URB2

URB2 ribosome biogenesis homolog, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 1:229626246-229660200

Previous symbols: [ "KIAA0133" ]

Links

ENSG00000135763 ∙ NCBI:9816 ∙ OMIM:619372 ∙ HGNC:28967 ∙ Uniprot:Q14146 ∙ 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 URB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the URB2 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	1	3
missense			74	10	3	87
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	75	12	4

Variants in URB2

This is a list of pathogenic ClinVar variants found in the URB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-229627718-G-C		not specified	Uncertain significance (Mar 20, 2023)
1-229632298-G-T		not specified	Uncertain significance (May 30, 2024)
1-229632324-A-G		not specified	Uncertain significance (Nov 14, 2023)
1-229632378-A-G		not specified	Uncertain significance (Jun 17, 2024)
1-229632382-C-G		not specified	Uncertain significance (Dec 14, 2023)
1-229632390-T-G		not specified	Uncertain significance (Sep 16, 2021)
1-229632419-A-G		not specified	Likely benign (Sep 15, 2022)
1-229634933-T-C		not specified	Uncertain significance (Nov 08, 2022)
1-229634943-C-A		not specified	Uncertain significance (Nov 07, 2022)
1-229634980-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-229634984-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-229635014-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-229635086-G-C		not specified	Uncertain significance (Sep 16, 2021)
1-229635097-G-A		not specified	Uncertain significance (Apr 04, 2024)
1-229635178-A-C		not specified	Uncertain significance (Feb 05, 2024)
1-229635302-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-229635374-A-G		not specified	Uncertain significance (Aug 07, 2023)
1-229635527-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-229635688-G-A		not specified	Uncertain significance (Oct 05, 2021)
1-229635716-C-A		not specified	Uncertain significance (May 16, 2023)
1-229635723-C-G		not specified	Uncertain significance (Mar 07, 2023)
1-229635725-A-G		not specified	Uncertain significance (Mar 15, 2024)
1-229635729-C-G		not specified	Uncertain significance (Dec 15, 2023)
1-229635739-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-229635784-C-T		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
URB2	protein_coding	protein_coding	ENST00000258243	9	33966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-17	0.965	125574	0	174	125748	0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.376	847	817	1.04	0.0000455	9862
Missense in Polyphen		210	199.61	1.052		2568
Synonymous	0.331	349	357	0.978	0.0000216	3174
Loss of Function	2.50	36	56.2	0.640	0.00000291	661

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00136	0.00136
Ashkenazi Jewish	0.000116	0.0000992
East Asian	0.000707	0.000707
Finnish	0.000647	0.000647
European (Non-Finnish)	0.000813	0.000809
Middle Eastern	0.000707	0.000707
South Asian	0.000360	0.000359
Other	0.000980	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0888

Intolerance Scores

• loftool: 0.922
• rvis_EVS: -1.31
• rvis_percentile_EVS: 4.82

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.172
• ghis: 0.549

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Urb2

Gene ontology

• Biological process: ribosome biogenesis
• Cellular component: nucleolus;aggresome;midbody