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    SGSM3 small G protein signaling modulator 3 [ Homo sapiens (human) ]

    Gene ID: 27352, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SGSM3provided by HGNC
    Official Full Name
    small G protein signaling modulator 3provided by HGNC
    Primary source
    HGNC:HGNC:25228
    See related
    Ensembl:ENSG00000100359 MIM:610440; AllianceGenome:HGNC:25228
    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
    MAP; CIP85; RUSC3; RUTBC3; RABGAP5; RabGAP-5; rabGAPLP
    Summary
    Enables GTPase activator activity and small GTPase binding activity. Involved in several processes, including Rap protein signal transduction; positive regulation of GTPase activity; and regulation of Rab protein signal transduction. Located in cytosol. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in stomach (RPKM 33.5), prostate (RPKM 23.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SGSM3 in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (40370594..40410289)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (40842001..40880672)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (40766598..40806293)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene trinucleotide repeat containing adaptor 6B Neighboring gene ribosomal protein L7 pseudogene 52 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19082 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40591286-40591820 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40591821-40592353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40624195-40624696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40633809-40634710 Neighboring gene uncharacterized LOC124905121 Neighboring gene MPRA-validated peak4496 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr22:40740204-40740376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40742019-40742532 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40742533-40743046 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40743047-40743559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19086 Neighboring gene adenylosuccinate lyase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40812395-40812894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19091 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:40851734-40851957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19093 Neighboring gene myocardin related transcription factor A Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40867879-40868537 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40894439-40894938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40906589-40907133 Neighboring gene MRTFA antisense RNA 1 Neighboring gene uncharacterized LOC105373037

    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. Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews. Birnbaum R, et al. J Med Genet, 2024 Feb 21. PMID 37833060
    2. Evaluation of 4-bp insertion/deletion polymorphism within the 3'UTR of SGSM3 in bladder cancer using mismatch PCR-RFLP method: A preliminary report. Hashemi M, et al. J Cell Biochem, 2018 Aug. PMID 29693742
    3. Association between an insertion/deletion polymorphism within 3'UTR of SGSM3 and risk of hepatocellular carcinoma. Wang C, et al. Tumour Biol, 2014 Jan. PMID 23918301
    4. MAP, a protein interacting with a tumor suppressor, merlin, through the run domain. Lee IK, et al. Biochem Biophys Res Commun, 2004 Dec 17. PMID 15541357
    5. Genetic variants of ESR1 and SGSM3 are associated with the susceptibility of breast cancer in the Chinese population. Tan T, et al. Breast Cancer, 2017 May. PMID 27432265

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews.
      Title: Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews.
    2. findings support an association between 4-bp ins/del polymorphism in the 3'UTR of SGSM3 and the risk of bladder cancer in an Iranian population.
      Title: Evaluation of 4-bp insertion/deletion polymorphism within the 3'UTR of SGSM3 in bladder cancer using mismatch PCR-RFLP method: A preliminary report.
    3. SGSM3 gene polymorphism is associated with the risk of breast cancer in Chinese population.
      Title: Genetic variants of ESR1 and SGSM3 are associated with the susceptibility of breast cancer in the Chinese population.
    4. The CIP85 was observed to interact with clathrin, which suggested a role for CIP85 in the clathrin-mediated internalization of Cx43.
      Title: The connexin43-interacting protein, CIP85, mediates the internalization of connexin43 from the plasma membrane.
    5. rs56228771 may contribute to hepatocarcinogenesis, possibly by affecting SGSM3 expression through a miRNA-mediated regulation.
      Title: Association between an insertion/deletion polymorphism within 3'UTR of SGSM3 and risk of hepatocellular carcinoma.
    6. Identification of novel protein SGSM3 which modulates 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.
    7. MAP decreased the AP-1-dependent promoter activity additively with merlin in NIH3T3 cells.Results suggest that MAP may play a cooperative role in the merlin-mediated growth suppression of cells.
      Title: MAP, a protein interacting with a tumor suppressor, merlin, through the run domain.
    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
    A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide signaling pathway in the etiology of human height variation.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp761D051

    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 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 Rap protein signal transduction IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in plasma membrane to endosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of Rab protein signal transduction IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in regulation of cell cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT involved_in regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in gap junction IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    small G protein signaling modulator 3
    Names
    RUN and SH3 containing 3
    RUN and TBC1 domain containing 3
    RUN and TBC1 domain-containing protein 3
    merlin binding protein
    merlin-associated protein
    rab-GTPase-activating protein-like protein
    small G protein signaling modulator 3 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_001301849.2 → NP_001288778.1  small G protein signaling modulator 3 isoform 2

      See identical proteins and their annotated locations for NP_001288778.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region, one of which results in the use of an alternate start codon compared to variant 1. It encodes isoform 2 which has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK301042, AW512418, BC008078, BP283990, HY229847
      UniProtKB/TrEMBL
      B4DMS2, B4DVE3, E9PEL5
      Conserved Domains (3) summary
      cd11813
      Location:421 → 473
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:51 → 262
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:480 → 628
      RUN; RUN domain

    2. NM_001350039.2 → NP_001336968.1  small G protein signaling modulator 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL022238, AW512418, BC008078, BP283990, HY229847
      Conserved Domains (3) summary
      cd11813
      Location:484 → 536
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:114 → 325
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:563 → 731
      RUN; RUN domain

    3. NM_001350040.2 → NP_001336969.1  small G protein signaling modulator 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL022238, AW512418, BC008078, BP283990, HY231525
      Conserved Domains (3) summary
      cd11813
      Location:484 → 536
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:114 → 325
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:563 → 731
      RUN; RUN domain

    4. NM_001350041.2 → NP_001336970.1  small G protein signaling modulator 3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AW512418, BC008078, BP283990, BU684524
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5

    5. NM_001350042.2 → NP_001336971.1  small G protein signaling modulator 3 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AK301042, AL022238, AW512418, BC008078, BP283990, HY229847
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5
      Conserved Domains (3) summary
      cd11813
      Location:421 → 473
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:51 → 262
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:500 → 668
      RUN; RUN domain

    6. NM_001350043.2 → NP_001336972.1  small G protein signaling modulator 3 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL022238, AW512418, BC008078, BX424691, HY229847
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5
      Conserved Domains (3) summary
      cd11813
      Location:417 → 469
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:47 → 258
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:496 → 664
      RUN; RUN domain

    7. NM_001350044.2 → NP_001336973.1  small G protein signaling modulator 3 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AK301042, AW512418, BC008078, BP283990, BX388288, DC389110, HY229847
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5
      Conserved Domains (3) summary
      cd11813
      Location:421 → 473
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:51 → 262
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:500 → 651
      RUN; RUN domain

    8. NM_001350045.2 → NP_001336974.1  small G protein signaling modulator 3 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AK301042, AW512418, BC008078, BP283990, BX388288, HY229847
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5
      Conserved Domains (3) summary
      cd11813
      Location:421 → 473
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:51 → 262
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:500 → 651
      RUN; RUN domain

    9. NM_001350046.2 → NP_001336975.1  small G protein signaling modulator 3 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AW512418, BC008078, BX424691, HY149764, HY229847
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5
      Conserved Domains (3) summary
      cd11813
      Location:417 → 469
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:47 → 258
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:496 → 647
      RUN; RUN domain

    10. NM_001350047.2 → NP_001336976.1  small G protein signaling modulator 3 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AW512418, BC008078, BX430401, HY231525
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5

    11. NM_001350048.2 → NP_001336977.1  small G protein signaling modulator 3 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AW512418, BC008078, BX428466, BX430401, HY149764, HY229847
      UniProtKB/TrEMBL
      B4DMS2, E9PEL5
      Conserved Domains (3) summary
      cd11813
      Location:318 → 370
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      pfam00566
      Location:7 → 159
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam02759
      Location:397 → 548
      RUN; RUN domain

    12. NM_015705.6 → NP_056520.2  small G protein signaling modulator 3 isoform 1

      See identical proteins and their annotated locations for NP_056520.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AW512418, BC008078, BP283990, HY229847
      Consensus CDS
      CCDS14002.1
      UniProtKB/Swiss-Prot
      B0QY79, Q7Z709, Q96HU1, Q9NT69
      UniProtKB/TrEMBL
      B9A6J5
      Related
      ENSP00000248929.8, ENST00000248929.14
      Conserved Domains (3) summary
      cd11813
      Location:484 → 536
      SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
      smart00164
      Location:114 → 325
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam02759
      Location:563 → 714
      RUN; RUN domain

    RNA

    1. NR_146412.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL022238, AW512418, BC008078, BP283990, HY229847

    2. NR_146413.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL022238, AW512418, BC008078, BX424691, HY149764, HY229847

    3. NR_146414.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL022238, AW512418, BC008078, BX428466, DC386475, HY229847

    4. NR_146415.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL022238, AW512418, BC008078, BX428466, BX430401, HY149764, HY229847

    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
      40370594..40410289
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441336.1 → XP_047297292.1  small G protein signaling modulator 3 isoform X1

    2. XM_047441337.1 → XP_047297293.1  small G protein signaling modulator 3 isoform X2

    3. XM_047441338.1 → XP_047297294.1  small G protein signaling modulator 3 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      40842001..40880672
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325558.1 → XP_054181533.1  small G protein signaling modulator 3 isoform X1

    2. XM_054325559.1 → XP_054181534.1  small G protein signaling modulator 3 isoform X2

    3. XM_054325560.1 → XP_054181535.1  small G protein signaling modulator 3 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96HU1.1 GenPept UniProtKB/Swiss-Prot:Q96HU1

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