Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SBF1 Gene

Aliases for SBF1 Gene

  • SET Binding Factor 1 2 3 5
  • DENN/MADD Domain Containing 7A 2 3
  • MTMR5 3 4
  • Myotubularin-Related Protein 5 3
  • Myotubularin Related 5 2
  • SET-Binding Factor 1 4
  • DENND7A 3
  • CMT4B3 3
  • Sbf1 4

External Ids for SBF1 Gene

Previous GeneCards Identifiers for SBF1 Gene

  • GC22M047389
  • GC22M049017
  • GC22M049175
  • GC22M050885
  • GC22M033773

Summaries for SBF1 Gene

Entrez Gene Summary for SBF1 Gene

  • This gene encodes a member of the protein-tyrosine phosphatase family. However, the encoded protein does not appear to be a catalytically active phosphatase because it lacks several amino acids in the catalytic pocket. This protein contains a Guanine nucleotide exchange factor (GEF) domain which is necessary for its role in growth and differentiation. Mutations in this gene have been associated with Charcot-Marie-Tooth disease 4B3. Pseudogenes of this gene have been defined on chromosomes 1 and 8. [provided by RefSeq, Dec 2014]

GeneCards Summary for SBF1 Gene

SBF1 (SET Binding Factor 1) is a Protein Coding gene. Diseases associated with SBF1 include Charcot-Marie-Tooth Disease, Type 4B3 and Charcot-Marie-Tooth Neuropathy Type 4B3. Among its related pathways are Vesicle-mediated transport and RAB GEFs exchange GTP for GDP on RABs. GO annotations related to this gene include phosphatase activity and Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is SBF2.

UniProtKB/Swiss-Prot for SBF1 Gene

  • Probable pseudophosphatase. Lacks several amino acids in the catalytic pocket which renders it catalytically inactive as a phosphatase. The pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases. Inhibits myoblast differentiation in vitro and induces oncogenic transformation in fibroblasts. According to PubMed:20937701, may function as a guanine nucleotide exchange factor (GEF) activating RAB28. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form.

Gene Wiki entry for SBF1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SBF1 Gene

Genomics for SBF1 Gene

Regulatory Elements for SBF1 Gene

Enhancers for SBF1 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
GH22G050443 1 ENCODE dbSUPER 13.4 +35.3 35334 2.5 KLF1 AGO1 CEBPG ZEB1 HIC1 ZFHX2 GLIS2 POLR2A PATZ1 SCRT2 PLXNB2 ADM2 SBF1 MIOX CHKB MAPK8IP2 SYCE3 PPP6R2 PIR32267 GC22P050437
GH22G050446 0.5 dbSUPER 13.4 +33.3 33260 0.9 ZNF740 POLR2A AGO1 BCL11B PLXNB2 SBF1 ADM2 MIOX CHKB MAPK8IP2 SYCE3 DENND6B ARSA GC22P050437
GH22G050467 1.7 FANTOM5 ENCODE dbSUPER 3.2 +8.5 8468 7.9 HDGF ARID4B SIN3A GLI4 ZNF48 YY1 GLIS2 ZNF143 KLF7 ZNF263 TUBGCP6 CPT1B DENND6B MIOX RPL23AP82 PLXNB2 RABL2B CHKB HDAC10 SBF1
GH22G050619 1.8 FANTOM5 Ensembl ENCODE dbSUPER 1.9 -141.6 -141561 3.7 PKNOX1 ATF1 MLX ZFP64 WRNIP1 ARID4B SIN3A DMAP1 ZNF48 YY1 ARSA CPT1B CHKB TUBGCP6 SYCE3 MAPK8IP2 HDAC10 NCAPH2 PPP6R2 SBF1
GH22G050271 1.4 FANTOM5 ENCODE dbSUPER 1.7 +208.5 208454 0.3 RB1 FUS ARID4B BMI1 KLF13 SP3 SP5 GATAD2B REST SP1 DENND6B MAPK8IP2 MAPK11 SHANK3 PPP6R2 MOV10L1 MLC1 SBF1 ACR PIR50517
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SBF1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SBF1 Gene

Chromosome:
22
Start:
50,444,630 bp from pter
End:
50,480,296 bp from pter
Size:
35,667 bases
Orientation:
Minus strand

Genomic View for SBF1 Gene

Genes around SBF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SBF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SBF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SBF1 Gene

