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

Gene ID: 129049, updated on 5-Mar-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 be involved in activation of GTPase activity and intracellular protein transport. 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, Apr 2022]
Expression
Broad expression in brain (RPKM 6.6), heart (RPKM 5.6) and 15 other tissues See more
Orthologs
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Genomic context

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Location:
22q11.23
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (24806211..24927578)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (25267600..25389136)
105.20220307 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
  • 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 (20) 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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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
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 small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in activation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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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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_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
    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

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