U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SBF2 SET binding factor 2 [ Homo sapiens (human) ]

Gene ID: 81846, updated on 3-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
SBF2provided by HGNC
Official Full Name
SET binding factor 2provided by HGNC
Primary source
HGNC:HGNC:2135
See related
Ensembl:ENSG00000133812 MIM:607697; AllianceGenome:HGNC:2135
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
CMT4B2; MTMR13; DENND7B
Summary
This gene encodes a pseudophosphatase and member of the myotubularin-related protein family. This gene maps within the CMT4B2 candidate region of chromosome 11p15 and mutations in this gene have been associated with Charcot-Marie-Tooth Disease, type 4B2. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 7.7), fat (RPKM 7.5) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SBF2 in Genome Data Viewer
Location:
11p15.4
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (9778668..10303837, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (9863048..10388341, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (9800215..10315766, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9733231-9733731 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9740773-9741273 Neighboring gene RN7SK pseudogene 50 Neighboring gene switching B cell complex subunit SWAP70 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3138 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9785216-9785716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9786625-9787448 Neighboring gene uncharacterized LOC105369149 Neighboring gene long intergenic non-protein coding RNA 2709 Neighboring gene SBF2 antisense RNA 1 Neighboring gene protein GVQW1-like Neighboring gene uncharacterized LOC101928008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4426 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:9884465-9885024 Neighboring gene RNA, U7 small nuclear 28 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9915190-9915690 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9915691-9916191 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:9927555-9928139 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:10004023-10005222 Neighboring gene glutamate-ammonia ligase pseudogene 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:10065715-10066914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10098213-10098818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4428 Neighboring gene G protein subunit gamma 10 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3147 Neighboring gene Sharpr-MPRA regulatory region 210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3149 Neighboring gene Sharpr-MPRA regulatory region 6386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10361038-10361538 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10361539-10362039 Neighboring gene uncharacterized LOC100130460 Neighboring gene VISTA enhancer hs2289 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10375005-10375536 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10375537-10376067 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:10388109-10388608 Neighboring gene Sharpr-MPRA regulatory region 7754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10413861-10414740 Neighboring gene adrenomedullin Neighboring gene RNA, U6atac small nuclear 33, pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. The impact of SBF2 on taxane-induced peripheral neuropathy. Cunningham GM, et al. PLoS Genet, 2022 Jan. PMID 34986146, Free PMC Article
  2. Charcot-Marie-Tooth gene, SBF2, associated with taxane-induced peripheral neuropathy in African Americans. Schneider BP, et al. Oncotarget, 2016 Dec 13. PMID 27732968, Free PMC Article
  3. Identification of a novel SBF2 frameshift mutation in charcot-marie-tooth disease type 4B2 using whole-exome sequencing. Chen M, et al. Genomics Proteomics Bioinformatics, 2014 Oct. PMID 25462154, Free PMC Article
  4. Identification of a novel SBF2 missense mutation associated with a rare case of thrombocytopenia using whole-exome sequencing. Abuzenadah AM, et al. J Thromb Thrombolysis, 2013 Nov. PMID 23334996
  5. A new SBF2 mutation in a family with recessive demyelinating Charcot-Marie-Tooth (CMT4B2). Conforti FL, et al. Neurology, 2004 Oct 12. PMID 15477569

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The impact of SBF2 on taxane-induced peripheral neuropathy.
    Title: The impact of SBF2 on taxane-induced peripheral neuropathy.
  2. Rare variants in SBF2 predict an increased risk of taxane-induced peripheral neuropathy in African American breast cancer patients receiving paclitaxel.
    Title: Charcot-Marie-Tooth gene, SBF2, associated with taxane-induced peripheral neuropathy in African Americans.
  3. Starvation-induced MTMR13 and RAB21 activity regulates VAMP8 to promote autophagosome-lysosome fusion.
    Title: Starvation-induced MTMR13 and RAB21 activity regulates VAMP8 to promote autophagosome-lysosome fusion.
  4. SBF2 frameshift mutation is associated with charcot-marie-tooth disease type 4B2.
    Title: Identification of a novel SBF2 frameshift mutation in charcot-marie-tooth disease type 4B2 using whole-exome sequencing.
  5. Identification of a novel SBF2 missense mutation associated with a rare case of thrombocytopenia using whole-exome sequencing.
    Title: Identification of a novel SBF2 missense mutation associated with a rare case of thrombocytopenia using whole-exome sequencing.
  6. Germline genetic variation in the SBF2 locus was associated with overall survival in patients with pancreatic adenocarcinoma of European and Asian ancestry.
    Title: Genome-wide association study of survival in patients with pancreatic adenocarcinoma.
  7. REVIEW : MTMR13 and homologous proteins are mutated in several neuromuscular diseases
    Title: Endosomal phosphoinositides and human diseases.
  8. A phylogenetic study revealing co-evolution of myotubularins with PI 3-kinase class III complex
    Title: PtdIns5P regulation through evolution: roles in membrane trafficking?
  9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  10. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Charcot-Marie-Tooth disease type 4B2
MedGen: C1858278 OMIM: 604563 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of smoking behaviours among Bangladeshi adults.
EBI GWAS Catalog
Genome-wide association study of survival in patients with pancreatic adenocarcinoma.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Replication interactions

Interaction Pubs
Knockdown of SET binding factor 2 (SBF2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ22918, FLJ41627, KIAA1766, DKFZp779B2327

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
  
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatase binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatase regulator activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in myelination NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in vacuolar membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
myotubularin-related protein 13
Names
DENN/MADD domain containing 7B
inactive phosphatidylinositol 3-phosphatase 13

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_008074.1 RefSeqGene

    Range
    5001..520541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_267

mRNA and Protein(s)

