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.

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.

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						0
missense			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in BRIX1

This is a list of pathogenic ClinVar variants found in the BRIX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-34915752-A-G		not specified	Uncertain significance (May 02, 2024)
5-34915770-G-A		not specified	Uncertain significance (Aug 16, 2021)
5-34915791-A-G		not specified	Uncertain significance (Nov 25, 2024)
5-34915815-C-G		not specified	Uncertain significance (Jan 09, 2025)
5-34915817-G-A		not specified	Likely benign (Nov 17, 2022)
5-34915845-C-A		not specified	Uncertain significance (Sep 26, 2022)
5-34918372-G-C		not specified	Uncertain significance (Nov 07, 2024)
5-34918425-C-G		not specified	Uncertain significance (May 15, 2024)
5-34918425-C-T		not specified	Uncertain significance (Sep 22, 2022)
5-34919846-A-C		not specified	Uncertain significance (Jun 22, 2024)
5-34919851-G-T		not specified	Uncertain significance (Feb 22, 2023)
5-34919854-C-A		not specified	Uncertain significance (Nov 21, 2024)
5-34919880-C-G		not specified	Uncertain significance (Oct 29, 2024)
5-34922227-T-C		not specified	Uncertain significance (Apr 20, 2024)
5-34922260-C-T		not specified	Uncertain significance (Oct 27, 2021)
5-34922281-A-C		not specified	Uncertain significance (Oct 25, 2024)
5-34922557-C-T		not specified	Likely benign (Feb 06, 2025)
5-34922576-C-A		not specified	Uncertain significance (Feb 15, 2025)
5-34922737-A-G		not specified	Uncertain significance (Jan 27, 2022)
5-34922748-C-A		not specified	Uncertain significance (Mar 01, 2024)
5-34922767-C-G		not specified	Uncertain significance (Feb 04, 2025)
5-34923137-T-G		not specified	Uncertain significance (Feb 15, 2023)
5-34923169-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-34923175-G-A		not specified	Uncertain significance (Apr 08, 2024)
5-34923182-A-G		not specified	Uncertain significance (Dec 20, 2023)

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