Aliases for CLPTM1 Gene

Aliases for CLPTM1 Gene

  • CLPTM1 Regulator Of GABA Type A Receptor Forward Trafficking 2 3 5
  • Cleft Lip And Palate Associated Transmembrane Protein 1 2 3
  • Cleft Lip And Palate Transmembrane Protein 1 3 4
  • CLPTM1, Transmembrane Protein 2 3
  • CLPTM1 5

External Ids for CLPTM1 Gene

Previous GeneCards Identifiers for CLPTM1 Gene

  • GC19P046103
  • GC19P045849
  • GC19P050134
  • GC19P050150
  • GC19P045458
  • GC19P041889

Summaries for CLPTM1 Gene

GeneCards Summary for CLPTM1 Gene

CLPTM1 (CLPTM1 Regulator Of GABA Type A Receptor Forward Trafficking) is a Protein Coding gene. Diseases associated with CLPTM1 include Cleft Lip and Cleft Lip/Palate-Ectodermal Dysplasia Syndrome. An important paralog of this gene is CLPTM1L.

UniProtKB/Swiss-Prot Summary for CLPTM1 Gene

Gene Wiki entry for CLPTM1 Gene

Additional gene information for CLPTM1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLPTM1 Gene

Genomics for CLPTM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLPTM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J044953 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 618.2 +1.1 1101 4.2 BRCA1 ARHGAP35 SP1 CREB1 PRDM10 ZNF629 LEF1 IKZF1 RFX5 POLR2A CLPTM1 ENSG00000267114 MN297597 APOC2 DMPK NECTIN2 lnc-ZNF296-5 RELB
GH19J044945 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 600.4 -8.6 -8635 1.8 HNRNPL GATAD2A REST TFE3 RBFOX2 RXRB SP1 GABPA CEBPA SOX13 APOC2 CLPTM1 ZNF180 ZNF234 ENSG00000269148 ZNF224 CLASRP ZNF155 FBXO46 NECTIN2
GH19J045005 Enhancer 1 Ensembl ENCODE 14.9 +52.7 52727 4.3 ZNF629 IKZF1 JUND MTA2 ZNF24 NR2C1 BRD9 DPF2 HDAC1 ATF7 APOC2 CLPTM1 CLASRP ENSG00000267114 RNU6-611P ZNF296 GEMIN7 PPP1R37 ZNF223 ZNF227
GH19J045000 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 6 +47.2 47171 2.5 SP1 CREB1 PRDM10 ZNF629 TFE3 KDM1A POLR2A RCOR2 ZNF174 BACH1 RELB ZNF225 ZNF180 ZNF234 ZNF224 ZNF284 ZNF227 APOC2 CCDC61 CLASRP
GH19J044939 Enhancer 0.8 Ensembl 10.2 -14.7 -14684 1.4 GATAD2A NFKBIZ RCOR2 RXRB SP1 CEBPA SOX13 CEBPB FOXA2 ATF3 L13714-240 APOC2 CLPTM1 APOC4 APOC1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLPTM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLPTM1

Top Transcription factor binding sites by QIAGEN in the CLPTM1 gene promoter:
  • AhR
  • Arnt
  • CBF(2)
  • GATA-1
  • NF-Y
  • Pax-5
  • RREB-1
  • Sox5
  • ZID

Genomic Locations for CLPTM1 Gene

Genomic Locations for CLPTM1 Gene
chr19:44,954,585-44,993,346
(GRCh38/hg38)
Size:
38,762 bases
Orientation:
Plus strand
chr19:45,457,842-45,496,604
(GRCh37/hg19)
Size:
38,763 bases
Orientation:
Plus strand

Genomic View for CLPTM1 Gene

Genes around CLPTM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLPTM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLPTM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLPTM1 Gene

Proteins for CLPTM1 Gene

  • Protein details for CLPTM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O96005-CLPT1_HUMAN
    Recommended name:
    Cleft lip and palate transmembrane protein 1
    Protein Accession:
    O96005
    Secondary Accessions:
    • B3KQH2
    • B4DDS3
    • B4E2X9
    • B7Z9X9
    • F5H8J3
    • Q53ET6
    • Q9BSS5