  1. NM_001386339.1 → NP_001373268.1  myotubularin-related protein 13 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC011092, AC026250, AC080023, AC100763
    Consensus CDS
    CCDS91440.1
    UniProtKB/TrEMBL
    A0A6Q8PH13, A0A8I5KQ02
    Related
    ENSP00000509587.1, ENST00000689128.1
    Conserved Domains (7) summary
    smart00801
    Location:352 → 420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:1 → 86
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:1774 → 1879
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    cd13339
    Location:882 → 1000
    PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    cd14589
    Location:1138 → 1517
    PTP-MTMR13; protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 13
    pfam02141
    Location:116 → 298
    DENN; DENN (AEX-3) domain
    pfam12335
    Location:531 → 754
    SBF2; Myotubularin protein

  2. NM_001386342.1 → NP_001373271.1  myotubularin-related protein 13 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC011092, AC026250, AC080023, AC100763
    Consensus CDS
    CCDS91439.1
    UniProtKB/TrEMBL
    A0A8I5KWY5, A0A8I5KY55
    Related
    ENSP00000509545.1, ENST00000692716.1
    Conserved Domains (7) summary
    smart00801
    Location:352 → 421
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:1 → 86
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:1699 → 1804
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    cd13339
    Location:839 → 957
    PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    cd14589
    Location:1095 → 1442
    PTP-MTMR13; protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 13
    pfam02141
    Location:116 → 298
    DENN; DENN (AEX-3) domain
    pfam12335
    Location:488 → 711
    SBF2; Myotubularin protein

  3. NM_001424318.1 → NP_001411247.1  myotubularin-related protein 13 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC011092, AC026250, AC080023, AC100763

  4. NM_001425069.1 → NP_001411998.1  myotubularin-related protein 13 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC011092, AC026250, AC080023, AC100763

  5. NM_001425070.1 → NP_001411999.1  myotubularin-related protein 13 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC011092, AC026250, AC080023, AC100763

  6. NM_030962.4 → NP_112224.1  myotubularin-related protein 13 isoform 2

    See identical proteins and their annotated locations for NP_112224.1

    Status: REVIEWED

    Source sequence(s)
    AC011092, AC026250, AC080023, AC100763
    Consensus CDS
    CCDS31427.1
    UniProtKB/Swiss-Prot
    Q3MJF0, Q68DQ3, Q6P459, Q6PJD1, Q7Z325, Q7Z621, Q86VE2, Q86WG5, Q96FE2, Q9C097
    UniProtKB/TrEMBL
    A0A8I5KWY5
    Related
    ENSP00000256190.8, ENST00000256190.13
    Conserved Domains (8) summary
    smart00801
    Location:352 → 420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:1 → 86
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:1742 → 1847
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    cd13339
    Location:882 → 1000
    PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    pfam00169
    Location:1747 → 1847
    PH; PH domain
    pfam02141
    Location:116 → 298
    DENN; DENN (AEX-3) domain
    pfam06602
    Location:1116 → 1519
    Myotub-related; Myotubularin-like phosphatase domain
    pfam12335
    Location:531 → 754
    SBF2; Myotubularin protein

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    9778668..10303837 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427657.1 → XP_047283613.1  myotubularin-related protein 13 isoform X1

  2. XM_011520395.4 → XP_011518697.1  myotubularin-related protein 13 isoform X2

    UniProtKB/TrEMBL
    A0A6Q8PH87
    Related
    ENSP00000502578.1, ENST00000676324.2
    Conserved Domains (6) summary
    smart00801
    Location:352 → 420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:1 → 86
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:116 → 298
    DENN; DENN (AEX-3) domain
    pfam12335
    Location:531 → 754
    SBF2; Myotubularin protein
    cl17171
    Location:882 → 1000
    PH-like; Pleckstrin homology-like domain
    cl21483
    Location:1116 → 1248
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  3. XM_047427658.1 → XP_047283614.1  myotubularin-related protein 13 isoform X4

  4. XM_011520396.4 → XP_011518698.1  myotubularin-related protein 13 isoform X3

    Related
    ENSP00000509247.1, ENST00000533770.6
    Conserved Domains (5) summary
    smart00801
    Location:352 → 420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:1 → 86
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:116 → 298
    DENN; DENN (AEX-3) domain
    pfam12335
    Location:531 → 754
    SBF2; Myotubularin protein
    cl17171
    Location:882 → 1000
    PH-like; Pleckstrin homology-like domain

  5. XM_017018377.3 → XP_016873866.1  myotubularin-related protein 13 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    9863048..10388341 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370087.1 → XP_054226062.1  myotubularin-related protein 13 isoform X10

  2. XM_054370086.1 → XP_054226061.1  myotubularin-related protein 13 isoform X9

  3. XM_054370082.1 → XP_054226057.1  myotubularin-related protein 13 isoform X6

  4. XM_054370083.1 → XP_054226058.1  myotubularin-related protein 13 isoform X7

  5. XM_054370085.1 → XP_054226060.1  myotubularin-related protein 13 isoform X8

  6. XM_054370084.1 → XP_054226059.1  myotubularin-related protein 13 isoform X8

  7. XM_054370088.1 → XP_054226063.1  myotubularin-related protein 13 isoform X1

  8. XM_054370089.1 → XP_054226064.1  myotubularin-related protein 13 isoform X2

    UniProtKB/TrEMBL
    A0A6Q8PH87

  9. XM_054370090.1 → XP_054226065.1  myotubularin-related protein 13 isoform X3

  10. XM_054370091.1 → XP_054226066.1  myotubularin-related protein 13 isoform X4

  11. XM_054370092.1 → XP_054226067.1  myotubularin-related protein 13 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86WG5.1 GenPept UniProtKB/Swiss-Prot:Q86WG5

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous