BEX3

brain expressed X-linked 3, the group of Brain expressed X-linked family

Basic information

Region (hg38): X:103376394-103378164

Previous symbols: [ "NGFRAP1" ]

Links

ENSG00000166681 ∙ NCBI:27018 ∙ OMIM:300361 ∙ HGNC:13388 ∙ Uniprot:Q00994 ∙ 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 BEX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEX3 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in BEX3

This is a list of pathogenic ClinVar variants found in the BEX3 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-103377782-C-T			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEX3	protein_coding	protein_coding	ENST00000372645	1	1738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.621	0.349	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.995	28	47.2	0.593	0.00000352	748
Missense in Polyphen		3	11.083	0.27067		223
Synonymous	-0.757	17	13.5	1.26	8.64e-7	197
Loss of Function	1.63	0	3.09	0.00	2.78e-7	37

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 be a signaling adapter molecule involved in p75NTR- mediated apoptosis induced by NGF. Plays a role in zinc-triggered neuronal death (By similarity). May play an important role in the pathogenesis of neurogenetic diseases. {ECO:0000250}.
• Pathway: Neurotrophin signaling pathway - Homo sapiens (human);Apoptosis-related network due to altered Notch3 in ovarian cancer;Signal Transduction;NADE modulates death signalling;Death Receptor Signalling;p75 NTR receptor-mediated signalling;p75(NTR)-mediated signaling;Cell death signalling via NRAGE, NRIF and NADE (Consensus)

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.162
• hipred: Y
• hipred_score: 0.618
• ghis: 0.625

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Bex3

Gene ontology

• Biological process: activation of cysteine-type endopeptidase activity involved in apoptotic process;multicellular organism development;extrinsic apoptotic signaling pathway via death domain receptors;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;regulation of cysteine-type endopeptidase activity involved in apoptotic process
• Cellular component: nucleus;cytosol
• Molecular function: nerve growth factor receptor binding;protein binding;cysteine-type endopeptidase activator activity involved in apoptotic process;identical protein binding;metal ion binding