UBA3

ubiquitin like modifier activating enzyme 3, the group of Ubiquitin like modifier activating enzymes

Basic information

Region (hg38): 3:69054730-69080408

Previous symbols: [ "UBE1C" ]

Links

ENSG00000144744 ∙ NCBI:9039 ∙ OMIM:603172 ∙ HGNC:12470 ∙ Uniprot:Q8TBC4 ∙ 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 UBA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBA3 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			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	10	0	0

Variants in UBA3

This is a list of pathogenic ClinVar variants found in the UBA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-69055442-A-C		not specified	Uncertain significance (Dec 05, 2022)
3-69055495-G-A		not specified	Uncertain significance (Jul 14, 2022)
3-69055893-T-C		not specified	Uncertain significance (May 26, 2024)
3-69056002-G-A			Uncertain significance (Aug 01, 2024)
3-69057304-C-G		not specified	Uncertain significance (Aug 04, 2021)
3-69062080-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-69062095-T-G		not specified	Uncertain significance (May 15, 2024)
3-69062139-A-C		not specified	Uncertain significance (Jul 05, 2023)
3-69063025-A-T		not specified	Uncertain significance (Aug 22, 2023)
3-69063471-T-C		not specified	Uncertain significance (Jul 25, 2023)
3-69064073-T-C		not specified	Uncertain significance (Feb 03, 2022)
3-69067941-A-C		not specified	Uncertain significance (Sep 20, 2023)
3-69071601-C-G		not specified	Uncertain significance (Dec 11, 2023)
3-69080327-T-C			Uncertain significance (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBA3	protein_coding	protein_coding	ENST00000361055	18	25679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.504	0.496	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	187	238	0.787	0.0000113	3014
Missense in Polyphen		61	99.968	0.6102		1243
Synonymous	0.668	78	85.9	0.908	0.00000446	859
Loss of Function	4.14	7	32.5	0.216	0.00000180	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000585	0.0000544
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.0000717	0.0000703
Middle Eastern	0.0000585	0.0000544
South Asian	0.0000338	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Down-regulates steroid receptor activity. Necessary for cell cycle progression. {ECO:0000269|PubMed:10207026, ECO:0000269|PubMed:12740388, ECO:0000269|PubMed:9694792}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation;Coregulation of Androgen receptor activity;Validated nuclear estrogen receptor alpha network;Validated nuclear estrogen receptor beta network (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.552
• rvis_EVS: -0.74
• rvis_percentile_EVS: 13.94

Haploinsufficiency Scores

• pHI: 0.733
• hipred: Y
• hipred_score: 0.696
• ghis: 0.678

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uba3
• Phenotype: cellular phenotype; embryo 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: cellular protein modification process;proteolysis;endomitotic cell cycle;protein modification by small protein conjugation;post-translational protein modification;protein neddylation;negative regulation of transcription, DNA-templated;regulation of cell cycle
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: protein binding;ATP binding;acid-amino acid ligase activity;nuclear receptor binding;NEDD8 activating enzyme activity;NEDD8 transferase activity;identical protein binding;protein heterodimerization activity