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Aliases for SH3PXD2B Gene

Aliases for SH3PXD2B Gene

  • SH3 And PX Domains 2B 2 3 5
  • KIAA1295 2 3 4
  • Tyrosine Kinase Substrate With Four SH3 Domains 3 4
  • Factor For Adipocyte Differentiation 49 3 4
  • Adapter Protein HOFI 3 4
  • FAD49 3 4
  • TKS4 3 4
  • SH3 And PX Domain-Containing Protein 2B 3
  • Adaptor Protein HOFI 3
  • FTHS 3
  • HOFI 3
  • TSK4 3

External Ids for SH3PXD2B Gene

Previous HGNC Symbols for SH3PXD2B Gene

  • KIAA1295

Previous GeneCards Identifiers for SH3PXD2B Gene

  • GC05M171693
  • GC05M166855

Summaries for SH3PXD2B Gene

Entrez Gene Summary for SH3PXD2B Gene

  • This gene encodes an adapter protein that is characterized by a PX domain and four Src homology 3 domains. The encoded protein is required for podosome formation and is involved in cell adhesion and migration of numerous cell types. Mutations in this gene are the cause of Frank-ter Haar syndrome (FTHS), and also Borrone Dermato-Cardio-Skeletal (BDCS) syndrome. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]

GeneCards Summary for SH3PXD2B Gene

SH3PXD2B (SH3 And PX Domains 2B) is a Protein Coding gene. Diseases associated with SH3PXD2B include Frank-Ter Haar Syndrome and Moved To 249420. GO annotations related to this gene include phosphatidylinositol binding and phosphatidylinositol-3-phosphate binding. An important paralog of this gene is SH3PXD2A.

UniProtKB/Swiss-Prot for SH3PXD2B Gene

  • Adapter protein involved in invadopodia and podosome formation and extracellular matrix degradation. Binds matrix metalloproteinases (ADAMs), NADPH oxidases (NOXs) and phosphoinositides. Acts as an organizer protein that allows NOX1- or NOX3-dependent reactive oxygen species (ROS) generation and ROS localization. Plays a role in mitotic clonal expansion during the immediate early stage of adipocyte differentiation (By similarity).

Additional gene information for SH3PXD2B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SH3PXD2B Gene

Genomics for SH3PXD2B Gene

Regulatory Elements for SH3PXD2B Gene

Enhancers for SH3PXD2B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H173322 1.7 Ensembl ENCODE dbSUPER 36.2 -873.1 -873081 9.6 MLX FEZF1 DMAP1 SLC30A9 ZNF143 SP3 NFYC ZFP41 SSRP1 ZNF610 SH3PXD2B BOD1 LOC102724551 ENSG00000253172 ENSG00000253628 RPL12P22 ENSG00000254011 LOC100268168 RNU6-500P LOC285593
GH05H172409 1.9 FANTOM5 Ensembl ENCODE dbSUPER 26.5 +41.6 41552 6.3 MLX DMAP1 FOS RUNX3 MXD4 NFYC JUNB REST MIER2 PPARG SH3PXD2B UBTD2 DUSP1 STK10 GC05P172400
GH05H172360 1.6 FANTOM5 Ensembl ENCODE 30 +92.6 92565 2.3 TBP BATF ZNF366 ZNF350 FOS ZNF548 ETV6 ATF7 RUNX3 CREM SH3PXD2B NPM1 CREBRF UBTD2 STK10 DUSP1 PIR48158 PIR48190
GH05H172787 2.1 FANTOM5 Ensembl ENCODE dbSUPER 20.7 -341.2 -341220 16.6 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B YBX1 ZBTB7B YY1 ZNF766 ERGIC1 CREBRF BOD1 SH3PXD2B DUSP1 FBXW11 LOC401218 LOC105377730 LOC100130394 ENSG00000270243
GH05H172894 2 FANTOM5 Ensembl ENCODE dbSUPER 20.3 -446.4 -446425 12.7 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A FEZF1 ZNF2 ZBTB7B KLF3P1 BOD1 BNIP1 SH3PXD2B UBTD2 ERGIC1 DUSP1 ENSG00000253628 ENSG00000253172 CREBRF
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SH3PXD2B on UCSC Golden Path with GeneCards custom track

