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    SCAMP4 secretory carrier membrane protein 4 [ Homo sapiens (human) ]

    Gene ID: 113178, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SCAMP4provided by HGNC
    Official Full Name
    secretory carrier membrane protein 4provided by HGNC
    Primary source
    HGNC:HGNC:30385
    See related
    Ensembl:ENSG00000227500 MIM:613764; AllianceGenome:HGNC:30385
    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
    SCAMP-4
    Summary
    Secretory carrier membrane proteins (SCAMPs) are widely distributed integral membrane proteins implicated in membrane trafficking. Most SCAMPs (e.g., SCAMP1; MIM 606911) have N-terminal cytoplasmic NPF (arg-pro-phe) repeats, 4 central transmembrane regions, and a short C-terminal cytoplasmic tail. These SCAMPs likely have a role in endocytosis that is mediated by their NPF repeats. Other SCAMPs, such as SCAMP4, lack the NPF repeats and are therefore unlikely to function in endocytosis (summary by Fernandez-Chacon and Sudhof, 2000 [PubMed 11050114]).[supplied by OMIM, Feb 2011]
    Expression
    Ubiquitous expression in prostate (RPKM 16.8), thyroid (RPKM 14.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SCAMP4 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1905399..1926013)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1876716..1897325)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1905398..1926012)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1853940-1854496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1854497-1855054 Neighboring gene Sharpr-MPRA regulatory region 8340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1861121-1862006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9749 Neighboring gene KLF16 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1865114-1865668 Neighboring gene KLF transcription factor 16 Neighboring gene KLF16-I enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1873541-1874256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1875445-1876145 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1876146-1876845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1876846-1877546 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1884760-1884907 Neighboring gene abhydrolase domain containing 17A, depalmitoylase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1887074-1887578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1887579-1888084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1897455-1898150 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1898955-1899127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13635 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1907977-1908788 Neighboring gene adenosine deaminase tRNA specific 3 Neighboring gene Sharpr-MPRA regulatory region 4132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13636 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1938387-1938587 Neighboring gene uncharacterized LOC105372238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1946998-1947718 Neighboring gene casein kinase 1 gamma 2 Neighboring gene CSNK1G2 antisense RNA 1

    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. SCAMP4 enhances the senescent cell secretome. Kim KM, et al. Genes Dev, 2018 Jul 1. PMID 29967290, Free PMC Article
    2. Expression of the SCAMP-4 gene, a new member of the secretory carrier membrane protein family, is repressed by progesterone in brain regions associated with female sexual behavior. Krebs CJ, et al. Brain Res Mol Brain Res, 2001 Mar 31. PMID 11295240
    3. Ubiquitously expressed secretory carrier membrane proteins (SCAMPs) 1-4 mark different pathways and exhibit limited constitutive trafficking to and from the cell surface. Castle A, et al. J Cell Sci, 2005 Aug 15. PMID 16105885
    4. Novel SCAMPs lacking NPF repeats: ubiquitous and synaptic vesicle-specific forms implicate SCAMPs in multiple membrane-trafficking functions. Fernández-Chacón R, et al. J Neurosci, 2000 Nov 1. PMID 11050114, Free PMC Article
    5. High-resolution photocatalytic mapping of SARS-CoV-2 spike interactions on the cell surface. Datta S, et al. Cell Chem Biol, 2023 Oct 19. PMID 37499664

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. secretory carrier membrane protein 4 (SCAMP4) levels were strikingly elevated on the surface of senescent cells compared with proliferating cells
      Title: SCAMP4 enhances the senescent cell secretome.
    2. 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.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ33847, FLJ90105

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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 4

    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_001329539.2 → NP_001316468.1  secretory carrier-associated membrane protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream translation start site compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AC012615, AK074586, AK307641, BC062598, CA417608
      UniProtKB/Swiss-Prot
      Q969E2
      Conserved Domains (1) summary
      pfam04144
      Location:1 → 134
      SCAMP; SCAMP family

    2. NM_001329540.2 → NP_001316469.1  secretory carrier-associated membrane protein 4 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC012615, AK092056, BC062598, CA417608
      Consensus CDS
      CCDS86689.1
      UniProtKB/Swiss-Prot
      Q969E2
      Related
      ENSP00000386865.1, ENST00000409472.6
      Conserved Domains (1) summary
      pfam04144
      Location:5 → 145
      SCAMP; SCAMP family

    3. NM_079834.4 → NP_524558.1  secretory carrier-associated membrane protein 4 isoform 1

      See identical proteins and their annotated locations for NP_524558.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK074586, AL832731, BC062598, CA417608
      Consensus CDS
      CCDS45903.1
      UniProtKB/Swiss-Prot
      Q8N2N1, Q8NAV0, Q969E2
      Related
      ENSP00000316007.7, ENST00000316097.13
      Conserved Domains (1) summary
      pfam04144
      Location:5 → 178
      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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      1905399..1926013
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      1876716..1897325
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969E2.1 GenPept UniProtKB/Swiss-Prot:Q969E2

    Gene LinkOut

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

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