    Protein attributes for CLPTM1 Gene

    Size:
    669 amino acids
    Molecular mass:
    76097 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH04865.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=AAP35926.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Alternative splice isoforms for CLPTM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLPTM1 Gene

Post-translational modifications for CLPTM1 Gene

  • Glycosylation at Asn28, Asn119, Asn161, Asn241, Asn295, and Asn413
  • Ubiquitination at Lys209, Lys224, and Lys534
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • CLPT1_HUMAN (1116)

Antibody Products

  • Abcam antibodies for CLPTM1

No data available for DME Specific Peptides for CLPTM1 Gene

Domains & Families for CLPTM1 Gene

Gene Families for CLPTM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CLPTM1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLPTM1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59465, highly similar to Cleft lip and palate transmembrane protein 1 (B4DDS3_HUMAN)
  • Cleft lip and palate transmembrane protein 1 (CLPT1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O96005

UniProtKB/Swiss-Prot:

CLPT1_HUMAN :
  • Belongs to the CLPTM1 family.
Family:
  • Belongs to the CLPTM1 family.
genes like me logo Genes that share domains with CLPTM1: view

Function for CLPTM1 Gene

Molecular function for CLPTM1 Gene

UniProtKB/Swiss-Prot Function:
May play a role in T-cell development.
GENATLAS Biochemistry:
putative transmembrane protein,strongly homolog to C elegans R166.2,disrupted by a balanced translocation t(2;19)(q11.2;q13.3) in a family with cleft lip and palate

Phenotypes From GWAS Catalog for CLPTM1 Gene

Gene Ontology (GO) - Molecular Function for CLPTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21903422
genes like me logo Genes that share ontologies with CLPTM1: view
genes like me logo Genes that share phenotypes with CLPTM1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLPTM1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLPTM1 Gene

Localization for CLPTM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLPTM1 Gene

Membrane. Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLPTM1 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centriolar satellite (2)
  • Nuclear membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLPTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane TAS 9828125
GO:0009897 external side of plasma membrane ISS --
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CLPTM1: view

Pathways & Interactions for CLPTM1 Gene

PathCards logo

SuperPathways for CLPTM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CLPTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development TAS,IEA --
GO:0030154 cell differentiation IEA --
GO:0033081 regulation of T cell differentiation in thymus ISS --
genes like me logo Genes that share ontologies with CLPTM1: view

No data available for Pathways by source and SIGNOR curated interactions for CLPTM1 Gene

Drugs & Compounds for CLPTM1 Gene

No Compound Related Data Available

Transcripts for CLPTM1 Gene

mRNA/cDNA for CLPTM1 Gene

4 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLPTM1

Alternative Splicing Database (ASD) splice patterns (SP) for CLPTM1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b · 17c ·
SP1: - - - -
SP2: - - - - - - -
SP3: - -
SP4: - - -
SP5: - - - - - - - - - - - - - - - - - - -
SP6: -
SP7:
SP8: -
SP9:

ExUns: 17d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for CLPTM1 Gene

GeneLoc Exon Structure for
CLPTM1

Expression for CLPTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLPTM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLPTM1 Gene

This gene is overexpressed in Nasal epithelium (56.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLPTM1 Gene



Protein tissue co-expression partners for CLPTM1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLPTM1

SOURCE GeneReport for Unigene cluster for CLPTM1 Gene:

Hs.444441

mRNA Expression by UniProt/SwissProt for CLPTM1 Gene:

O96005-CLPT1_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for CLPTM1 Gene

  • Nervous system(4.9)
  • Kidney(4.5)
  • Liver(4.5)
  • Blood(4.3)
  • Skin(2.9)
  • Lung(2.5)
  • Muscle(2.4)
  • Intestine(2.3)
  • Stomach(2)
  • Heart(2)
genes like me logo Genes that share expression patterns with CLPTM1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLPTM1 Gene

