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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SGSM1 Gene

protein-coding   GIFtS: 45
GCID: GC22P025202

Small G Protein Signaling Modulator 1

(Previous name: RUN and TBC1 domain containing 2)
(Previous symbol: RUTBC2)
  Search for SGSM1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Small G Protein Signaling Modulator 11 2
RUTBC21 2 3
RUN And TBC1 Domain Containing 21 2
RUN And TBC1 Domain-Containing Protein 22 3
Small G Protein Signaling Modulator 1 Protein2
KIAA19413

External Ids:    HGNC: 294101   Entrez Gene: 1290492   Ensembl: ENSG000001670377   OMIM: 6114175   UniProtKB: Q2NKQ13   

Export aliases for SGSM1 gene to outside databases

Previous GC identifers: GC22P023532 GC22P008151


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for SGSM1 Gene: 
SGSM1 (small G protein signaling modulator 1) is a protein-coding gene. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is TBC1D17.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000022.10  NC_018933.2  NT_011520.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SGSM1 gene promoter:
         LUN-1   NF-E2 p45   LCR-F1   FAC1   ARP-1   STAT3   FOXO1a   NF-E2   Zic3   FOXO1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SGSM1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SGSM1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q11.23   Ensembl cytogenetic band:  22q11.23   HGNC cytogenetic band: 22q11.23

SGSM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SGSM1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P025202:  view genomic region     (about GC identifiers)

Start:
25,202,136 bp from pter      End:
25,323,545 bp from pter
Size:
121,410 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SGSM1_HUMAN, Q2NKQ1 (See protein sequence)
Recommended Name: Small G protein signaling modulator 1  
Size: 1148 amino acids; 129718 Da
Subunit: Interacts with RAB3A, RAB4A, RAB5A, RAB8A, RAB11A, RAP1A, RAP1B, RAP2A and RAP2B. No interaction with
RAB27A
Subcellular location: Golgi apparatus, trans-Golgi network (By similarity)
Sequence caution: Sequence=BAB85527.1; Type=Erroneous initiation;
Secondary accessions: A5LGW1 A8MUT4 B0QYW0 B0QYW1 B5MEG1 Q5TFL3 Q8TF60
Alternative splicing: 3 isoforms:  Q2NKQ1-1   Q2NKQ1-3   Q2NKQ1-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SGSM1: NX_Q2NKQ1

Explore proteomics data for SGSM1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q2NKQ1

  • SGSM1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SGSM1 Protein Expression
    REFSEQ proteins (4 alternative transcripts): 
    NP_001035037.1  NP_001091967.1  NP_001091968.1  NP_597711.1  

    ENSEMBL proteins: 
     ENSP00000383211   ENSP00000383212  

    Human Recombinant Protein Products for SGSM1: 
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    Cloud-Clone Corp. Proteins for SGSM1 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005794Golgi apparatus IEA--

    SGSM1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    SGSM: Small G protein signaling modulators

    2 InterPro protein domains:
     IPR000195 Rab-GTPase-TBC_dom
     IPR004012 Run

    Graphical View of Domain Structure for InterPro Entry Q2NKQ1

    ProtoNet protein and cluster: Q2NKQ1

    1 Blocks protein domain: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: SGSM1_HUMAN, Q2NKQ1
    Similarity: Belongs to the RUTBC family
    Similarity: Contains 1 Rab-GAP TBC domain
    Similarity: Contains 1 RUN domain


    SGSM1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--
         
    SGSM1 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SGSM1

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032313regulation of Rab GTPase activity ----

    SGSM1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SGSM1

    Search CenterWatch for drugs/clinical trials and news about SGSM1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SGSM1 gene (4 alternative transcripts): 
    NM_001039948.2  NM_001098497.1  NM_001098498.1  NM_133454.2  

    Unigene Cluster for SGSM1:

    Small G protein signaling modulator 1
    Hs.474397  [show with all ESTs]
    Unigene Representative Sequence: AB275761
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000400358(uc003abf.2 uc003abg.2 uc010guu.1 uc003abh.2 uc003abj.2 uc003abi.1)
    ENST00000470591 ENST00000400359 ENST00000473458 ENST00000480523
    miRNA
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    8/18 QIAGEN miScript miRNA Assays for microRNAs that regulate SGSM1 (see all 18):
    hsa-miR-140-5p hsa-miR-1197 hsa-miR-575 hsa-miR-218 hsa-miR-507 hsa-miR-9 hsa-miR-133a hsa-miR-2113
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Additional mRNA sequence: 

    AB275761.1 AB449879.1 AK123162.1 AK124850.1 BC036915.1 BC111698.1 

    8 DOTS entries:

    DT.101979627  DT.406131  DT.120663514  DT.406130  DT.100744234  DT.95259482  DT.121234906  DT.75182573 

    24/57 AceView cDNA sequences (see all 57):

