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

Gene ID: 1209, updated on 3-Nov-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, Nov 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 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. 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
  2. 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
  3. 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
  4. Lung Cancer Risk in Never-Smokers of European Descent is Associated With Genetic Variation in the 5(p)15.33 TERT-CLPTM1Ll Region. Hung RJ, et al. J Thorac Oncol, 2019 Aug. PMID 31009812, 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 (90) 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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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
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)

Genotypes

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
  
Component Evidence Code Pubs
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

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Chemical Information
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