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

Gene ID: 10067, updated on 3-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 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)

Genotypes

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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