UBA7

ubiquitin like modifier activating enzyme 7, the group of Ubiquitin like modifier activating enzymes|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:49805209-49813953

Previous symbols: [ "UBE1L" ]

Links

ENSG00000182179 ∙ NCBI:7318 ∙ OMIM:191325 ∙ HGNC:12471 ∙ Uniprot:P41226 ∙ 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 UBA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBA7 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				1	1	2
missense			80	10	1	91
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	81	11	2

Variants in UBA7

This is a list of pathogenic ClinVar variants found in the UBA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49805382-C-T		not specified	Uncertain significance (Dec 05, 2024)
3-49805385-G-A		not specified	Uncertain significance (Jan 18, 2023)
3-49805446-G-A		UBA7-related disorder	Likely benign (May 25, 2023)
3-49805945-T-C		not specified	Uncertain significance (Apr 25, 2023)
3-49805955-C-T		not specified	Uncertain significance (Jan 05, 2022)
3-49805958-A-G		not specified	Likely benign (Feb 07, 2023)
3-49806096-C-T		not specified	Uncertain significance (Aug 19, 2024)
3-49806114-G-T		not specified	Uncertain significance (Apr 04, 2023)
3-49807779-T-C		not specified	Uncertain significance (Mar 31, 2023)
3-49807795-G-C		not specified	Uncertain significance (Apr 06, 2022)
3-49807806-C-T		not specified	Uncertain significance (Sep 08, 2024)
3-49807819-G-A			Likely benign (Dec 31, 2019)
3-49807822-G-A		not specified	Uncertain significance (Sep 27, 2021)
3-49807824-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-49807864-G-C		not specified	Uncertain significance (Nov 09, 2022)
3-49807866-C-T		not specified	Uncertain significance (Aug 28, 2024)
3-49807881-G-A		not specified	Uncertain significance (Feb 03, 2022)
3-49807906-T-C		not specified	Uncertain significance (Oct 01, 2024)
3-49807920-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-49808027-C-G		UBA7-related disorder	Benign (Mar 20, 2019)
3-49808027-C-T		not specified	Uncertain significance (Apr 20, 2023)
3-49808028-G-A		not specified	Uncertain significance (May 03, 2023)
3-49808036-G-A		not specified	Uncertain significance (Nov 08, 2024)
3-49808060-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-49808075-G-A		not specified	Uncertain significance (Oct 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBA7	protein_coding	protein_coding	ENST00000333486	24	8740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.82e-17	0.870	125314	4	430	125748	0.00173

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.988	507	574	0.884	0.0000328	6504
Missense in Polyphen		130	174.05	0.74692		2179
Synonymous	0.308	232	238	0.975	0.0000133	2131
Loss of Function	2.18	34	50.8	0.670	0.00000246	570

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00326	0.00325
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000495	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00125	0.00124
Middle Eastern	0.000495	0.000489
South Asian	0.00598	0.00577
Other	0.00313	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates ubiquitin by first adenylating with ATP its C- terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin- E1 thioester and free AMP. Catalyzes the ISGylation of influenza A virus NS1 protein. {ECO:0000269|PubMed:16254333, ECO:0000269|PubMed:20133869}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Proteasome Degradation;Parkinsons Disease Pathway;DNA Repair;Cytokine Signaling in Immune system;DDX58/IFIH1-mediated induction of interferon-alpha/beta;protein ubiquitylation;Innate Immune System;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;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: 0.145

Intolerance Scores

• loftool: 0.935
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.66

Haploinsufficiency Scores

• pHI: 0.0862
• hipred: N
• hipred_score: 0.258
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uba7
• Phenotype: normal phenotype; cellular phenotype

Gene ontology

• Biological process: cellular protein modification process;cellular response to DNA damage stimulus;protein ubiquitination;modification-dependent protein catabolic process;ISG15-protein conjugation;protein modification by small protein conjugation;negative regulation of type I interferon production
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding;ATP binding;ISG15 activating enzyme activity