UBR3

ubiquitin protein ligase E3 component n-recognin 3, the group of Ubiquitin protein ligase E3 component n-recognins

Basic information

Region (hg38): 2:169827454-170084131

Previous symbols: [ "ZNF650" ]

Links

ENSG00000144357 ∙ NCBI:130507 ∙ OMIM:613831 ∙ HGNC:30467 ∙ Uniprot:Q6ZT12 ∙ 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 UBR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBR3 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				8	6	14
missense			55	3		58
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				2		2
non coding				1		1
Total	0	0	56	13	6

Variants in UBR3

This is a list of pathogenic ClinVar variants found in the UBR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-169827526-G-C		not specified	Uncertain significance (Dec 15, 2023)
2-169827533-T-G		not specified	Uncertain significance (Dec 03, 2021)
2-169827599-C-T		not specified	Uncertain significance (Aug 11, 2022)
2-169827691-G-A		not specified	Uncertain significance (Mar 07, 2024)
2-169827762-G-A		UBR3-related disorder	Likely benign (Apr 19, 2020)
2-169827914-G-A		UBR3-related disorder	Uncertain significance (May 11, 2023)
2-169827930-C-T		UBR3-related disorder	Likely benign (Jun 07, 2019)
2-169828049-G-A		not specified	Uncertain significance (Jan 10, 2022)
2-169828062-G-A		UBR3-related disorder	Likely benign (Jun 12, 2019)
2-169872270-A-G		not specified	Uncertain significance (Feb 15, 2023)
2-169872302-G-C		not specified	Uncertain significance (Oct 31, 2022)
2-169872302-GAT-G		UBR3-related disorder	Uncertain significance (May 15, 2023)
2-169872312-T-C		not specified	Uncertain significance (Dec 02, 2022)
2-169872330-A-G		UBR3-related disorder	Likely benign (Apr 01, 2019)
2-169875809-A-G		not specified	Uncertain significance (May 18, 2022)
2-169875812-A-T		not specified	Uncertain significance (Apr 09, 2024)
2-169875931-T-C		not specified	Uncertain significance (Dec 21, 2022)
2-169877534-G-C		not specified	Uncertain significance (Oct 02, 2023)
2-169877562-C-G			Uncertain significance (Aug 01, 2017)
2-169877592-G-A		not specified	Uncertain significance (Jan 03, 2022)
2-169877619-A-C		not specified	Uncertain significance (Sep 22, 2022)
2-169878535-C-T			Benign (Mar 01, 2023)
2-169878539-A-G		not specified	Uncertain significance (Dec 26, 2023)
2-169878572-G-A		not specified	Uncertain significance (Feb 28, 2024)
2-169895228-C-A		not specified	Uncertain significance (Apr 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBR3	protein_coding	protein_coding	ENST00000418381	39	256674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.17e-11	125731	0	13	125744	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.43	468	826	0.566	0.0000410	12375
Missense in Polyphen		159	375.34	0.42362		5576
Synonymous	2.02	244	288	0.848	0.0000149	3446
Loss of Function	8.25	6	90.9	0.0660	0.00000452	1296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000186
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000717	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end rule pathway (By similarity). Does not bind to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation (By similarity). May play a role in Shh signaling by mediating the ubiquitination of Kif7 (By similarity). May be important for MYH9 function in certain tissues, possibly by regulating the ubiquitination of MYH9 and consequently affecting its interaction with MYO7A (PubMed:27331610). {ECO:0000250|UniProtKB:Q5U430, ECO:0000269|PubMed:27331610}.

Intolerance Scores

• loftool: 0.401
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.71

Haploinsufficiency Scores

• pHI: 0.356
• hipred: Y
• hipred_score: 0.677
• ghis: 0.675

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubr3
• Phenotype: homeostasis/metabolism phenotype; taste/olfaction 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); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: ubr3
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: has extra parts of type

Gene ontology

• Biological process: in utero embryonic development;suckling behavior;ubiquitin-dependent protein catabolic process;sensory perception of smell;embryo development ending in birth or egg hatching;protein ubiquitination;olfactory behavior;ubiquitin-dependent protein catabolic process via the N-end rule pathway
• Cellular component: ubiquitin ligase complex;cytoplasm;integral component of membrane
• Molecular function: ubiquitin-protein transferase activity;zinc ion binding;ubiquitin protein ligase activity