    BF507540 H55488 BM668881 AK123162 H38281 AW292307 BI768965 H55305 
    H55245 CA390592 AA622692 BU680772 AI692308 AI378446 BX116718 BU740613 
    AW028652 BM725760 BM693560 BX107450 AI797011 BC036915 AW592693 BU584769 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SGSM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGACGGTCAG
    SGSM1 Expression
    About this image


    See SGSM1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SGSM1

    SOURCE GeneReport for Unigene cluster: Hs.474397

    UniProtKB/Swiss-Prot: SGSM1_HUMAN, Q2NKQ1
    Tissue specificity: Mainly expressed in brain, heart and testis

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SGSM1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SGSM1 gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sgsm11 , 5 small G protein signaling modulator 11, 5 86.54(n)1
    94.05(a)1
      5 (55.45 cM)5
    528501  NM_172718.31  NP_766306.21 
     1132432205 
    chicken
    (Gallus gallus)
    Aves SGSM11 small G protein signaling modulator 1 78.77(n)
    83.06(a)
      430664  XM_003642204.1  XP_003642252.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sgsm11 small G protein signaling modulator 1 69.92(n)
    75.82(a)
      100270734  XM_003198619.1  XP_003198667.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG16951 CG1695 57.95(n)
    52.21(a)
      33046  NM_167705.1  NP_728346.1 
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-81 Protein TBC-8 47.86(n)
    39.81(a)
      176454  NM_066891.3  NP_499292.2 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GYP76
    GTPase-activating protein for yeast Rab family mem...
    15(a)
    1 → many
    IV(34237-36477)


    ENSEMBL Gene Tree for SGSM1 (if available)
    TreeFam Gene Tree for SGSM1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SGSM1 gene
    TBC1D172  TBC1D162  SGSM22  TBC1D152  TBC1D252  
    4 SIMAP similar genes for SGSM1 using alignment to 1 protein entry:     SGSM1_HUMAN:
    RUTBC2    DKFZp761D0223    RUTBC1    SGSM2

    SGSM1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SGSM1
    PGOHUM00000263069


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/3351 SNPs in SGSM1 are shown (see all 3351)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs600276921,2
    C--9131164(+) AAAAA-/AGAAAA 4 -- int10--------
    rs347944821,2
    C--9159055(+) CTCTCT/-TTTTT 4 -- int12Minor allele frequency- -:0.25NA 4
    rs1132853311,2
    C--9230980(+) AAAGGAA/-AAAAA 4 -- int11Minor allele frequency- -:0.50CSA 2
    rs1418316961,2
    --25200291(+) CAGTTC/TATTTC 4 -- us2k10--------
    rs1466017041,2
    --25200336(+) GCTTAC/TGGCCA 4 -- us2k10--------
    rs412815591,2
    C--25200426(+) TAGTCC/TTTCTG 4 -- us2k10--------
    rs1445441321,2
    C--25200456(+) GGGGA-/CCCTAA 4 -- us2k10--------
    rs796320141,2
    C,F--25200513(+) TTGGCC/TCTGCA 4 -- us2k11Minor allele frequency- T:0.04WA 118
    rs1436717471,2
    --25200598(+) TCACTA/GTTTGA 4 -- us2k10--------
    rs1471952271,2
    C--25200605(+) TTGACA/TGGACA 4 -- us2k10--------

    HapMap Linkage Disequilibrium report for SGSM1 (25202136 - 25323545 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for SGSM1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2670598CNV Deletion23128226
    esv2724070CNV Deletion23290073
    esv2724071CNV Deletion23290073
    esv25685CNV Loss19812545
    nsv819966CNV Gain19587683
    nsv834161CNV Gain17160897
    nsv7350OTHER Inversion18451855

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SGSM1 for disorders           About MalaCards
    OMIM gene information: 611417    OMIM disorders: --


    SGSM1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SGSM1
    Human Genome Epidemiology (HuGE) Navigator: SGSM1 (4 documents)

    Export disorders for SGSM1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SGSM1 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with SGSM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of three novel proteins (SGSM1, 2, 3) which modulate small G protein (RAP and RAB)-mediated signaling pathway. (PubMed id 17509819)1, 2, 3 Yang H....Shimizu N. (2007)
    2. Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins. (PubMed id 11853319)1, 2, 3 Nagase T.... Ohara O. (2001)
    3. RUTBC2 protein, a Rab9A effector and GTPase-activating protein for Rab36. (PubMed id 22637480)1, 3 Nottingham R.M....Pfeffer S.R. (2012)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    5. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    6. Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)
    7. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PubMed id 19077034)1 Ishibashi K.... Fukuda M. (2009)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    10. The DNA sequence of human chromosome 22. (PubMed id 10591208)2 Dunham I....O'Brien K.P. (1999)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 129049 HGNC: 29410 AceView: RUTBC2 Ensembl:ENSG00000167037 euGenes: HUgn129049
    ECgene: SGSM1 H-InvDB: SGSM1

    (According to HUGE)
    About This Section
    HUGE: KIAA1941

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SGSM1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SGSM1 gene:
    Search GeneIP for patents involving SGSM1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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