Proteins for SBF1 Gene

  • Protein details for SBF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95248-MTMR5_HUMAN
    Recommended name:
    Myotubularin-related protein 5
    Protein Accession:
    O95248
    Secondary Accessions:
    • A6PVG9
    • O60228
    • Q5JXD8
    • Q5PPM2
    • Q96GR9
    • Q9UGB8

    Protein attributes for SBF1 Gene

    Size:
    1867 amino acids
    Molecular mass:
    208315 Da
    Quaternary structure:
    • Interacts with the SET domain of KMT2A/MLL1. Interacts with SUV39H1.
    SequenceCaution:
    • Sequence=AAC39675.1; Type=Frameshift; Positions=1603, 1627, 1631, 1864; Evidence={ECO:0000305};

    Alternative splice isoforms for SBF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SBF1 Gene

Post-translational modifications for SBF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SBF1 Gene

No data available for DME Specific Peptides for SBF1 Gene

Domains & Families for SBF1 Gene

Graphical View of Domain Structure for InterPro Entry

O95248

UniProtKB/Swiss-Prot:

MTMR5_HUMAN :
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class myotubularin subfamily.
Family:
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class myotubularin subfamily.
genes like me logo Genes that share domains with SBF1: view

Function for SBF1 Gene

Molecular function for SBF1 Gene

GENATLAS Biochemistry:
SET binding factor 1,expressed in skeletal muscle,heart,placenta,brain,liver and pancreas
UniProtKB/Swiss-Prot Function:
Probable pseudophosphatase. Lacks several amino acids in the catalytic pocket which renders it catalytically inactive as a phosphatase. The pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases. Inhibits myoblast differentiation in vitro and induces oncogenic transformation in fibroblasts. According to PubMed:20937701, may function as a guanine nucleotide exchange factor (GEF) activating RAB28. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form.

Gene Ontology (GO) - Molecular Function for SBF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008138 protein tyrosine/serine/threonine phosphatase activity TAS 9736772
GO:0017112 Rab guanyl-nucleotide exchange factor activity TAS --
GO:0019208 phosphatase regulator activity IEA --
genes like me logo Genes that share ontologies with SBF1: view
genes like me logo Genes that share phenotypes with SBF1: view

Human Phenotype Ontology for SBF1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SBF1 Gene

MGI Knock Outs for SBF1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SBF1 Gene

Localization for SBF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SBF1 Gene

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 SBF1 gene
Compartment Confidence
cytosol 5
nucleus 4
plasma membrane 1
extracellular 1
mitochondrion 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SBF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005829 cytosol TAS --
GO:0016021 integral component of membrane TAS 9736772
genes like me logo Genes that share ontologies with SBF1: view

Pathways & Interactions for SBF1 Gene

genes like me logo Genes that share pathways with SBF1: view

Pathways by source for SBF1 Gene

Gene Ontology (GO) - Biological Process for SBF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation TAS 9736772
GO:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0007283 spermatogenesis IEA --
GO:0043087 regulation of GTPase activity IEA --
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with SBF1: view

No data available for SIGNOR curated interactions for SBF1 Gene

Drugs & Compounds for SBF1 Gene

No Compound Related Data Available

Transcripts for SBF1 Gene

Unigene Clusters for SBF1 Gene

SET binding factor 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SBF1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: -
SP2:
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30a · 30b ^ 31a · 31b ^ 32a · 32b ^ 33a · 33b · 33c ^ 34 ^ 35a · 35b · 35c ^ 36a · 36b · 36c ^ 37 ^ 38 ^ 39 ^
SP1: - -
SP2: - - -
SP3:
SP4: - -
SP5: - -
SP6: -
SP7:
SP8:
SP9:
SP10: -

ExUns: 40 ^ 41a · 41b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for SBF1 Gene

GeneLoc Exon Structure for
SBF1
ECgene alternative splicing isoforms for
SBF1

Expression for SBF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SBF1 Gene

Protein differential expression in normal tissues from HIPED for SBF1 Gene

This gene is overexpressed in Plasma (21.8), Frontal cortex (11.0), Peripheral blood mononuclear cells (9.1), and Brain (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SBF1 Gene



Protein tissue co-expression partners for SBF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SBF1 Gene:

SBF1

SOURCE GeneReport for Unigene cluster for SBF1 Gene:

Hs.589924

Evidence on tissue expression from TISSUES for SBF1 Gene

  • Muscle(4.3)
  • Blood(4.2)
  • Liver(4.1)
  • Nervous system(4)
  • Pancreas(2.2)
  • Lung(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SBF1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • head
  • skull
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
Limb:
  • foot
  • lower limb
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SBF1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SBF1 Gene

