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    CLPTM1 CLPTM1 regulator of GABA type A receptor forward trafficking [ Homo sapiens (human) ]

    Gene ID: 1209, updated on 17-Jun-2019

    Summary

    Official Symbol
    CLPTM1provided by HGNC
    Official Full Name
    CLPTM1 regulator of GABA type A receptor forward traffickingprovided by HGNC
    Primary source
    HGNC:HGNC:2087
    See related
    Ensembl:ENSG00000104853 MIM:604783
    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
    Expression
    Ubiquitous expression in kidney (RPKM 40.5), brain (RPKM 32.5) and 25 other tissues See more
    Orthologs

    Genomic context

    See CLPTM1 in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (44954585..44993346)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (45457842..45496604)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene APOC4-APOC2 readthrough (NMD candidate) Neighboring gene apolipoprotein C4 Neighboring gene apolipoprotein C2 Neighboring gene RELB proto-oncogene, NF-kB subunit Neighboring gene CLK4 associating serine/arginine rich protein Neighboring gene RNA, U6 small nuclear 611, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of cleft lip and palate associated transmembrane protein 1 (CLPTM1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ14792

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of T cell differentiation in thymus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    external side of plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    membrane HDA PubMed 

    General protein information

    Preferred Names
    cleft lip and palate transmembrane protein 1
    Names
    CLPTM1, transmembrane protein
    cleft lip and palate associated transmembrane protein 1

    NCBI Reference Sequences (RefSeq)

    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_001282175.1NP_001269104.1  cleft lip and palate transmembrane protein 1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' terminal exon, and thus differs in the 5' UTR and 5' coding region, compared to variant 2. These differences cause translation initiation at an alternate AUG and result in an isoform (3) with a shorter and distinct N-terminus, compared to isoform 2.
      Source sequence(s)
      AK074935, AK304480, BC012359, BI916245, BM676309, BQ574654, DC313765
      Consensus CDS
      CCDS74394.1
      UniProtKB/Swiss-Prot
      O96005
      Related
      ENSP00000442011.1, ENST00000541297.6
      Conserved Domains (1) summary
      pfam05602
      Location:46482
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)
    2. NM_001282176.1NP_001269105.1  cleft lip and palate transmembrane protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001269105.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate 5' exon structure, and thus differs in the 5' UTR and 5' coding region, compared to variant 2. These differences cause translation initiation at a downstream AUG and result in an isoform (4) with a shorter N-terminus, compared to isoform 2.
      Source sequence(s)
      AK074935, AK316094, BC012359, BI916245, BM676309, BQ574654, DC383798
      Consensus CDS
      CCDS74395.1
      UniProtKB/Swiss-Prot
      O96005
      Related
      ENSP00000443192.1, ENST00000546079.5
      Conserved Domains (1) summary
      pfam05602
      Location:1394
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)
    3. NM_001294.4NP_001285.1  cleft lip and palate transmembrane protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001285.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AK074935, BC012359, BI916245, BM676309, BQ574654, DB033341
      Consensus CDS
      CCDS12651.1
      UniProtKB/Swiss-Prot
      O96005
      UniProtKB/TrEMBL
      A0A0S2Z3H2
      Related
      ENSP00000336994.4, ENST00000337392.10
      Conserved Domains (1) summary
      pfam05602
      Location:60496
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

      Range
      44954585..44993346
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001199468.1: Suppressed sequence

      Description
      NM_001199468.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript.
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