BRIX1

biogenesis of ribosomes BRX1, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 5:34915677-34925996

Previous symbols: [ "BXDC2" ]

Links

ENSG00000113460 ∙ NCBI:55299 ∙ OMIM:618466 ∙ HGNC:24170 ∙ Uniprot:Q8TDN6 ∙ 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 BRIX1 gene.

• not_specified (48 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRIX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018321.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			46	1		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRIX1	protein_coding	protein_coding	ENST00000336767	10	10621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.728	0.272	125726	0	3	125729	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.631	162	186	0.870	0.00000960	2331
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for biogenesis of the 60S ribosomal subunit.
• Pathway: Gastric Cancer Network 2 (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.192
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.876
• hipred: Y
• hipred_score: 0.783
• ghis: 0.579

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brix1

Gene ontology

• Biological process: ribosomal large subunit assembly
• Cellular component: nucleus;nucleolus
• Molecular function: RNA binding