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

    Gene ID: 1209, updated on 10-Dec-2024

    Summary

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    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; AllianceGenome:HGNC:2087
    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
    Summary
    Predicted to enable GABA receptor binding activity. Predicted to be involved in regulation of T cell differentiation in thymus and regulation of postsynaptic membrane neurotransmitter receptor levels. Located in membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 40.5), brain (RPKM 32.5) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See CLPTM1 in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (44954585..44993341)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (47779419..47818179)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (45457842..45496599)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene APOC4-APOC2 readthrough (NMD candidate) Neighboring gene apolipoprotein C4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10745 Neighboring gene apolipoprotein C2 Neighboring gene MPRA-validated peak3513 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14775 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:45464990-45465143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10747 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10748 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:45514891-45515392 Neighboring gene RELB proto-oncogene, NF-kB subunit Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10749 Neighboring gene Sharpr-MPRA regulatory region 3318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45541977-45542846 Neighboring gene Sharpr-MPRA regulatory region 2438 Neighboring gene CLK4 associating serine/arginine rich protein Neighboring gene RNA, U6 small nuclear 611, pseudogene

    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. De novo CLPTM1 variants with reduced GABA(A) R current response in patients with epilepsy. Liu N, et al. Epilepsia, 2023 Nov. PMID 37577761, Free PMC Article
    2. Long telomere length and a TERT-CLPTM1 locus polymorphism association with melanoma risk. Llorca-Cardeñosa MJ, et al. Eur J Cancer, 2014 Dec. PMID 25457634
    3. Pathobiological role of cleft palate transmembrane protein 1 family proteins in oral squamous cell carcinoma. Inoue K, et al. J Cancer Res Clin Oncol, 2019 Apr. PMID 30635792
    4. Assessing a single SNP located at TERT/CLPTM1L multi-cancer risk region as a genetic modifier for risk of pancreatic cancer and melanoma in Dutch CDKN2A mutation carriers. Christodoulou E, et al. Fam Cancer, 2019 Oct. PMID 31203567, Free PMC Article
    5. Mutation analysis of CLPTM 1 and PVRL 1 genes in patients with non-syndromic clefts of lip, alveolus and palate. Turhani D, et al. J Craniomaxillofac Surg, 2005 Oct. PMID 16122939

    See all (91) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. De novo CLPTM1 variants with reduced GABAA R current response in patients with epilepsy.
      Title: De novo CLPTM1 variants with reduced GABA(A) R current response in patients with epilepsy.
    2. Authors detected three genome-wide statistically significant single nucleotide polymorphisms mapped to Chromosome 5 CLPTM1L-TERT region.
      Title: Lung Cancer Risk in Never-Smokers of European Descent is Associated With Genetic Variation in the 5(p)15.33 TERT-CLPTM1Ll Region.
    3. a single SNP located at TERT/CLPTM1L multi-cancer risk region as a genetic modifier for risk of pancreatic cancer and melanoma in Dutch CDKN2A mutation carriers
      Title: Assessing a single SNP located at TERT/CLPTM1L multi-cancer risk region as a genetic modifier for risk of pancreatic cancer and melanoma in Dutch CDKN2A mutation carriers.
    4. Non-tumorous oral squamous cells exhibited vague, weak, or little cytoplasmic staining with anti-Clptm1 and CRR9 antibodies. By contrast, robust Clptm1 and CRR9 immunoreactivity was found at the cancer invasion front in 55 and 54 of the 98 OSCC tissue specimens, respectively.
      Title: Pathobiological role of cleft palate transmembrane protein 1 family proteins in oral squamous cell carcinoma.
    5. that the rs401681 polymorphism in the TERT-CLPTM1L locus contributes to lung carcinogenesis only in patients harboring an EGFR mutation
      Title: A TERT-CLPTM1 locus polymorphism (rs401681) is associated with EGFR mutation in non-small cell lung cancer.
    6. Results suggest that single nucleotide polymorphism in CLPTM1 influences telomere length and so increases risk of melanoma.
      Title: Long telomere length and a TERT-CLPTM1 locus polymorphism association with melanoma risk.
    7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in COL2A1, COL11A2, and IRF6 contribute risk to nonsyndromic cleft palate.
    9. Identification of inactivating mutations in the JAK1, SYNJ2, and CLPTM1 genes in prostate cancer cells
      Title: Identification of inactivating mutations in the JAK1, SYNJ2, and CLPTM1 genes in prostate cancer cells using inhibition of nonsense-mediated decay and microarray analysis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14792

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GABA receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of T cell differentiation in thymus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endomembrane system IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in external side of plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    putative lipid scramblase CLPTM1
    Names
    CLPTM1, transmembrane protein
    cleft lip and palate associated transmembrane protein 1
    cleft lip and palate transmembrane protein 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_001282175.2 → NP_001269104.1  putative lipid scramblase CLPTM1 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/TrEMBL
      A0A0S2Z3H6
      Related
      ENSP00000442011.1, ENST00000541297.6
      Conserved Domains (1) summary
      pfam05602
      Location:43 → 483
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

    2. NM_001282176.2 → NP_001269105.1  putative lipid scramblase CLPTM1 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/TrEMBL
      A0A0S2Z3H6
      Related
      ENSP00000443192.1, ENST00000546079.5
      Conserved Domains (1) summary
      pfam05602
      Location:1 → 394
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

    3. NM_001294.4 → NP_001285.1  putative lipid scramblase CLPTM1 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
      B3KQH2, B4DDS3, B4E2X9, B7Z9X9, F5H8J3, O96005, Q53ET6, Q9BSS5
      UniProtKB/TrEMBL
      A0A0S2Z3H2, A0A0S2Z3H6
      Related
      ENSP00000336994.4, ENST00000337392.10
      Conserved Domains (1) summary
      pfam05602
      Location:57 → 497
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

    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
      44954585..44993341
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      47779419..47818179
      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.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O96005.1 GenPept UniProtKB/Swiss-Prot:O96005

    Gene LinkOut

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

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