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 splic... See more...

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
  • SH3 And PX Domain-Containing Protein 2B 3 4
  • Factor For Adipocyte Differentiation 49 3 4
  • Adapter Protein HOFI 3 4
  • FAD49 3 4
  • TKS4 3 4
  • Adaptor Protein HOFI 3
  • SH3PXD2B 5
  • FLJ20831 2
  • 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 Borrone Di Rocco Crovato Syndrome. Gene Ontology (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 Summary 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).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SH3PXD2B Gene

Genomics for SH3PXD2B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SH3PXD2B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SH3PXD2B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SH3PXD2B

Top Transcription factor binding sites by QIAGEN in the SH3PXD2B gene promoter:
  • AML1a
  • c-Myc
  • CUTL1
  • GATA-1
  • GATA-2
  • HNF-4alpha1
  • Max1
  • NCX
  • POU2F1
  • POU2F1a

Genomic Locations for SH3PXD2B Gene

Genomic Locations for SH3PXD2B Gene
chr5:172,325,000-172,454,525
(GRCh38/hg38)
Size:
129,526 bases
Orientation:
Minus strand
chr5:171,752,185-171,881,527
(GRCh37/hg19)
Size:
129,343 bases
Orientation:
Minus strand

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:
  • Tyrosine kinase substrate with four SH3 domains (SPD2B_HUMAN)

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 IBA,ISS --
GO:0016176 superoxide-generating NADPH oxidase activator activity IBA 21873635
GO:0032266 phosphatidylinositol-3-phosphate binding IBA,ISS --
GO:0035091 phosphatidylinositol binding IBA --
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

  • Taconic Biosciences Mouse Models for SH3PXD2B

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SH3PXD2B

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 4
plasma membrane 3
nucleus 3
cytosol 3
extracellular 2
mitochondrion 2
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (2)
  • Nucleoplasm (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 --
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

PathCards logo

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 IBA,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

mRNA/cDNA for SH3PXD2B Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SH3PXD2B

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

No ASD Table

Relevant External Links for SH3PXD2B Gene

GeneLoc Exon Structure for
SH3PXD2B

Expression for SH3PXD2B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for SH3PXD2B Gene



Protein tissue co-expression partners for SH3PXD2B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.5)
  • Heart(2.3)
  • Spleen(2.2)

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
Regions:
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

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 30 31
  • 97.69 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SH3PXD2B 30 31
  • 88.62 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SH3PXD2B 30 31
  • 86.77 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sh3pxd2b 30
  • 86.03 (n)
Mouse
(Mus musculus)
Mammalia Sh3pxd2b 30 17 31
  • 85.18 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SH3PXD2B 31
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SH3PXD2B 31
  • 75 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SH3PXD2B 30 31
  • 73.05 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SH3PXD2B 31
  • 70 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sh3pxd2b 30
  • 62.71 (n)
Zebrafish
(Danio rerio)
Actinopterygii sh3pxd2b 30 31
  • 61.36 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BEM1 33
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 53 (a)
OneToMany
Species where no ortholog for SH3PXD2B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SH3PXD2B: view image

Paralogs for SH3PXD2B Gene

Paralogs for SH3PXD2B Gene

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

  • SPD2B_HUMAN
  • G3V144_HUMAN
  • H0YAU1_HUMAN
  • L8EC68_HUMAN
genes like me logo Genes that share paralogs with SH3PXD2B: view

Variants for SH3PXD2B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SH3PXD2B Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
709897 Likely Benign: not provided 172,350,405(-) G/A MISSENSE_VARIANT
715874 Likely Benign: not provided 172,339,761(-) C/A SYNONYMOUS_VARIANT,INTRON_VARIANT
718614 Likely Benign: not provided 172,422,458(-) G/A SYNONYMOUS_VARIANT
721446 Likely Benign: not provided 172,339,821(-) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT
722184 Likely Benign: not provided 172,338,977(-) G/C MISSENSE_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for SH3PXD2B Gene

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

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

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)

Additional Variant Information 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

(10) MalaCards diseases for SH3PXD2B Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
frank-ter haar syndrome
  • fths
borrone di rocco crovato syndrome
  • borrone dermatocardioskeletal syndrome
otopalatodigital syndrome spectrum disorder
  • fronto-otopalatodigital osteodysplasia
pontocerebellar hypoplasia, type 9
  • pch9
megalocornea
  • anterior megalophthalmos
- 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.

Additional Disease Information for SH3PXD2B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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
  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
  3. 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
  4. 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 41
  5. Identification of SH3 domain interaction partners of human FasL (CD178) by phage display screening. (PMID: 19807924) Voss M … Janssen O (BMC immunology 2009) 3 4

Products for SH3PXD2B Gene

Sources for SH3PXD2B Gene