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GeneBe

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:15464245-15556529

Links

ENSG00000102010NCBI:660OMIM:300101HGNC:1079Uniprot:P51813AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
2
clinvar
3
missense
14
clinvar
2
clinvar
1
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
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-15511457-T-A Benign (Feb 08, 2018)726139
X-15516129-C-T not specified Uncertain significance (Aug 18, 2021)2228484
X-15516168-G-T not specified Uncertain significance (Feb 12, 2024)3134637
X-15516211-G-A not specified Uncertain significance (Dec 28, 2022)2339979
X-15517947-C-T not specified Uncertain significance (Dec 17, 2023)3134638
X-15517955-G-A not specified Uncertain significance (Feb 22, 2023)2487358
X-15522377-A-G not specified Likely benign (Mar 01, 2023)2491784
X-15522470-G-C not specified Likely benign (Nov 07, 2022)2367891
X-15522475-G-A not specified Uncertain significance (Jan 16, 2024)3134639
X-15522476-C-T Benign (Dec 19, 2017)728813
X-15529992-T-G not specified Uncertain significance (May 24, 2023)2516141
X-15537153-A-G Likely benign (Jan 01, 2023)2660054
X-15541995-C-G not specified Uncertain significance (Sep 01, 2021)2345989
X-15542086-A-T not specified Uncertain significance (Feb 22, 2023)2472382
X-15542189-C-T Benign (Mar 29, 2018)722714
X-15542204-C-A Likely benign (Apr 01, 2023)2660055
X-15546837-G-A not specified Uncertain significance (Sep 15, 2021)2249252
X-15546837-G-C not specified Uncertain significance (Dec 20, 2023)3134635
X-15549831-G-C Benign (May 18, 2018)739305
X-15549906-T-C not specified Uncertain significance (Mar 07, 2024)3134636
X-15549941-C-T not specified Uncertain significance (Aug 19, 2023)2592450
X-15549995-G-A not specified Uncertain significance (Nov 12, 2021)2260514

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BMXprotein_codingprotein_codingENST00000357607 1892284
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.006670.9931257111271257300.0000756
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9911972400.8200.00001744459
Missense in Polyphen70107.390.651832029
Synonymous-0.2189390.41.030.000006831182
Loss of Function3.31927.90.3230.00000183539

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001950.000161
Ashkenazi Jewish0.000.00
East Asian0.0003630.000272
Finnish0.000.00
European (Non-Finnish)0.00005290.0000352
Middle Eastern0.0003630.000272
South Asian0.0003220.000196
Other0.0002250.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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