BEX4

protein-coding

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

Gene summary

This gene is a member of the brain expressed X-linked gene family. The proteins encoded by some of the other members of this family act as transcription elongation factors which allow RNA polymerase II to escape pausing during elongation. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Aug 2011]

Previous symbols:

BEXL1

MANE transcript

NM_001080425.4

Inheritance

—

ClinVar variants

U:19B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:103,215,108-103,217,246

External References & Databases

Ensembl (ENSG00000102409)

Transcript & Mutation Effects

hg38 • Region Span ~2.1 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 BEX4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 18

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080425.4. 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			17 clinvar	1 clinvar		18
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	19	2	0	21

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080425.4	RefSeq	NP_001073894.1	1	MANE Select
ENST00000372695.6	Ensembl	ENSP00000361780.5	1	MANE Select
NM_001127688.2	RefSeq	NP_001121160.1	1	Standard
ENST00000372691.3	Ensembl	ENSP00000361776.3	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chromosome segregation
regulation of cell migration
regulation of cell population proliferation
negative regulation of tubulin deacetylation

Molecular Function

histone deacetylase binding
alpha-tubulin binding

Cellular Component

spindle pole
nucleus
cytoplasm
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372695
Coding exons: 1
Length: 2155
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	0.240	44	48.7	0.903	0.00000387	803
Missense (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

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

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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