Promoters for SH3PXD2B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000190782 623 2201 PKNOX1 INSM2 ARID4B SIN3A RAD21 GTF3C2 GLIS2 SCRT2 RCOR1 ZNF391

Genomic Locations for SH3PXD2B Gene

Genomic Locations for SH3PXD2B Gene
chr5:172,325,000-172,454,523
(GRCh38/hg38)
Size:
129,524 bases
Orientation:
Minus strand
chr5:171,752,185-171,881,527
(GRCh37/hg19)

Genomic View for SH3PXD2B Gene

Genes around SH3PXD2B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SH3PXD2B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SH3PXD2B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SH3PXD2B Gene

Proteins for SH3PXD2B Gene

  • Protein details for SH3PXD2B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A1X283-SPD2B_HUMAN
    Recommended name:
    SH3 and PX domain-containing protein 2B
    Protein Accession:
    A1X283
    Secondary Accessions:
    • B6F0V2
    • Q9P2Q1

    Protein attributes for SH3PXD2B Gene

    Size:
    911 amino acids
    Molecular mass:
    101579 Da
    Quaternary structure:
    • Interacts with ADAM15 (By similarity). Interacts with NOXO1. Interacts (via SH3 domains) with NOXA1; the interaction is direct. Interacts with FASLG.

neXtProt entry for SH3PXD2B Gene

Post-translational modifications for SH3PXD2B Gene

Other Protein References for SH3PXD2B Gene

No data available for DME Specific Peptides for SH3PXD2B Gene

Domains & Families for SH3PXD2B Gene

Gene Families for SH3PXD2B Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SH3PXD2B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A1X283

UniProtKB/Swiss-Prot:

SPD2B_HUMAN :
  • The PX domain is required for podosome localization because of its ability to bind phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) and, to a lesser extent, phosphatidylinositol 4-phosphate (PtdIns(4)P), phosphatidylinositol 5-phosphate (PtdIns(5)P), and phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). Binds to the third intramolecular SH3 domain (By similarity).
  • Belongs to the SH3PXD2 family.
Domain:
  • The PX domain is required for podosome localization because of its ability to bind phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) and, to a lesser extent, phosphatidylinositol 4-phosphate (PtdIns(4)P), phosphatidylinositol 5-phosphate (PtdIns(5)P), and phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). Binds to the third intramolecular SH3 domain (By similarity).
Family:
  • Belongs to the SH3PXD2 family.
genes like me logo Genes that share domains with SH3PXD2B: view

Function for SH3PXD2B Gene

Molecular function for SH3PXD2B Gene

UniProtKB/Swiss-Prot Function:
Adapter protein involved in invadopodia and podosome formation and extracellular matrix degradation. Binds matrix metalloproteinases (ADAMs), NADPH oxidases (NOXs) and phosphoinositides. Acts as an organizer protein that allows NOX1- or NOX3-dependent reactive oxygen species (ROS) generation and ROS localization. Plays a role in mitotic clonal expansion during the immediate early stage of adipocyte differentiation (By similarity).

Phenotypes From GWAS Catalog for SH3PXD2B Gene

Gene Ontology (GO) - Molecular Function for SH3PXD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19755710
GO:0010314 phosphatidylinositol-5-phosphate binding IEA,ISS --
GO:0016176 superoxide-generating NADPH oxidase activator activity IBA --
GO:0032266 phosphatidylinositol-3-phosphate binding IEA,ISS --
GO:0035091 phosphatidylinositol binding IEA --
genes like me logo Genes that share ontologies with SH3PXD2B: view
genes like me logo Genes that share phenotypes with SH3PXD2B: view

