URB1

protein-coding

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

Gene summary

Enables RNA binding activity. Predicted to be involved in maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in fibrillar center. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C21orf108

MANE transcript

NM_014825.3

Inheritance

—

ClinVar variants

U:365B:50

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr21:32,311,018-32,393,012

External References & Databases

Ensembl (ENSG00000142207)

Transcript & Mutation Effects

hg38 • Region Span ~82.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to URB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 391

not providedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014825.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	7 clinvar	4 clinvar	13
missense			361 clinvar	37 clinvar	2 clinvar	400
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	365	44	6	415

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014825.3	RefSeq	NP_055640.2	39	MANE Select
ENST00000382751.4	Ensembl	ENSP00000372199.3	39	MANE Select
ENST00000864001.1	Ensembl	ENSP00000534060.1	38	Standard
ENST00000864001.2	Ensembl	ENSP00000534060.1	38	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

RNA binding

Cellular Component

fibrillar center
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382751
Coding exons: 39
Length: 82007
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.09	996	1.20e+3	0.830	0.0000714	14692
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0943

Intolerance Scores

RVIS EVS: 2.7
RVIS percentile EVS: 98.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.880

Gene Damage Prediction

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