BEX1

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

Basic information

Region (hg38): X:103062650-103064171

Links

ENSG00000133169 ∙ NCBI:55859 ∙ OMIM:300690 ∙ HGNC:1036 ∙ Uniprot:Q9HBH7 ∙ 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 BEX1 gene.

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			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)
X-103063067-G-A		not specified	Uncertain significance (Jan 26, 2022)
X-103063171-G-A		not specified	Conflicting classifications of pathogenicity (Feb 23, 2023)
X-103063180-T-C		not specified	Uncertain significance (Feb 22, 2023)
X-103063225-G-T		not specified	Uncertain significance (Sep 27, 2022)
X-103063229-T-C		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEX1	protein_coding	protein_coding	ENST00000372728	1	1590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.543	0.406	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.374	42	49.4	0.850	0.00000388	844
Missense in Polyphen		8	9.7147	0.8235		211
Synonymous	-0.915	21	16.3	1.29	0.00000113	218
Loss of Function	1.41	0	2.33	0.00	1.55e-7	43

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: 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

• 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

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

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