URB1

URB1 ribosome biogenesis homolog, the group of Armadillo like helical domain containing|Ribosomal biogenesis factors|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 21:32311018-32393012

Previous symbols: [ "C21orf108" ]

Links

ENSG00000142207 ∙ NCBI:9875 ∙ OMIM:608865 ∙ HGNC:17344 ∙ Uniprot:O60287 ∙ 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 URB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the URB1 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				6	4	10
missense			203	21	3	227
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	7	4	26
Total	0	0	218	34	11

Variants in URB1

This is a list of pathogenic ClinVar variants found in the URB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32311682-AG-A		Inborn genetic diseases	Uncertain significance (Jun 10, 2022)
21-32311687-C-A		Inborn genetic diseases	Uncertain significance (Jan 08, 2025)
21-32311696-G-A		Glucocorticoid deficiency 2	Uncertain significance (Jan 13, 2018)
21-32311711-C-G		Glucocorticoid deficiency 2	Benign (Dec 31, 2019)
21-32311719-G-T		MRAP-related disorder	Uncertain significance (Aug 18, 2024)
21-32311732-C-A		Inborn genetic diseases	Uncertain significance (Dec 19, 2023)
21-32311748-C-A		Glucocorticoid deficiency 2	Uncertain significance (Jan 13, 2018)
21-32311762-G-A			Likely benign (Jan 01, 2023)
21-32311799-G-A		Inborn genetic diseases	Uncertain significance (Aug 17, 2022)
21-32311800-C-T		Inborn genetic diseases	Uncertain significance (Jul 08, 2024)
21-32311801-G-A			Likely benign (Apr 01, 2023)
21-32311804-C-A		Inborn genetic diseases	Likely benign (Sep 20, 2023)
21-32311830-G-A		Inborn genetic diseases	Likely benign (Dec 14, 2021)
21-32311842-C-T			Likely benign (Jun 01, 2022)
21-32311852-G-C		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
21-32311866-C-T		Glucocorticoid deficiency 2	Benign (Dec 31, 2019)
21-32311867-C-G		Glucocorticoid deficiency 2	Benign (Jan 13, 2018)
21-32311877-G-A		Inborn genetic diseases	Uncertain significance (Mar 25, 2021)
21-32311912-A-C		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
21-32311923-A-G		Glucocorticoid deficiency 2	Likely benign (Jan 13, 2018)
21-32311928-G-A		Glucocorticoid deficiency 2	Uncertain significance (Jan 13, 2018)
21-32311963-C-G		Glucocorticoid deficiency 2	Uncertain significance (Jan 12, 2018)
21-32311985-T-A		Glucocorticoid deficiency 2 • MRAP-related disorder	Uncertain significance (Jan 13, 2018)
21-32312010-T-A		Glucocorticoid deficiency 2	Uncertain significance (Jan 13, 2018)
21-32312104-A-G		Glucocorticoid deficiency 2	Benign (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
URB1	protein_coding	protein_coding	ENST00000382751	39	82007

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	1.00	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	996	1.20e+3	0.830	0.0000714	14692
Missense in Polyphen		246	309.89	0.79383		4262
Synonymous	2.76	450	531	0.848	0.0000340	4629
Loss of Function	5.02	46	100	0.459	0.00000551	1189

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0943

Intolerance Scores

• rvis_EVS: 2.7
• rvis_percentile_EVS: 98.89

Haploinsufficiency Scores

• pHI: 0.199
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.880

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Urb1

Gene ontology

• Biological process: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);biological_process
• Cellular component: fibrillar center;nucleolus
• Molecular function: RNA binding