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

Gene ID: 1209, updated on 22-Sep-2022

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; 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 be involved in regulation of T cell differentiation in thymus. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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

See CLPTM1 in Genome Data Viewer
Location:
19q13.32
Exon count:
16
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (44954585..44993341)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (47779419..47818179)
105.20220307 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 apolipoprotein C2 Neighboring gene RELB proto-oncogene, NF-kB subunit Neighboring gene Sharpr-MPRA regulatory region 3318 Neighboring gene Sharpr-MPRA regulatory region 2438 Neighboring gene CLK4 associating serine/arginine rich protein

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 Functions

What's a GeneRIF?

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
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
 
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
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
PubMed 

General protein information

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_001282175.2NP_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/Swiss-Prot
    O96005
    Related
    ENSP00000442011.1, ENST00000541297.6
    Conserved Domains (1) summary
    pfam05602
    Location:43483
    CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)
  2. NM_001282176.2NP_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/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  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
    O96005, Q9BSS5
    UniProtKB/TrEMBL
    A0A0S2Z3H2
    Related
    ENSP00000336994.4, ENST00000337392.10
    Conserved Domains (1) summary
    pfam05602
    Location:57497
    CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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.