BMX

BMX non-receptor tyrosine kinase, the group of Tec family tyrosine kinases|Pleckstrin homology domain containing|SH2 domain containing

Basic information

Region (hg38): X:15464246-15556529

Links

ENSG00000102010 ∙ NCBI:660 ∙ OMIM:300101 ∙ HGNC:1079 ∙ Uniprot:P51813 ∙ 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 BMX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMX 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	2	3
missense			14	2	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	14	3	4

Variants in BMX

This is a list of pathogenic ClinVar variants found in the BMX 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-15479812-G-T		not specified	Uncertain significance (Jun 07, 2024)
X-15479820-A-G		not specified	Uncertain significance (Jun 07, 2024)
X-15511457-T-A			Benign (Feb 08, 2018)
X-15516129-C-T		not specified	Uncertain significance (Aug 18, 2021)
X-15516168-G-T		not specified	Uncertain significance (Feb 12, 2024)
X-15516211-G-A		not specified	Uncertain significance (Dec 28, 2022)
X-15517947-C-T		not specified	Uncertain significance (Dec 17, 2023)
X-15517955-G-A		not specified	Uncertain significance (Feb 22, 2023)
X-15522377-A-G		not specified	Likely benign (Mar 01, 2023)
X-15522470-G-C		not specified	Likely benign (Nov 07, 2022)
X-15522475-G-A		not specified	Uncertain significance (Jan 16, 2024)
X-15522476-C-T			Benign (Dec 19, 2017)
X-15529992-T-G		not specified	Uncertain significance (May 24, 2023)
X-15536403-C-T		not specified	Uncertain significance (May 13, 2024)
X-15537153-A-G			Likely benign (Jan 01, 2023)
X-15541995-C-G		not specified	Uncertain significance (Sep 01, 2021)
X-15542086-A-T		not specified	Uncertain significance (Feb 22, 2023)
X-15542189-C-T			Benign (Mar 29, 2018)
X-15542204-C-A			Likely benign (Apr 01, 2023)
X-15546837-G-A		not specified	Uncertain significance (Sep 15, 2021)
X-15546837-G-C		not specified	Uncertain significance (Dec 20, 2023)
X-15549831-G-C			Benign (May 18, 2018)
X-15549906-T-C		not specified	Uncertain significance (Mar 07, 2024)
X-15549941-C-T		not specified	Uncertain significance (Aug 19, 2023)
X-15549995-G-A		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMX	protein_coding	protein_coding	ENST00000357607	18	92284

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00667	0.993	125711	12	7	125730	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.991	197	240	0.820	0.0000174	4459
Missense in Polyphen		70	107.39	0.65183		2029
Synonymous	-0.218	93	90.4	1.03	0.00000683	1182
Loss of Function	3.31	9	27.9	0.323	0.00000183	539

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000195	0.000161
Ashkenazi Jewish	0.00	0.00
East Asian	0.000363	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000352
Middle Eastern	0.000363	0.000272
South Asian	0.000322	0.000196
Other	0.000225	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-receptor tyrosine kinase that plays central but diverse modulatory roles in various signaling processes involved in the regulation of actin reorganization, cell migration, cell proliferation and survival, cell adhesion, and apoptosis. Participates in signal transduction stimulated by growth factor receptors, cytokine receptors, G-protein coupled receptors, antigen receptors and integrins. Induces tyrosine phosphorylation of BCAR1 in response to integrin regulation. Activation of BMX by integrins is mediated by PTK2/FAK1, a key mediator of integrin signaling events leading to the regulation of actin cytoskeleton and cell motility. Plays a critical role in TNF-induced angiogenesis, and implicated in the signaling of TEK and FLT1 receptors, 2 important receptor families essential for angiogenesis. Required for the phosphorylation and activation of STAT3, a transcription factor involved in cell differentiation. Also involved in interleukin-6 (IL6) induced differentiation. Plays also a role in programming adaptive cytoprotection against extracellular stress in different cell systems, salivary epithelial cells, brain endothelial cells, and dermal fibroblasts. May be involved in regulation of endocytosis through its interaction with an endosomal protein RUFY1. May also play a role in the growth and differentiation of hematopoietic cells; as well as in signal transduction in endocardial and arterial endothelial cells. {ECO:0000269|PubMed:10688651, ECO:0000269|PubMed:11331870, ECO:0000269|PubMed:12370298, ECO:0000269|PubMed:12832404, ECO:0000269|PubMed:15788485, ECO:0000269|PubMed:18292575, ECO:0000269|PubMed:9520419}.
• Pathway: Angiogenesis overview;Metabolism of lipids;Apoptotic cleavage of cellular proteins;Metabolism;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Synthesis of PIPs at the plasma membrane;Angiopoietin receptor Tie2-mediated signaling;PI Metabolism;Phospholipid metabolism;IL6;Signaling events mediated by focal adhesion kinase (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.320
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.480
• hipred: Y
• hipred_score: 0.736
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bmx
• Phenotype: skeleton phenotype; normal phenotype; immune system phenotype

Gene ontology

• Biological process: adaptive immune response;protein phosphorylation;phosphatidylinositol biosynthetic process;apoptotic process;cell adhesion;signal transduction;mesoderm development;intracellular signal transduction;peptidyl-tyrosine autophosphorylation;protein autophosphorylation;B cell receptor signaling pathway
• Cellular component: nucleoplasm;cytosol;plasma membrane;ruffle membrane
• Molecular function: protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding;metal ion binding