Human Phenotype Ontology for SH3PXD2B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SH3PXD2B Gene

MGI Knock Outs for SH3PXD2B:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SH3PXD2B Gene

Localization for SH3PXD2B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SH3PXD2B Gene

Cytoplasm. Cell projection, podosome. Note=Cytoplasmic in normal cells and localizes to podosomes in SRC-transformed cells. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SH3PXD2B gene
Compartment Confidence
cytoskeleton 5
nucleus 3
plasma membrane 2
mitochondrion 2
cytosol 2
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (2)
  • Nucleus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SH3PXD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002102 podosome ISS,IBA --
GO:0005737 cytoplasm ISS --
GO:0030054 cell junction IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with SH3PXD2B: view

Pathways & Interactions for SH3PXD2B Gene

SuperPathways for SH3PXD2B Gene

No Data Available

Gene Ontology (GO) - Biological Process for SH3PXD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IMP 20137777
GO:0001654 eye development IMP 20137777
GO:0002051 osteoblast fate commitment IEA --
GO:0006801 superoxide metabolic process IDA 19755710
GO:0007507 heart development IMP 20137777
genes like me logo Genes that share ontologies with SH3PXD2B: view

No data available for Pathways by source and SIGNOR curated interactions for SH3PXD2B Gene

Drugs & Compounds for SH3PXD2B Gene

No Compound Related Data Available

Transcripts for SH3PXD2B Gene

Unigene Clusters for SH3PXD2B Gene

SH3 and PX domains 2B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SH3PXD2B Gene

No ASD Table

Relevant External Links for SH3PXD2B Gene

GeneLoc Exon Structure for
SH3PXD2B
ECgene alternative splicing isoforms for
SH3PXD2B

Expression for SH3PXD2B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SH3PXD2B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SH3PXD2B Gene

This gene is overexpressed in Bone marrow stromal cell (10.7), Pancreas (7.8), and Fetal Brain (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SH3PXD2B Gene



Protein tissue co-expression partners for SH3PXD2B Gene

NURSA nuclear receptor signaling pathways regulating expression of SH3PXD2B Gene:

SH3PXD2B

SOURCE GeneReport for Unigene cluster for SH3PXD2B Gene:

Hs.285666

mRNA Expression by UniProt/SwissProt for SH3PXD2B Gene:

A1X283-SPD2B_HUMAN
Tissue specificity: Expressed in fibroblasts.

Evidence on tissue expression from TISSUES for SH3PXD2B Gene

  • Nervous system(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SH3PXD2B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • intestine
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SH3PXD2B: view

Primer Products

No data available for mRNA differential expression in normal tissues for SH3PXD2B Gene

Orthologs for SH3PXD2B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SH3PXD2B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SH3PXD2B 33 34
  • 97.69 (n)
dog
(Canis familiaris)
Mammalia SH3PXD2B 33 34
  • 88.62 (n)
cow
(Bos Taurus)
Mammalia SH3PXD2B 33 34
  • 86.77 (n)
rat
(Rattus norvegicus)
Mammalia Sh3pxd2b 33
  • 86.03 (n)
mouse
(Mus musculus)
Mammalia Sh3pxd2b 33 16 34
  • 85.18 (n)
oppossum
(Monodelphis domestica)
Mammalia SH3PXD2B 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SH3PXD2B 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves SH3PXD2B 33 34
  • 73.05 (n)
lizard
(Anolis carolinensis)
Reptilia SH3PXD2B 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sh3pxd2b 33
  • 62.71 (n)
zebrafish
(Danio rerio)
Actinopterygii sh3pxd2b 33 34
  • 61.36 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BEM1 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
OneToMany
Species where no ortholog for SH3PXD2B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SH3PXD2B Gene

ENSEMBL:
Gene Tree for SH3PXD2B (if available)
TreeFam:
Gene Tree for SH3PXD2B (if available)

Paralogs for SH3PXD2B Gene

Paralogs for SH3PXD2B Gene

(6) SIMAP similar genes for SH3PXD2B Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SH3PXD2B: view

