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Clptm1 cleft lip and palate associated transmembrane protein 1 [ Mus musculus (house mouse) ]

Gene ID: 56457, updated on 14-Nov-2024

Summary

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Official Symbol
Clptm1provided by MGI
Official Full Name
cleft lip and palate associated transmembrane protein 1provided by MGI
Primary source
MGI:MGI:1927155
See related
Ensembl:ENSMUSG00000002981 AllianceGenome:MGI:1927155
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
HS9; N14
Summary
Enables GABA receptor binding activity. Involved in regulation of T cell differentiation in thymus. Located in external side of plasma membrane. Is expressed in lymph node; spleen white pulp; thymus cortex; thymus primordium; and thymus thin fibrous capsule. Orthologous to human CLPTM1 (CLPTM1 regulator of GABA type A receptor forward trafficking). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in adrenal adult (RPKM 72.9), colon adult (RPKM 61.5) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Clptm1 in Genome Data Viewer
Location:
7 A3; 7 9.93 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (19365505..19398955, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (19631580..19665030, complement)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene CLK4-associating serine/arginine rich protein Neighboring gene avian reticuloendotheliosis viral (v-rel) oncogene related B Neighboring gene STARR-positive B cell enhancer ABC_E1720 Neighboring gene STARR-positive B cell enhancer ABC_E4901 Neighboring gene apolipoprotein C2 like Neighboring gene apolipoprotein C2 Neighboring gene apolipoprotein C-IV

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Structure and promoter region of the surface membrane protein HS9 gene expressed on the thymic epithelial cells. Miyazawa H, et al. Biochim Biophys Acta, 1999 Mar 19. PMID 10095063
  2. Haploinsufficiency of GABA(A) Receptor-Associated Clptm1 Enhances Phasic and Tonic Inhibitory Neurotransmission, Suppresses Excitatory Synaptic Plasticity, and Impairs Memory. Ge Y, et al. J Neurosci, 2024 Aug 7. PMID 38942471,
  3. Characterization of a 50 kDa surface membrane protein on thymic stromal cells as an important factor for early T cell development. Takeuchi T, et al. Int Immunol, 1995 Apr. PMID 7547685
  4. Characterization of a novel gene disrupted by a balanced chromosomal translocation t(2;19)(q11.2;q13.3) in a family with cleft lip and palate. Yoshiura K, et al. Genomics, 1998 Dec 1. PMID 9828125
  5. Clptm1 Limits Forward Trafficking of GABA(A) Receptors to Scale Inhibitory Synaptic Strength. Ge Y, et al. Neuron, 2018 Feb 7. PMID 29395912, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Targeted (1)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables GABA receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of T cell differentiation in thymus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in GABA-ergic synapse ISO
Inferred from Sequence Orthology
more info
  
is_active_in endomembrane system IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
putative lipid scramblase CLPTM1
Names
cleft lip and palate transmembrane protein 1 homolog
thymic epithelial cell surface antigen

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_019649.2 → NP_062623.2  putative lipid scramblase CLPTM1

    See identical proteins and their annotated locations for NP_062623.2

    Status: VALIDATED

    Source sequence(s)
    AI844337, AK152410, AK165742, BY288640
    Consensus CDS
    CCDS39800.1
    UniProtKB/Swiss-Prot
    O08708, Q3U758, Q3U823, Q3UG77, Q8VBZ3, Q8VEJ6
    Related
    ENSMUSP00000051293.10, ENSMUST00000055242.11
    Conserved Domains (1) summary
    pfam05602
    Location:60 → 496
    CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    19365505..19398955 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006540227.1 → XP_006540290.1  putative lipid scramblase CLPTM1 isoform X1

    Conserved Domains (1) summary
    pfam05602
    Location:1 → 395
    CLPTM1; Cleft lip and palate transmembrane protein 1 (CLPTM1)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8VBZ3.1 GenPept UniProtKB/Swiss-Prot:Q8VBZ3

Gene LinkOut

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

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