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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
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Genomic context

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See CLPTM1L in Genome Data Viewer
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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