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

Gene ID: 6305, updated on 7-Jan-2024

Summary

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

See SBF1 in Genome Data Viewer
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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC99700, DKFZp761D0422

Gene Ontology Provided by GOA

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

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_001365819.1NP_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:365433
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:130311
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:17611866
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    pfam06602
    Location:11291532
    Myotub-related; Myotubularin-like phosphatase domain
    pfam12335
    Location:544765
    SBF2; Myotubularin protein
    cl17171
    Location:8941012
    PH-like; Pleckstrin homology-like domain
  2. NM_001410794.1NP_001397723.1  myotubularin-related protein 5 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL096767
    Consensus CDS
    CCDS93187.1
    UniProtKB/TrEMBL
    A0A8I5KVF2
    Related
    ENSP00000509117.1, ENST00000684986.1
  3. NM_001410795.1NP_001397724.1  myotubularin-related protein 5 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL096767
    Consensus CDS
    CCDS93185.1
    UniProtKB/TrEMBL
    A0A8I5KXX8, A0A8J8YTQ8
    Related
    ENSP00000252027.8, ENST00000348911.11
  4. NM_002972.4NP_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:364432
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:129310
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:17861891
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    pfam00169
    Location:17901891
    PH; PH domain
    pfam06602
    Location:11281556
    Myotub-related; Myotubularin-like phosphatase domain
    pfam12335
    Location:543764
    SBF2; Myotubularin protein
    cl17171
    Location:8931011
    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)