BEX2

brain expressed X-linked 2, the group of Brain expressed X-linked family

Basic information

Region (hg38): X:103309345-103311007

Links

ENSG00000133134 ∙ NCBI:84707 ∙ OMIM:300691 ∙ HGNC:30933 ∙ Uniprot:Q9BXY8 ∙ 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 BEX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEX2 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			10	1	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			4			4
Total	0	0	14	1	1

Variants in BEX2

This is a list of pathogenic ClinVar variants found in the BEX2 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-103309596-C-A		not specified	Uncertain significance (Dec 14, 2023)
X-103309600-A-G		not specified	Uncertain significance (Oct 13, 2023)
X-103309652-G-A		not specified	Uncertain significance (Apr 16, 2024)
X-103309724-T-C		not specified	Uncertain significance (Jan 19, 2024)
X-103309728-C-G		not specified	Uncertain significance (Jun 07, 2024)
X-103309775-C-G		not specified	Uncertain significance (Feb 03, 2022)
X-103309783-T-C			Likely benign (Mar 01, 2023)
X-103309802-T-C		not specified	Uncertain significance (Oct 03, 2023)
X-103309808-G-A		not specified	Uncertain significance (Oct 05, 2023)
X-103309820-G-A		not specified	Uncertain significance (Mar 12, 2024)
X-103309820-G-T		not specified	Uncertain significance (Apr 06, 2023)
X-103309883-T-C			Benign (Feb 25, 2018)
X-103309958-G-C		not specified	Uncertain significance (Feb 27, 2023)
X-103309961-C-T		not specified	Uncertain significance (Dec 20, 2023)
X-103310359-T-C			Likely benign (Jun 01, 2022)
X-103310361-G-T			Uncertain significance (Jan 13, 2020)
X-103310364-C-T		not specified	Uncertain significance (Sep 30, 2021)
X-103310417-C-T		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-103310424-C-T		not specified	Uncertain significance (Dec 16, 2023)
X-103310427-C-G		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEX2	protein_coding	protein_coding	ENST00000536889	3	1701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.101	0.783	125737	1	0	125738	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0138	67	66.7	1.00	0.00000525	1075
Missense in Polyphen		8	11.874	0.67377		253
Synonymous	0.383	21	23.4	0.899	0.00000180	273
Loss of Function	1.21	2	4.89	0.409	3.93e-7	81

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	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of mitochondrial apoptosis and G1 cell cycle in breast cancer. Protects the breast cancer cells against mitochondrial apoptosis and this effect is mediated through the modulation of BCL2 protein family, which involves the positive regulation of anti-apoptotic member BCL2 and the negative regulation of pro-apoptotic members BAD, BAK1 and PUMA. Required for the normal cell cycle progression during G1 in breast cancer cells through the regulation of CCND1 and CDKN1A. Regulates the level of PP2A regulatory subunit B and PP2A phosphatase activity. {ECO:0000269|PubMed:19711341}.

Recessive Scores

• pRec: 0.0953

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.63

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.112
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bex1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: apoptotic process;cell cycle;regulation of apoptotic process;regulation of cell cycle
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding