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    SCAMP3 secretory carrier membrane protein 3 [ Homo sapiens (human) ]

    Gene ID: 10067, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SCAMP3provided by HGNC
    Official Full Name
    secretory carrier membrane protein 3provided by HGNC
    Primary source
    HGNC:HGNC:10565
    See related
    Ensembl:ENSG00000116521 MIM:606913; AllianceGenome:HGNC:10565
    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
    C1orf3
    Summary
    This gene encodes an integral membrane protein that belongs to the secretory carrier membrane protein family. The encoded protein functions as a carrier to the cell surface in post-golgi recycling pathways. This protein is also involved in protein trafficking in endosomal pathways. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 20.0), placenta (RPKM 19.2) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SCAMP3 in Genome Data Viewer
    Location:
    1q22
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (155255981..155262360, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (154394539..154400920, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (155225772..155232151, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene GBA recombination region Neighboring gene glucosylceramidase beta 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:155213585-155214548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:155219706-155220308 Neighboring gene endosomal transmembrane epsin interactor 3 Neighboring gene CDC like kinase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:155243888-155244388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:155254443-155254943 Neighboring gene hyperpolarization activated cyclic nucleotide gated potassium channel 3 Neighboring gene pyruvate kinase L/R

    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. SCAMP 3 is a novel regulator of endosomal morphology and composition. Thomas P, et al. Biochem Biophys Res Commun, 2016 Sep 23. PMID 27507217
    2. Regulation of the MVB pathway by SCAMP3. Falguières T, et al. Traffic, 2012 Jan. PMID 21951651
    3. SCAMP3 is a component of the Salmonella-induced tubular network and reveals an interaction between bacterial effectors and post-Golgi trafficking. Mota LJ, et al. Cell Microbiol, 2009 Aug. PMID 19438519, Free PMC Article
    4. Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation. Naboulsi W, et al. Biochim Biophys Acta, 2016 Nov. PMID 27519163
    5. Secretory Carrier Membrane Protein 3 Interacts with 3A Viral Protein of Enterovirus and Participates in Viral Replication. Lu JY, et al. Microbiol Spectr, 2021 Sep 3. PMID 34378951, Free PMC Article

    See all (116) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Secretory Carrier Membrane Protein 3 Interacts with 3A Viral Protein of Enterovirus and Participates in Viral Replication.
      Title: Secretory Carrier Membrane Protein 3 Interacts with 3A Viral Protein of Enterovirus and Participates in Viral Replication.
    2. MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis.
      Title: MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis.
    3. The novel association of several endocytosis-associated proteins has been demonstrated, in particular, of CLTC and SCAMP3 with hepatocellular carcinoma progression.
      Title: Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation.
    4. SCAMP 3 is a novel regulator of endosomal morphology and composition.
      Title: SCAMP 3 is a novel regulator of endosomal morphology and composition.
    5. SCAMP3 has a positive role in sorting into and budding of intralumenal vesicles and thereby controls the process of multivesicular endosome biogenesis.
      Title: Regulation of the MVB pathway by SCAMP3.
    6. SCAMP3 tubules reflect a manipulation of specific post-Golgi trafficking that might allow Salmonella to acquire nutrients and membrane, or to control host immune responses.
      Title: SCAMP3 is a component of the Salmonella-induced tubular network and reveals an interaction between bacterial effectors and post-Golgi trafficking.
    7. Depletion of SCAMP3 in HeLa cells by inhibitory RNA accelerated degradation of epidermal growth factor receptor (EGFR) and EGF while inhibiting recycling
      Title: SCAMP3 negatively regulates epidermal growth factor receptor degradation and promotes receptor recycling.
    8. the SCAMPs may largely function at the same sites during vesicular transport rather than in separate post-Golgi recycling pathways.
      Title: Three mammalian SCAMPs (secretory carrier membrane proteins) are highly related products of distinct genes having similar subcellular distributions.
    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 meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of secretory carrier membrane protein 3 (SCAMP3) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with secretory carrier membrane protein 3 (SCAMP3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in post-Golgi vesicle-mediated transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in recycling endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in trans-Golgi network membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    secretory carrier-associated membrane protein 3
    Names
    propin 1

    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_005698.4 → NP_005689.2  secretory carrier-associated membrane protein 3 isoform 1

      See identical proteins and their annotated locations for NP_005689.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL713999, BC000161, BU193466
      Consensus CDS
      CCDS1105.1
      UniProtKB/Swiss-Prot
      A9Z1W6, B1AVS6, O14828, O15128, Q96FR8, Q9BPY0
      UniProtKB/TrEMBL
      Q6FHJ5
      Related
      ENSP00000307275.3, ENST00000302631.8
      Conserved Domains (1) summary
      pfam04144
      Location:132 → 307
      SCAMP; SCAMP family

    2. NM_052837.3 → NP_443069.1  secretory carrier-associated membrane protein 3 isoform 2

      See identical proteins and their annotated locations for NP_443069.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BC010505, BM790077, BU193466
      Consensus CDS
      CCDS1106.1
      UniProtKB/TrEMBL
      Q6FHJ5
      Related
      ENSP00000347540.3, ENST00000355379.3
      Conserved Domains (1) summary
      pfam04144
      Location:106 → 281
      SCAMP; SCAMP family

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      155255981..155262360 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418254.1 → XP_047274210.1  secretory carrier-associated membrane protein 3 isoform X4

    2. XM_047418240.1 → XP_047274196.1  secretory carrier-associated membrane protein 3 isoform X3

      UniProtKB/TrEMBL
      A0AAQ5BHR7
      Related
      ENSP00000519502.1, ENST00000714219.1

    3. XM_047418222.1 → XP_047274178.1  secretory carrier-associated membrane protein 3 isoform X2

      UniProtKB/TrEMBL
      A0AAQ5BHP8
      Related
      ENSP00000519503.1, ENST00000714220.1

    4. XM_047418195.1 → XP_047274151.1  secretory carrier-associated membrane protein 3 isoform X1

      UniProtKB/TrEMBL
      A0AAQ5BHS3
      Related
      ENSP00000519499.1, ENST00000714216.1

    5. XM_047418271.1 → XP_047274227.1  secretory carrier-associated membrane protein 3 isoform X5

      UniProtKB/TrEMBL
      A0AAQ5BHM9
      Related
      ENSP00000519482.1, ENST00000478737.6

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315906.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      61004..67383 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329466.1 → XP_054185441.1  secretory carrier-associated membrane protein 3 isoform X4

    2. XM_054329465.1 → XP_054185440.1  secretory carrier-associated membrane protein 3 isoform X3

      UniProtKB/TrEMBL
      A0AAQ5BHR7

    3. XM_054329464.1 → XP_054185439.1  secretory carrier-associated membrane protein 3 isoform X2

      UniProtKB/TrEMBL
      A0AAQ5BHP8

    4. XM_054329463.1 → XP_054185438.1  secretory carrier-associated membrane protein 3 isoform X1

      UniProtKB/TrEMBL
      A0AAQ5BHS3

    5. XM_054329467.1 → XP_054185442.1  secretory carrier-associated membrane protein 3 isoform X5

      UniProtKB/TrEMBL
      A0AAQ5BHM9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      154394539..154400920 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333705.1 → XP_054189680.1  secretory carrier-associated membrane protein 3 isoform X4

    2. XM_054333704.1 → XP_054189679.1  secretory carrier-associated membrane protein 3 isoform X3

      UniProtKB/TrEMBL
      A0AAQ5BHR7

    3. XM_054333703.1 → XP_054189678.1  secretory carrier-associated membrane protein 3 isoform X2

      UniProtKB/TrEMBL
      A0AAQ5BHP8

    4. XM_054333702.1 → XP_054189677.1  secretory carrier-associated membrane protein 3 isoform X1

      UniProtKB/TrEMBL
      A0AAQ5BHS3

    5. XM_054333706.1 → XP_054189681.1  secretory carrier-associated membrane protein 3 isoform X5

      UniProtKB/TrEMBL
      A0AAQ5BHM9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14828.3 GenPept UniProtKB/Swiss-Prot:O14828

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