Variants for SH3PXD2B Gene

Sequence variations from dbSNP and Humsavar for SH3PXD2B Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs267607046 Pathogenic, Frank-Ter Haar syndrome (FTHS) [MIM:249420] 172,422,445(-) TTTAC(C/T)GGCGC reference, missense
rs367543284 Pathogenic 172,382,035(-) AAAGA(A/G)TAAGT splice-donor-variant
rs775217258 Pathogenic 172,422,498(+) AGACC(G/T)GCGGG splice-acceptor-variant
rs794728005 Pathogenic 172,422,424(-) TTTTT(-/T)GACCT reference, frameshift-variant
rs794728006 Pathogenic 172,350,406(-) GACGG(-/G)CGGTT reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for SH3PXD2B Gene

Variant ID Type Subtype PubMed ID
nsv950442 CNV deletion 24416366
nsv830554 CNV loss 17160897
nsv600283 CNV loss 21841781
nsv475565 CNV novel sequence insertion 20440878
nsv471850 CNV novel sequence insertion 20440878
nsv1119048 CNV deletion 24896259
nsv1114760 CNV deletion 24896259
nsv1112888 CNV deletion 24896259
nsv1073934 CNV deletion 25765185
esv3567019 CNV deletion 23714750
esv3383499 CNV insertion 20981092
esv3379464 CNV insertion 20981092
esv3310125 CNV mobile element insertion 20981092
esv2731097 CNV deletion 23290073
esv2651986 CNV deletion 19546169

Variation tolerance for SH3PXD2B Gene

Residual Variation Intolerance Score: 56.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.16; 61.59% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SH3PXD2B Gene

Human Gene Mutation Database (HGMD)
SH3PXD2B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SH3PXD2B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SH3PXD2B Gene

Disorders for SH3PXD2B Gene

MalaCards: The human disease database

(5) MalaCards diseases for SH3PXD2B Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
frank-ter haar syndrome
  • borrone di rocco crovato syndrome
moved to 249420
  • dermato-cardio-skeletal syndrome, borrone type
borrone di rocco crovato syndrome
  • borrone dermatocardioskeletal syndrome
megalocornea
  • anterior megalophthalmos
glaucoma 3a, primary open angle, congenital, juvenile, or adult onset
  • buphthalmos
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SPD2B_HUMAN
  • Frank-Ter Haar syndrome (FTHS) [MIM:249420]: A syndrome characterized by brachycephaly, wide fontanels, prominent forehead, hypertelorism, prominent eyes, macrocornea with or without glaucoma, full cheeks, small chin, bowing of the long bones and flexion deformity of the fingers. {ECO:0000269 PubMed:20137777}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SH3PXD2B

Genetic Association Database (GAD)
SH3PXD2B
Human Genome Epidemiology (HuGE) Navigator
SH3PXD2B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SH3PXD2B
genes like me logo Genes that share disorders with SH3PXD2B: view

No data available for Genatlas for SH3PXD2B Gene

Publications for SH3PXD2B Gene

  1. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 60
  2. Direct interaction between Tks proteins and the N-terminal proline-rich region (PRR) of NoxA1 mediates Nox1-dependent ROS generation. (PMID: 20609497) Gianni D … Bokoch GM (European journal of cell biology 2011) 3 4 60
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  4. Disruption of the podosome adaptor protein TKS4 (SH3PXD2B) causes the skeletal dysplasia, eye, and cardiac abnormalities of Frank-Ter Haar Syndrome. (PMID: 20137777) Iqbal Z … van Bokhoven H (American journal of human genetics 2010) 3 4 60
  5. Novel p47(phox)-related organizers regulate localized NADPH oxidase 1 (Nox1) activity. (PMID: 19755710) Gianni D … Bokoch GM (Science signaling 2009) 3 4 60

Products for SH3PXD2B Gene

Sources for SH3PXD2B Gene

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