Orthologs for CLPTM1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CLPTM1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CLPTM1 30 31
  • 99.6 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CLPTM1 30 31
  • 92.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CLPTM1 30 31
  • 91.58 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Clptm1 30 17 31
  • 88.81 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Clptm1 30
  • 88.15 (n)
Oppossum
(Monodelphis domestica)
Mammalia CLPTM1 31
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CLPTM1 31
  • 46 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CLPTM1 31
  • 76 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia clptm1 30
  • 71.82 (n)
Str.753 30
Zebrafish
(Danio rerio)
Actinopterygii clptm1 30 31
  • 74.51 (n)
OneToOne
sbcb102 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6632 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007926 30
  • 59.74 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG3702 30 31 32
  • 59.63 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea C36B7.6 30 31 32
  • 56.19 (n)
OneToMany
R166.2 31 32
  • 47 (a)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G23575 30
  • 51.96 (n)
Rice
(Oryza sativa)
Liliopsida Os04g0441900 30
  • 52.05 (n)
Os.18612 30
Barley
(Hordeum vulgare)
Liliopsida Hv.6282 30
Wheat
(Triticum aestivum)
Liliopsida Ta.770 30
Corn
(Zea mays)
Liliopsida Zm.3148 30
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3480 30
Species where no ortholog for CLPTM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for CLPTM1 Gene

ENSEMBL:
Gene Tree for CLPTM1 (if available)
TreeFam:
Gene Tree for CLPTM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLPTM1: view image

Paralogs for CLPTM1 Gene

Paralogs for CLPTM1 Gene

(1) SIMAP similar genes for CLPTM1 Gene using alignment to 7 proteins:

  • CLPT1_HUMAN
  • B4DDS3_HUMAN
  • F5H8J3_HUMAN
  • K7EJ16_HUMAN
  • K7EKQ7_HUMAN
  • K7EQQ1_HUMAN
  • K7ERL5_HUMAN
genes like me logo Genes that share paralogs with CLPTM1: view

Variants for CLPTM1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for CLPTM1 Gene

CLPT1_HUMAN-O96005
A chromosomal translocation involving CLPTM1 is found in a family with cleft lip and palate. However, no etiologic link with the disease is characterized. Translocation t(2;19)(q11.2;q13.3).

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLPTM1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
708251 Benign: not provided 44,974,474(+) T/C SYNONYMOUS_VARIANT
709303 Benign: not provided 44,962,025(+) G/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
714889 Benign: not provided 44,977,430(+) C/T MISSENSE_VARIANT
716505 Benign: not provided 44,990,546(+) C/T SYNONYMOUS_VARIANT
717488 Benign: not provided 44,991,276(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for CLPTM1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CLPTM1 Gene

Variant ID Type Subtype PubMed ID
dgv14e24 CNV loss 17666407
dgv224e215 CNV deletion 23714750
esv22789 CNV loss 19812545
esv2656681 CNV deletion 23128226
esv32608 CNV loss 17666407
esv3644495 CNV loss 21293372
esv3644496 CNV gain 21293372
nsv1071535 CNV deletion 25765185
nsv1117220 CNV tandem duplication 24896259
nsv579864 CNV loss 21841781
nsv579865 CNV loss 21841781
nsv828562 CNV gain 20364138

Variation tolerance for CLPTM1 Gene

Residual Variation Intolerance Score: 38% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.95; 36.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLPTM1 Gene

Human Gene Mutation Database (HGMD)
CLPTM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLPTM1

Disorders for CLPTM1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CLPTM1 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLPTM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CLPTM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLPTM1 Gene

Publications for CLPTM1 Gene

  1. 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. (PMID: 9828125) Yoshiura K … Murray JC (Genomics 1998) 2 3 4
  2. Clptm1 Limits Forward Trafficking of GABAA Receptors to Scale Inhibitory Synaptic Strength. (PMID: 29395912) Ge Y … Craig AM (Neuron 2018) 2 3
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  4. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 41
  5. MTHFR and MSX1 contribute to the risk of nonsyndromic cleft lip/palate. (PMID: 20572854) Jagomägi T … Metspalu A (European journal of oral sciences 2010) 3 41

Products for CLPTM1 Gene

  • Signalway Proteins for CLPTM1

Sources for CLPTM1 Gene