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Aliases for CLPTM1 Gene

Aliases for CLPTM1 Gene

  • CLPTM1, Transmembrane Protein 2 3 5
  • Cleft Lip And Palate Associated Transmembrane Protein 1 2 3
  • Cleft Lip And Palate Transmembrane Protein 1 3

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, Transmembrane Protein) is a Protein Coding gene. Diseases associated with CLPTM1 include Cleft Lip and Orofacial Cleft. An important paralog of this gene is CLPTM1L.

UniProtKB/Swiss-Prot for CLPTM1 Gene

  • May play a role in T-cell development.

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 , fRNAdb sequence ontologies and piRNA Summary for CLPTM1 Gene

Genomics for CLPTM1 Gene

GeneHancer (GH) Regulatory Elements for CLPTM1 Gene

Promoters and enhancers for CLPTM1 Gene
GeneHancer (GH) Identifier GH Type GH
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 2.1 EPDnew Ensembl ENCODE 668.2 +0.7 696 3.4 HDGF PKNOX1 SMAD1 ARNT ARID4B NEUROD1 SIN3A FEZF1 DMAP1 ZNF2 CLPTM1 ENSG00000267114 APOC2 GC19M044995
GH19J044945 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 650.4 -8.6 -8635 1.8 ELF3 FOXA2 ARID4B DMAP1 THRB ZSCAN9 RAD21 RARA YY1 EGR1 APOC2 CLPTM1 APOC4-APOC2 APOC4
GH19J045005 Enhancer 0.9 ENCODE 14.9 +52.7 52727 4.3 HDAC1 ARNT GLI4 EGR1 ATF7 CREM SMARCA5 CEBPB USF2 ZEB2 APOC2 CLPTM1 CLASRP ENSG00000267114 RNU6-611P GEMIN7 ZNF296 PPP1R37 ZNF223 ZNF227
GH19J045000 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 6 +47.2 47171 2.5 HDGF ARID4B SIN3A IRF4 ZNF207 ZNF143 ZNF548 KLF13 SP3 SP5 RELB ZNF225 ZNF180 ZNF234 ZNF224 ZNF284 ZNF227 APOC2 CCDC61 CLASRP
GH19J044960 Enhancer 0.5 ENCODE 0.4 +6.8 6827 1.4 IKZF1 EBF1 DPF2 IKZF2 SPI1 APOC2 RELB GEMIN7 ZNF296 PPP1R37 RNU6-611P APOE CLPTM1 GC19M044995
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for CLPTM1 Gene

Genomic Locations for CLPTM1 Gene
38,762 bases
Plus strand
38,763 bases
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:
    Recommended name:
    Cleft lip and palate transmembrane protein 1
    Protein Accession:
    Secondary Accessions:
    • B3KQH2
    • B4DDS3
    • B4E2X9
    • B7Z9X9
    • F5H8J3
    • Q53ET6
    • Q9BSS5

    Protein attributes for CLPTM1 Gene

    669 amino acids
    Molecular mass:
    76097 Da
    Quaternary structure:
    No Data Available
    • 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


neXtProt entry for CLPTM1 Gene

Post-translational modifications for CLPTM1 Gene

  • Glycosylation at posLast=413413, Asn295, Asn241, Asn161, Asn119, and Asn28
  • Ubiquitination at Lys534, posLast=224224, and Lys209
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for CLPTM1
  • Boster Bio 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


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the CLPTM1 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

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
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubule organizing center (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

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

Unigene Clusters for CLPTM1 Gene

Cleft lip and palate associated transmembrane protein 1:
Representative Sequences:

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: -
SP8: -

ExUns: 17d

Relevant External Links for CLPTM1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLPTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of CLPTM1 Gene:


SOURCE GeneReport for Unigene cluster for CLPTM1 Gene:


mRNA Expression by UniProt/SwissProt for CLPTM1 Gene:

Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for CLPTM1 Gene

  • Nervous system(4.9)
  • Kidney(4.5)
  • Liver(4.4)
  • Blood(4.1)
  • Lung(2.4)
  • Muscle(2.4)
  • Skin(2.3)
  • Heart(2)
  • Stomach(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
(Pan troglodytes)
Mammalia CLPTM1 34 33
  • 99.6 (n)
(Bos Taurus)
Mammalia CLPTM1 34 33
  • 92.63 (n)
(Canis familiaris)
Mammalia CLPTM1 34 33
  • 91.58 (n)
(Mus musculus)
Mammalia Clptm1 16 34 33
  • 88.81 (n)
(Rattus norvegicus)
Mammalia Clptm1 33
  • 88.15 (n)
(Monodelphis domestica)
Mammalia CLPTM1 34
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia CLPTM1 34
  • 46 (a)
(Anolis carolinensis)
Reptilia CLPTM1 34
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clptm1 33
  • 71.82 (n)
Str.753 33
(Danio rerio)
Actinopterygii clptm1 34 33
  • 74.51 (n)
sbcb102 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6632 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007926 33
  • 59.74 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3702 34 35 33
  • 59.63 (n)
(Caenorhabditis elegans)
Secernentea C36B7.6 34 35 33
  • 56.19 (n)
R166.2 34 35
  • 47 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G23575 33
  • 51.96 (n)
(Oryza sativa)
Liliopsida Os04g0441900 33
  • 52.05 (n)
Os.18612 33
(Triticum aestivum)
Liliopsida Ta.770 33
(Zea mays)
Liliopsida Zm.3148 33
(Hordeum vulgare)
Liliopsida Hv.6282 33
sea squirt
(Ciona savignyi)
Ascidiacea Cin.3480 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3480 33
Species where no ortholog for CLPTM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

Gene Tree for CLPTM1 (if available)
Gene Tree for CLPTM1 (if available)
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:

  • F5H8J3_HUMAN
  • K7EJ16_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

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 from dbSNP and Humsavar for CLPTM1 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000005480 -- 44,955,400(+) C/T coding_sequence_variant, intron_variant, missense_variant
rs1000213473 -- 44,964,977(+) G/C intron_variant
rs1000326227 -- 44,966,556(+) G/T intron_variant
rs1000332121 -- 44,972,180(+) T/C intron_variant
rs1000419917 -- 44,969,260(+) TGTT/T intron_variant

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

Disorders for CLPTM1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLPTM1 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cleft lip
  • cheiloschisis
orofacial cleft
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLPTM1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  2. 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 44 58
  3. 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 44 58
  4. Testing reported associations of genetic risk factors for oral clefts in a large Irish study population. (PMID: 19937600) Carter TC … Mills JL (Birth defects research. Part A, Clinical and molecular teratology 2010) 3 44 58
  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 44 58

Products for CLPTM1 Gene

Sources for CLPTM1 Gene

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