BEX4

brain expressed X-linked 4, the group of Brain expressed X-linked family

Basic information

Region (hg38): X:103215107-103217246

Previous symbols: [ "BEXL1" ]

Links

ENSG00000102409 ∙ NCBI:56271 ∙ OMIM:300692 ∙ HGNC:25475 ∙ Uniprot:Q9NWD9 ∙ 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 BEX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEX4 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				1		1
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in BEX4

This is a list of pathogenic ClinVar variants found in the BEX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-103216161-C-T		not specified	Uncertain significance (Feb 28, 2024)
X-103216163-A-G		not specified	Uncertain significance (Jan 04, 2022)
X-103216185-A-G		not specified	Uncertain significance (Jul 20, 2022)
X-103216221-G-A		not specified	Uncertain significance (Sep 21, 2023)
X-103216307-C-T		not specified	Uncertain significance (Dec 06, 2023)
X-103216308-G-T		not specified	Likely benign (Jan 20, 2023)
X-103216347-C-T		not specified	Uncertain significance (Nov 08, 2021)
X-103216361-C-T		not specified	Uncertain significance (Nov 02, 2023)
X-103216413-T-C		not specified	Uncertain significance (Jul 12, 2023)
X-103216447-G-A			Likely benign (Jun 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEX4	protein_coding	protein_coding	ENST00000372695	1	2155

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.672	0.309	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.240	44	48.7	0.903	0.00000387	803
Missense in Polyphen		3	10.812	0.27747		214
Synonymous	-0.305	19	17.4	1.09	0.00000140	219
Loss of Function	1.77	0	3.63	0.00	4.27e-7	31

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

• Function: FUNCTION: May play a role in microtubule deacetylation by negatively regulating the SIRT2 deacetylase activity toward alpha- tubulin and thereby participate to the control of cell cycle progression and genomic stability. {ECO:0000269|PubMed:27512957}.

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.281
• hipred: N
• hipred_score: 0.132
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Bex4

Gene ontology

• Biological process: chromosome segregation;regulation of cell migration;regulation of cell population proliferation;negative regulation of tubulin deacetylation
• Cellular component: spindle pole;nucleus;cytoplasm;microtubule
• Molecular function: histone deacetylase binding;alpha-tubulin binding