Orthologs for SBF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SBF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SBF1 34 35
  • 99.31 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 92 (a)
OneToMany
SBF1 34
  • 89.23 (n)
-- 35
  • 86 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia SBF1 35
  • 89 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SBF1 34 35
  • 87.67 (n)
rat
(Rattus norvegicus)
Mammalia Sbf1 34
  • 87.66 (n)
mouse
(Mus musculus)
Mammalia Sbf1 34 16 35
  • 87.29 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 55 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SBF1 34 35
  • 76.68 (n)
lizard
(Anolis carolinensis)
Reptilia SBF1 35
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sbf1 34
  • 66.79 (n)
zebrafish
(Danio rerio)
Actinopterygii sbf1 34 35
  • 70.48 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sbf 36 35
  • 38 (a)
worm
(Caenorhabditis elegans)
Secernentea H28G03.6 36
  • 26 (a)
mtm-5 35
  • 25 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3355 35
  • 38 (a)
OneToMany
Species where no ortholog for SBF1 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • 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)

Evolution for SBF1 Gene

ENSEMBL:
Gene Tree for SBF1 (if available)
TreeFam:
Gene Tree for SBF1 (if available)

Paralogs for SBF1 Gene

(4) SIMAP similar genes for SBF1 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for SBF1 Gene

genes like me logo Genes that share paralogs with SBF1: view

Variants for SBF1 Gene

Sequence variations from dbSNP and Humsavar for SBF1 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
VAR_070046 Charcot-Marie-Tooth disease 4B3 (CMT4B3) [MIM:615284]
VAR_070047 Charcot-Marie-Tooth disease 4B3 (CMT4B3) [MIM:615284]
rs200488568 Pathogenic 50,454,858(+) AGGCG(C/T)CCTCT reference, missense
rs587776986 Pathogenic 50,465,084(+) CTTCA(C/T)CAGGA reference, missense
rs690016543 Pathogenic 50,465,006(-) TGTTC(A/G)ATGAG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SBF1 Gene

Variant ID Type Subtype PubMed ID
nsv1073191 CNV deletion 25765185
nsv1118959 CNV deletion 24896259
nsv1160782 CNV deletion 26073780
nsv471224 CNV loss 18288195
nsv829338 CNV gain 20364138
nsv834238 CNV loss 17160897
nsv955201 CNV deletion 24416366

Variation tolerance for SBF1 Gene

Residual Variation Intolerance Score: 0.548% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.31; 70.55% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SBF1 Gene

Human Gene Mutation Database (HGMD)
SBF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SBF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SBF1 Gene

Disorders for SBF1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SBF1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
charcot-marie-tooth disease, type 4b3
  • charcot-marie-tooth disease type 4b3
charcot-marie-tooth neuropathy type 4b3
  • cmt4b3
tooth disease
  • dental disorder
myopathy, centronuclear
  • centronuclear myopathy, autosomal, modifier of
charcot-marie-tooth disease
  • charcot marie tooth muscular atrophy
- elite association - COSMIC cancer census association via MalaCards
Search SBF1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

MTMR5_HUMAN
  • Charcot-Marie-Tooth disease 4B3 (CMT4B3) [MIM:615284]: A recessive demyelinating form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Demyelinating neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. By convention autosomal recessive forms of demyelinating Charcot-Marie-Tooth disease are designated CMT4. {ECO:0000269 PubMed:23749797}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SBF1

Genetic Association Database (GAD)
SBF1
Human Genome Epidemiology (HuGE) Navigator
SBF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SBF1
genes like me logo Genes that share disorders with SBF1: view

No data available for Genatlas for SBF1 Gene

Publications for SBF1 Gene

  1. Association of SET domain and myotubularin-related proteins modulates growth control. (PMID: 9537414) Cui X. … Cleary M.L. (Nat. Genet. 1998) 2 3 4 22 64
  2. Characterization of the myotubularin dual specificity phosphatase gene family from yeast to human. (PMID: 9736772) Laporte J. … Mandel J.-L. (Hum. Mol. Genet. 1998) 2 3 4 64
  3. SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3. (PMID: 23749797) Nakhro K. … Chung K.W. (Neurology 2013) 3 4 64
  4. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M. … Yamada Y. (Am. J. Hypertens. 2010) 3 46 64
  5. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T. … Yamada Y. (Int. J. Mol. Med. 2010) 3 46 64

Products for SBF1 Gene

Sources for SBF1 Gene

Content
Loading form....