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GeneBe

BEX1

brain expressed X-linked 1, the group of Brain expressed X-linked family

Basic information

Region (hg38): X:103062650-103064171

Links

ENSG00000133169NCBI:55859OMIM:300690HGNC:1036Uniprot:Q9HBH7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BEX1 gene.

  • Inborn genetic diseases (6 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEX1 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
5
clinvar
5
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 0 0

Variants in BEX1

This is a list of pathogenic ClinVar variants found in the BEX1 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-103062959-G-A not specified Uncertain significance (May 16, 2022)2352616
X-103063067-G-A not specified Uncertain significance (Jan 26, 2022)2273403
X-103063171-G-A not specified Conflicting classifications of pathogenicity (Feb 23, 2023)2454286
X-103063180-T-C not specified Uncertain significance (Feb 22, 2023)2487143
X-103063225-G-T not specified Uncertain significance (Sep 27, 2022)2313526
X-103063229-T-C not specified Uncertain significance (Sep 06, 2022)2310655

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BEX1protein_codingprotein_codingENST00000372728 11590
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5430.40600000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3744249.40.8500.00000388844
Missense in Polyphen89.71470.8235211
Synonymous-0.9152116.31.290.00000113218
Loss of Function1.4102.330.001.55e-743

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Signaling adapter molecule involved in p75NTR/NGFR signaling. Plays a role in cell cycle progression and neuronal differentiation. Inhibits neuronal differentiation in response to nerve growth factor (NGF). May act as a link between the cell cycle and neurotrophic factor signaling, possibly by functioning as an upstream modulator of receptor signaling, coordinating biological responses to external signals with internal cellular states (By similarity). {ECO:0000250}.;
Pathway
p75(NTR)-mediated signaling (Consensus)

Recessive Scores

pRec
0.431

Intolerance Scores

loftool
rvis_EVS
-0.05
rvis_percentile_EVS
49.39

Haploinsufficiency Scores

pHI
0.164
hipred
N
hipred_score
0.332
ghis
0.652

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bex2
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; hematopoietic system phenotype; vision/eye phenotype; homeostasis/metabolism phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process
nervous system development;cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of DNA-binding transcription factor activity
Cellular component
nucleus;transcription factor complex;cytoplasm
Molecular function
RNA polymerase II activating transcription factor binding;protein binding