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    SGSM1 small G protein signaling modulator 1 [ Homo sapiens (human) ]

    Gene ID: 129049, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SGSM1provided by HGNC
    Official Full Name
    small G protein signaling modulator 1provided by HGNC
    Primary source
    HGNC:HGNC:29410
    See related
    Ensembl:ENSG00000167037 MIM:611417; AllianceGenome:HGNC:29410
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RUTBC2
    Summary
    Enables GTPase activator activity and small GTPase binding activity. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasmic vesicle membrane and cytosol. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 6.6), heart (RPKM 5.6) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SGSM1 in Genome Data Viewer
    Location:
    22q11.23
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (24806211..24927578)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (25267600..25389136)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (25202178..25323545)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:25126732-25127306 Neighboring gene cysteine rich protein 1 pseudogene 4 Neighboring gene piwi like RNA-mediated gene silencing 3 Neighboring gene DNA topoisomerase I pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13556 Neighboring gene MPRA-validated peak4474 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25287609-25288110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25293734-25294234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25294235-25294735 Neighboring gene small nucleolar RNA SNORD56 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:25307870-25308029 Neighboring gene Sharpr-MPRA regulatory region 9438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13557 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:25354355-25354854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25365545-25366128 Neighboring gene LHFPL tetraspan subfamily member 7 Neighboring gene KIAA1671 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25390751-25391348 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:25398411-25398910 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:25421915-25423114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25457216-25458130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25462486-25463045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25465590-25466140 Neighboring gene Sharpr-MPRA regulatory region 10625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25494863-25495382 Neighboring gene KIAA1671 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:25506614-25507476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25507477-25508338

    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. Prognostic biomarker SGSM1 and its correlation with immune infiltration in gliomas. Li J, et al. BMC Cancer, 2022 Apr 28. PMID 35484511, Free PMC Article
    2. Hypermethylation of SHISA3 Promotes Nasopharyngeal Carcinoma Metastasis by Reducing SGSM1 Stability. Zhang J, et al. Cancer Res, 2019 Feb 15. PMID 30573520
    3. RUTBC2 protein, a Rab9A effector and GTPase-activating protein for Rab36. Nottingham RM, et al. J Biol Chem, 2012 Jun 29. PMID 22637480, Free PMC Article
    4. Identification of three novel proteins (SGSM1, 2, 3) which modulate small G protein (RAP and RAB)-mediated signaling pathway. Yang H, et al. Genomics, 2007 Aug. PMID 17509819
    5. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. Ishibashi K, et al. Genes Cells, 2009 Jan. PMID 19077034

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Prognostic biomarker SGSM1 and its correlation with immune infiltration in gliomas.
      Title: Prognostic biomarker SGSM1 and its correlation with immune infiltration in gliomas.
    2. Reduced SGSM1 Stability is associated with Nasopharyngeal Carcinoma Metastasis.
      Title: Hypermethylation of SHISA3 Promotes Nasopharyngeal Carcinoma Metastasis by Reducing SGSM1 Stability.
    3. These data show that RUTBC2 can act as a Rab36 GAP in cells and suggest that RUTBC2 links Rab9A function to Rab36 function in the endosomal system.
      Title: RUTBC2 protein, a Rab9A effector and GTPase-activating protein for Rab36.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    6. 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.
    7. Identification of novel protein SGSM1 which modulate small G protein (RAP and RAB)-mediated signaling pathway.
      Title: Identification of three novel proteins (SGSM1, 2, 3) which modulate small G protein (RAP and RAB)-mediated signaling pathway.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1941, MGC133298

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasmic vesicle membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    small G protein signaling modulator 1
    Names
    RUN and TBC1 domain containing 2
    RUN and TBC1 domain-containing protein 2
    small G protein signaling modulator 1 protein

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001039948.4 → NP_001035037.1  small G protein signaling modulator 1 isoform 1

      See identical proteins and their annotated locations for NP_001035037.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1) and includes two alternate in-frame exons.
      Source sequence(s)
      AB275761, AL050312, AP000359, AW028652, BC036915, BC111698, BM930881
      Consensus CDS
      CCDS46674.1
      UniProtKB/Swiss-Prot
      A5LGW1, A8MUT4, B0QYW0, B0QYW1, B5MEG1, B9A6J4, Q2NKQ1, Q5TFL3, Q8TF60
      Related
      ENSP00000383212.4, ENST00000400359.4
      Conserved Domains (3) summary
      smart00164
      Location:936 → 1105
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      cd15784
      Location:254 → 425
      PH_RUTBC; Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins
      pfam02759
      Location:44 → 188
      RUN; RUN domain

    2. NM_001098497.3 → NP_001091967.1  small G protein signaling modulator 1 isoform 3

      See identical proteins and their annotated locations for NP_001091967.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon, and includes an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AB275761, AL050312, AP000359, AW028652, BM930881
      Consensus CDS
      CCDS46675.1
      UniProtKB/Swiss-Prot
      Q2NKQ1
      Related
      ENSP00000383211.4, ENST00000400358.9
      Conserved Domains (3) summary
      smart00164
      Location:881 → 1050
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      cd15784
      Location:254 → 425
      PH_RUTBC; Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins
      pfam02759
      Location:44 → 188
      RUN; RUN domain

    3. NM_001098498.3 → NP_001091968.1  small G protein signaling modulator 1 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      AB075821, AB275761, AL050312, AP000359, AW028652, BC111698, BM930881
      UniProtKB/Swiss-Prot
      Q2NKQ1
      Conserved Domains (3) summary
      smart00164
      Location:820 → 989
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      cd15784
      Location:254 → 425
      PH_RUTBC; Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins
      pfam02759
      Location:44 → 188
      RUN; RUN domain

    4. NM_133454.4 → NP_597711.1  small G protein signaling modulator 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AB275761, AL050312, AP000359, AW028652, BC036915, BC111698, BM930881
      Consensus CDS
      CCDS74834.1
      UniProtKB/TrEMBL
      A0A087X241
      Related
      ENSP00000484682.1, ENST00000610372.4
      Conserved Domains (3) summary
      smart00164
      Location:875 → 1044
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      cd15784
      Location:254 → 425
      PH_RUTBC; Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins
      pfam02759
      Location:44 → 188
      RUN; RUN 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
      24806211..24927578
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      25267600..25389136
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2NKQ1.2 GenPept UniProtKB/Swiss-Prot:Q2NKQ1

    Gene LinkOut

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

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