, PubMed:20622874). {ECO:0000269|PubMed:16819549, ECO:0000269|PubMed:19820702, ECO:0000269|PubMed:19822757, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:22496338, ECO:0000269|PubMed:27259151}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;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: 0.122

Intolerance Scores

• loftool: 0.194
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.341
• hipred: Y
• hipred_score: 0.815
• ghis: 0.694

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.968

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2s

Gene ontology

• Biological process: cellular protein modification process;ubiquitin-dependent protein catabolic process;exit from mitosis;free ubiquitin chain polymerization;protein ubiquitination;anaphase-promoting complex-dependent catabolic process;protein K29-linked ubiquitination;protein K27-linked ubiquitination;cell division;protein K63-linked ubiquitination;protein K11-linked ubiquitination;protein K6-linked ubiquitination;positive regulation of ubiquitin protein ligase activity
• Cellular component: nucleoplasm;anaphase-promoting complex;cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding;ATP binding;anaphase-promoting complex binding;ubiquitin conjugating enzyme activity