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    CLPTM1L CLPTM1 like [ Homo sapiens (human) ]

    Gene ID: 81037, updated on 3-Apr-2024

    Summary

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    Official Symbol
    CLPTM1Lprovided by HGNC
    Official Full Name
    CLPTM1 likeprovided by HGNC
    Primary source
    HGNC:HGNC:24308
    See related
    Ensembl:ENSG00000049656 MIM:612585; AllianceGenome:HGNC:24308
    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
    CRR9
    Summary
    The protein encoded by this gene is a membrane protein whose overexpression in cisplatin-sensitive cells causes apoptosis. Polymorphisms in this gene have been reported to increase susceptibility to several cancers, including lung, pancreatic, and breast cancers. [provided by RefSeq, Nov 2015]
    Expression
    Ubiquitous expression in testis (RPKM 35.1), thyroid (RPKM 34.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    5p15.33
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (1317752..1345099, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (1225592..1255482, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (1317867..1345214, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1264322-1264939 Neighboring gene telomerase reverse transcriptase Neighboring gene Sharpr-MPRA regulatory region 13256 Neighboring gene TERT enhancer in intron 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1290609-1291360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1291361-1292111 Neighboring gene TERT 5' regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22307 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1320136 Neighboring gene microRNA 4457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1325297-1325797 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:1327650-1328264 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:1328265-1328877 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1330840 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1341101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1357815-1358370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1358371-1358926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1358927-1359482 Neighboring gene long intergenic non-protein coding RNA 1511 Neighboring gene MT-CO2 pseudogene 32 Neighboring gene Sharpr-MPRA regulatory region 8068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1386240-1386808 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:1404958-1406157 Neighboring gene solute carrier family 6 member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1412675-1413175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1414882-1415854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1415855-1416827 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1422785-1423310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1438947-1439628

    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. CLPTM1L is a GPI-anchoring pathway component targeted by HCMV. Kol I, et al. J Cell Biol, 2023 Sep 4. PMID 37389656, Free PMC Article
    2. Genome-wide CRISPR screen reveals CLPTM1L as a lipid scramblase required for efficient glycosylphosphatidylinositol biosynthesis. Wang Y, et al. Proc Natl Acad Sci U S A, 2022 Apr 5. PMID 35344438, Free PMC Article
    3. CLPTM1L induces estrogen receptor β signaling-mediated radioresistance in non-small cell lung cancer cells. Li H, et al. Cell Commun Signal, 2020 Sep 17. PMID 32943060, Free PMC Article
    4. Prognostic significance of CLPTM1L expression and its effects on migration and invasion of human lung cancer cells. Ni Z, et al. Cancer Biomark, 2016. PMID 27062701
    5. CLPTM1L polymorphism and lung cancer risk. Tang M, et al. Int J Clin Exp Med, 2015. PMID 26064290, Free PMC Article

    See all (139) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exploring the Relationship between CLPTM1L-MS2 Variants and Susceptibility to Bladder Cancer.
      Title: Exploring the Relationship between CLPTM1L-MS2 Variants and Susceptibility to Bladder Cancer.
    2. CLPTM1L is a GPI-anchoring pathway component targeted by HCMV.
      Title: CLPTM1L is a GPI-anchoring pathway component targeted by HCMV.
    3. Functional characterization of 5p15.33 risk locus in uveal melanoma reveals rs452384 as a functional variant and NKX2.4 as an allele-specific interactor.
      Title: Functional characterization of 5p15.33 risk locus in uveal melanoma reveals rs452384 as a functional variant and NKX2.4 as an allele-specific interactor.
    4. CLPTM1L induces estrogen receptor beta signaling-mediated radioresistance in non-small cell lung cancer cells.
      Title: CLPTM1L induces estrogen receptor β signaling-mediated radioresistance in non-small cell lung cancer cells.
    5. Genetic variation in cervical preinvasive and invasive disease: a genome-wide association study.
      Title: Genetic variation in cervical preinvasive and invasive disease: a genome-wide association study.
    6. Both TERT-rs33963617 and CLPTM1L-rs77518573 conferred reduced risk for Non small cell lung cancer in Chinese Han population.
      Title: TERT-rs33963617 and CLPTM1L-rs77518573 reduce the risk of non-small cell lung cancer in Chinese population.
    7. rs2736100 in CLPTM1L is associated with the risk of pharynx-larynx cancer.
      Title: Polymorphisms of the TERT-CLPTM1L Gene Are Associated with Pharynx-Larynx Cancer.
    8. Study in human pancreatic ductal adenocarcinoma cells revealed surface relocalization and survival signaling by CLPTM1L triggered by endoplasmic reticulum (ER) stress and demonstrated interaction of CLPTM1L with GRP78. Both chemoresistance and GRP78 interaction were dependent on the extracellular loop of CLPTM1L.
      Title: CLPTM1L/CRR9 ectodomain interaction with GRP78 at the cell surface signals for survival and chemoresistance upon ER stress in pancreatic adenocarcinoma cells.
    9. rs401681 and rs402710 single nucleotide polymorphism of CLPTM1L might be the causal SNPs for lung cancer in East Asian
      Title: rs401681 and rs402710 confer lung cancer susceptibility by regulating TERT expression instead of CLPTM1L in East Asian populations.
    10. using multivariate logistic regression, we observed that haplotype CLPTM1L is significantly associated with poor treatment response
      Title: Association of TERT-CLPTM1L and 8q24 Common Genetic Variants with Gallbladder Cancer Susceptibility and Prognosis in North Indian Population.
    Submit: New GeneRIF Correction See all GeneRIFs (73)

    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
    A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia.
    EBI GWAS Catalog
    A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33.
    EBI GWAS Catalog
    A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma.
    EBI GWAS Catalog
    A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.
    EBI GWAS Catalog
    Common 5p15.33 and 6p21.33 variants influence lung cancer risk.
    EBI GWAS Catalog
    Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study.
    EBI GWAS Catalog
    Genetic correction of PSA values using sequence variants associated with PSA levels.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with bladder cancer risk.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    EBI GWAS Catalog
    Genome-wide association study identifies three new melanoma susceptibility loci.
    EBI GWAS Catalog
    Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.
    EBI GWAS Catalog
    Identification of nine new susceptibility loci for testicular cancer, including variants near DAZL and PRDM14.
    EBI GWAS Catalog
    Lung cancer susceptibility locus at 5p15.33.
    EBI GWAS Catalog
    Sequence variants at the TERT-CLPTM1L locus associate with many cancer types.
    EBI GWAS Catalog
    The 5p15.33 locus is associated with risk of lung adenocarcinoma in never-smoking females in Asia.
    EBI GWAS Catalog
    Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14400, FLJ32533, DKFZp666M1010, DKFZp761M2324

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phospholipid scramblase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in plasma membrane phospholipid scrambling IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endomembrane system IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    lipid scramblase CLPTM1L
    Names
    CLPTM1-like protein
    cisplatin resistance related protein CRR9p
    cisplatin resistance-related protein 9
    cleft lip and palate transmembrane protein 1-like protein

    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.

    Genomic

    1. NG_046903.1 RefSeqGene

      Range
      4967..32314
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_030782.5 → NP_110409.2  lipid scramblase CLPTM1L

      See identical proteins and their annotated locations for NP_110409.2

      Status: REVIEWED

      Source sequence(s)
      AC026748, AC114291, BC025305, BQ019182, CD109529
      Consensus CDS
      CCDS3862.1
      UniProtKB/Swiss-Prot
      D3DTC1, Q658W6, Q7LG29, Q96AZ0, Q96KA5, Q9H3N4
      Related
      ENSP00000313854.5, ENST00000320895.10
      Conserved Domains (1) summary
      pfam05602
      Location:22 → 421
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      1317752..1345099 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514144.3 → XP_011512446.1  lipid scramblase CLPTM1L isoform X1

      Conserved Domains (1) summary
      pfam05602
      Location:22 → 420
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

    2. XM_024446222.2 → XP_024301990.1  lipid scramblase CLPTM1L isoform X2

      UniProtKB/TrEMBL
      G5E9Z2
      Related
      ENSP00000423321.1, ENST00000507807.3
      Conserved Domains (1) summary
      pfam05602
      Location:1 → 243
      CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187547.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      168910..195710
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      1225592..1255482 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353568.1 → XP_054209543.1  lipid scramblase CLPTM1L isoform X1

    2. XM_054353569.1 → XP_054209544.1  lipid scramblase CLPTM1L isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96KA5.1 GenPept UniProtKB/Swiss-Prot:Q96KA5

    Gene LinkOut

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

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