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

Gene ID: 6305, updated on 3-Apr-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
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Genomic context

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Location:
22q13.33
Exon count:
41
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50445000..50475035, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50954193..50984219, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. SBF1 mutations associated with autosomal recessive axonal neuropathy with cranial nerve involvement. Manole A, et al. Neurogenetics, 2017 Jan. PMID 28005197
  5. SET binding factor 1 (SBF1) mutation causes Charcot-Marie-tooth disease type 4B3. Alazami AM, et al. Neurology, 2014 May 6. PMID 24799518

See all (71) 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 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_2023_10

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

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