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    SBF1 SET binding factor 1 [ Homo sapiens (human) ]

    Gene ID: 6305, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SBF1provided by HGNC
    Official Full Name
    SET binding factor 1provided by HGNC
    Primary source
    HGNC:HGNC:10542
    See related
    Ensembl:ENSG00000100241 MIM:603560; AllianceGenome:HGNC:10542
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MTMR5; CMT4B3; DENND7A
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 38.3), brain (RPKM 19.4) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SBF1 in Genome Data Viewer
    Location:
    22q13.33
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50445000..50475035, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50954193..50984219, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50883429..50913464, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 6 regulatory subunit 2 Neighboring gene RNA, 7SL, cytoplasmic 500, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50836255-50836755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50838165-50838761 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:50844619-50845818 Neighboring gene microRNA 12114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50883030-50883876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50910985-50911896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50911897-50912806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50913717-50914626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13982 Neighboring gene adrenomedullin 2 Neighboring gene myo-inositol oxygenase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. SET binding factor 1 (SBF1) mutation causes Charcot-Marie-tooth disease type 4B3. Alazami AM, et al. Neurology, 2014 May 6. PMID 24799518
    2. Pseudo-phosphatase Sbf1 contains an N-terminal GEF homology domain that modulates its growth regulatory properties. Firestein R, et al. J Cell Sci, 2001 Aug. PMID 11686296
    3. A novel frameshift deletion in autosomal recessive SBF1-related syndromic neuropathy with necklace fibres. Gang Q, et al. J Neurol, 2020 Sep. PMID 32444983, Free PMC Article
    4. A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder. Khamse S, et al. Sci Rep, 2022 Sep 14. PMID 36104480, Free PMC Article
    5. Novel SBF1 splice-site null mutation broadens the clinical spectrum of Charcot-Marie-Tooth type 4B3 disease. Flusser H, et al. Clin Genet, 2018 Nov. PMID 30039846

    See all (78) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder.
      Title: A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder.
    2. A novel frameshift deletion in autosomal recessive SBF1-related syndromic neuropathy with necklace fibres.
      Title: A novel frameshift deletion in autosomal recessive SBF1-related syndromic neuropathy with necklace fibres.
    3. The novel SBF1 null mutation highlights distinct severe phenotypic manifestations, broadening the clinical spectrum of SBF1-related neuropathies: cerebellar and pyramidal signs evident in the first months of life with peripheral polyneuropathy emerging only toward the end of the first decade, together with unique MRI findings.
      Title: Novel SBF1 splice-site null mutation broadens the clinical spectrum of Charcot-Marie-Tooth type 4B3 disease.
    4. Novel sequence variants in SBF1 (c.1168C>G and c.2209_2210del) as the potential causative mutations in two siblings with severe axonal neuropathy, hearing loss, facial weakness and bulbar features.
      Title: SBF1 mutations associated with autosomal recessive axonal neuropathy with cranial nerve involvement.
    5. ZNF195 and SBF1 are potential biomarkers for gemcitabine sensitivity in head and neck squamous cell carcinoma cell lines.
      Title: DNA microarray reveals ZNF195 and SBF1 are potential biomarkers for gemcitabine sensitivity in head and neck squamous cell carcinoma cell lines.
    6. Compound heterozygous mutations in SBF1 appear to be the underlying causes of a novel Charcot-Marie-Tooth disease type 4B subtype (designated as CMT4B3) in a Korean family.
      Title: SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3.
    7. SBF1 (MTMR5) belongs to the myotubularin family of phosphoinositides phosphatases-like
      Title: Characterization of the myotubularin dual specificity phosphatase gene family from yeast to human.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    9. MTMR2 interacts with MTMR5 via its coiled-coil domain and that mutations in the coiled-coil domain of either MTMR2 or MTMR5 abrogate this interaction.
      Title: Regulation of myotubularin-related (MTMR)2 phosphatidylinositol phosphatase by MTMR5, a catalytically inactive phosphatase.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC99700, DKFZp761D0422

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
    		  
    NOT enables phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein tyrosine/serine/threonine phosphatase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein dephosphorylation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    myotubularin-related protein 5
    Names
    DENN/MADD domain containing 7A
    inactive phosphatidylinositol 3-phosphatase 5

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_041810.1 RefSeqGene

      Range
      5037..35072
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001365819.1 → NP_001352748.1  myotubularin-related protein 5 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL096767
      Consensus CDS
      CCDS93186.1
      UniProtKB/Swiss-Prot
      A0A024R4Z9, A6PVG9, G5E933, O60228, O95248, Q5JXD8, Q5PPM2, Q96GR9, Q9UGB8
      UniProtKB/TrEMBL
      A0A8I5KXX8
      Related
      ENSP00000510414.1, ENST00000689129.1
      Conserved Domains (7) summary
      smart00801
      Location:365 → 433
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:130 → 311
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1761 → 1866
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam06602
      Location:1129 → 1532
      Myotub-related; Myotubularin-like phosphatase domain
      pfam12335
      Location:544 → 765
      SBF2; Myotubularin protein
      cl17171
      Location:894 → 1012
      PH-like; Pleckstrin homology-like domain

    2. NM_001410794.1 → NP_001397723.1  myotubularin-related protein 5 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL096767
      Consensus CDS
      CCDS93187.1
      Related
      ENSP00000509117.1, ENST00000684986.1

    3. NM_001410795.1 → NP_001397724.1  myotubularin-related protein 5 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL096767
      Consensus CDS
      CCDS93185.1
      UniProtKB/TrEMBL
      A0A8J8YTQ8
      Related
      ENSP00000252027.8, ENST00000348911.11

    4. NM_002972.4 → NP_002963.2  myotubularin-related protein 5 isoform 1

      See identical proteins and their annotated locations for NP_002963.2

      Status: REVIEWED

      Source sequence(s)
      AL096767, BC087612, BM975530, HY035781
      Consensus CDS
      CCDS14091.2
      UniProtKB/TrEMBL
      A0A8I5KVF2
      Related
      ENSP00000370196.2, ENST00000380817.8
      Conserved Domains (8) summary
      smart00801
      Location:364 → 432
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:129 → 310
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1786 → 1891
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam00169
      Location:1790 → 1891
      PH; PH domain
      pfam06602
      Location:1128 → 1556
      Myotub-related; Myotubularin-like phosphatase domain
      pfam12335
      Location:543 → 764
      SBF2; Myotubularin protein
      cl17171
      Location:893 → 1011
      PH-like; Pleckstrin homology-like domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      50445000..50475035 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      50954193..50984219 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95248.4 GenPept UniProtKB/Swiss-Prot:O95248

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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