BRIX1

protein-coding

biogenesis of ribosomes BRX1, the group of Ribosomal biogenesis factors

Gene summary

Enables RNA binding activity. Predicted to be involved in ribosomal large subunit assembly. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

BXDC2

MANE transcript

NM_018321.4

Inheritance

—

ClinVar variants

U:59B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr5:34,915,677-34,925,996

External References & Databases

Ensembl (ENSG00000113460)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 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 BRIX1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 55

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018321.4. 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				1 clinvar		1
missense			55 clinvar	1 clinvar		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	59	2	0	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018321.4	RefSeq	NP_060791.3	10	MANE Select
ENST00000336767.6	Ensembl	ENSP00000338862.5	10	MANE Select
ENST00000938601.1	Ensembl	ENSP00000608660.1	10	Standard
ENST00000938602.1	Ensembl	ENSP00000608661.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gastric Cancer Network 2

Biological Process

ribosomal large subunit assembly

Molecular Function

RNA binding

Cellular Component

nucleus
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336767
Coding exons: 10
Length: 10621
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125729
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.631	162	186	0.870	0.00000960	2331
Missense (PolyPhen)		59	71.727	0.82257		951
Synonymous	0.470	54	58.6	0.922	0.00000295	617
Loss of Function	3.20	3	17.4	0.172	7.30e-7	251

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for biogenesis of the 60S ribosomal subunit.;

Recessive Scores

pRec: 0.168

Intolerance Scores

LoFtool: 0.192
RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.948

Gene Damage Prediction

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