UBR7

ubiquitin protein ligase E3 component n-recognin 7, the group of Ubiquitin protein ligase E3 component n-recognins

Basic information

Region (hg38): 14:93207240-93229215

Previous symbols: [ "C14orf130" ]

Links

ENSG00000012963 ∙ NCBI:55148 ∙ OMIM:613816 ∙ HGNC:20344 ∙ Uniprot:Q8N806 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR
• Li-Campeau syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Li-Campeau syndrome	AR	Cardiovascular; Endocrine	The condition can involve congenital cardiac anomalies, and awareness may allow early management; Among other features, the condition can include hypothyroidism, and awareness may allow medical management	Cardiovascular; Craniofacial; Endocrine; Genitourinary; Neurologic; Musculoskeletal	33340455

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBR7 gene.

• Li-Campeau syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBR7 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				4		4
missense			15	2		17
nonsense		3				3
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding						0
Total	1	3	16	6	0

Variants in UBR7

This is a list of pathogenic ClinVar variants found in the UBR7 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-93207298-G-C		not specified	Uncertain significance (Nov 10, 2022)
14-93207313-G-A		not specified	Uncertain significance (Dec 28, 2022)
14-93207314-C-A		not specified	Uncertain significance (Dec 28, 2022)
14-93207320-G-A		not specified	Uncertain significance (Apr 13, 2023)
14-93207325-T-TCGGAGCTGGAGCCCGTGGTA		Intellectual disability, mild	Pathogenic (Aug 11, 2020)
14-93207328-G-T		Li-Campeau syndrome	Pathogenic (Feb 18, 2021)
14-93207350-T-G		not specified	Uncertain significance (Oct 13, 2023)
14-93209839-C-T		Li-Campeau syndrome	Likely pathogenic (Feb 04, 2022)
14-93209900-T-G		Li-Campeau syndrome	Likely pathogenic (-)
14-93209909-G-C		not specified	Uncertain significance (Jul 22, 2022)
14-93209922-T-C			Likely benign (Apr 01, 2023)
14-93209949-C-T			Likely benign (Mar 01, 2022)
14-93210656-G-A		Long QT syndrome	Likely benign (-)
14-93212092-A-G		not specified	Uncertain significance (May 25, 2022)
14-93214953-G-A			Likely benign (Nov 01, 2022)
14-93214955-A-G			Likely benign (Mar 01, 2023)
14-93215174-A-G		Li-Campeau syndrome	Pathogenic (Feb 17, 2021)
14-93215243-G-GTT		Li-Campeau syndrome	Pathogenic (Feb 18, 2021)
14-93215254-T-C			Likely benign (Oct 01, 2022)
14-93215267-C-T		not specified	Uncertain significance (Apr 06, 2022)
14-93218542-CT-C		Li-Campeau syndrome	Conflicting classifications of pathogenicity (Mar 25, 2024)
14-93218575-G-T		not specified	Uncertain significance (Jun 05, 2023)
14-93218661-G-A		not specified	Uncertain significance (Apr 12, 2023)
14-93218680-A-C		not specified	Uncertain significance (Dec 28, 2023)
14-93219263-C-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBR7	protein_coding	protein_coding	ENST00000013070	11	22161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.494	0.505	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	145	223	0.651	0.0000108	2821
Missense in Polyphen		38	89.644	0.4239		1195
Synonymous	1.04	68	79.9	0.851	0.00000403	712
Loss of Function	3.54	5	23.5	0.212	9.92e-7	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000389	0.000343
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000813	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. {ECO:0000250}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.470
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.302
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubr7

Gene ontology

• Biological process: biological_process;protein ubiquitination
• Cellular component: cytoplasm
• Molecular function: molecular_function;zinc ion binding;ubiquitin protein ligase activity