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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

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. 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

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLPTM1 Gene

Genomics for CLPTM1 Gene

Regulatory Elements for CLPTM1 Gene

Enhancers for CLPTM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19F044953 0.7 ENCODE 18.3 +0.7 697 3.4 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 APOC2 CLPTM1 MRPS15P2 ZNF234 ENSG00000267395 SIX5 SNRPD2 ZNF180 ENSG00000259605 GC19M044995
GH19F045005 0.7 ENCODE 14.9 +52.7 52728 4.3 HDGF ATF1 PKNOX1 ARNT ARID4B SIN3A GLI4 YBX1 GLIS2 ZNF143 APOC2 CLPTM1 CLASRP RNU6-611P GEMIN7 ZNF296 PPP1R37 APOE RELB
GH19F045000 0.2 ENCODE 5.9 +47.2 47172 2.5 HDGF PKNOX1 CREB3L1 SIN3A ARID4B YY1 ZNF766 ZNF143 ZNF207 ZNF548 ZNF180 CCDC61 ZNF234 ZNF224 FBXO46 ENSG00000266958 ENSG00000269148 ZNF284 APOC2 NECTIN2
GH19F044960 0.8 Ensembl ENCODE 0.4 +6.8 6827 1.4 HDGF BCOR CTCF ZMYM3 CEBPG NFXL1 RAD21 ZNF664 GATA3 ADNP APOC2 RELB GEMIN7 ZNF296 PPP1R37 RNU6-611P APOE CLPTM1 GC19M044995
GH19F044989 0.2 ENCODE 0.3 +34.8 34783 0.2 HDGF PKNOX1 RAD21 ZNF335 ZNF121 GLIS2 ZNF143 ETV6 CREM SMARCA5 APOC2 GC19M044995 CLPTM1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CLPTM1 on UCSC Golden Path with GeneCards custom track

Promoters for CLPTM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000347299 515 2201 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for CLPTM1 Gene

Chromosome:
19
Start:
44,954,585 bp from pter
End:
44,993,346 bp from pter
Size:
38,762 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

  • Ubiquitination at Lys 209, Lys 224, and Lys 534
  • Glycosylation at Asn 28, Asn 119, Asn 161, Asn 241, Asn 295, and Asn 413
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLPTM1 Gene

Domains & Families for CLPTM1 Gene

Protein Domains for CLPTM1 Gene

InterPro:
ProtoNet:

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

No data available for Gene Families for CLPTM1 Gene

Function for CLPTM1 Gene

Molecular function for CLPTM1 Gene

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
UniProtKB/Swiss-Prot Function:
May play a role in T-cell development.

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

miRNA for CLPTM1 Gene

miRTarBase miRNAs that target CLPTM1

Inhibitory RNA Products

Flow Cytometry Products

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
Jensen Localization Image for CLPTM1 Gene COMPARTMENTS Subcellular localization image for CLPTM1 gene
Compartment Confidence
plasma membrane 5
peroxisome 1

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 IEA,ISS --
GO:0016020 membrane IEA,IDA 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

Interacting Proteins for CLPTM1 Gene

Gene Ontology (GO) - Biological Process for CLPTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0030154 cell differentiation IEA --
GO:0033081 regulation of T cell differentiation in thymus IEA,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

Transcripts for CLPTM1 Gene

Unigene Clusters for CLPTM1 Gene

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

Inhibitory RNA Products

Flow Cytometry Products

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
ECgene alternative splicing isoforms for
CLPTM1

Expression for CLPTM1 Gene

mRNA expression in normal human tissues 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:

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.
genes like me logo Genes that share expression patterns with CLPTM1: view

Primer Products

No data available for mRNA differential expression in normal tissues 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 34 35
  • 99.6 (n)
cow
(Bos Taurus)
Mammalia CLPTM1 34 35
  • 92.63 (n)
dog
(Canis familiaris)
Mammalia CLPTM1 34 35
  • 91.58 (n)
mouse
(Mus musculus)
Mammalia Clptm1 34 16 35
  • 88.81 (n)
rat
(Rattus norvegicus)
Mammalia Clptm1 34
  • 88.15 (n)
oppossum
(Monodelphis domestica)
Mammalia CLPTM1 35
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLPTM1 35
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLPTM1 35
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clptm1 34
  • 71.82 (n)
Str.753 34
zebrafish
(Danio rerio)
Actinopterygii clptm1 34 35
  • 74.51 (n)
sbcb102 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6632 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007926 34
  • 59.74 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3702 36 34 35
  • 59.63 (n)
worm
(Caenorhabditis elegans)
Secernentea C36B7.6 36 34 35
  • 56.19 (n)
R166.2 36 35
  • 49 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G23575 34
  • 51.96 (n)
rice
(Oryza sativa)
Liliopsida Os04g0441900 34
  • 52.05 (n)
Os.18612 34
barley
(Hordeum vulgare)
Liliopsida Hv.6282 34
wheat
(Triticum aestivum)
Liliopsida Ta.770 34
corn
(Zea mays)
Liliopsida Zm.3148 34
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3480 34
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

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

Paralogs for CLPTM1 Gene

Paralogs for CLPTM1 Gene

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

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 from dbSNP and Humsavar for CLPTM1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs10404137 -- 44,967,168(+) taaaa(A/G)attag intron-variant
rs10405184 -- 44,967,397(+) ctcac(A/G)cctgt intron-variant
rs10406100 -- 44,954,529(+) TTCAC(A/G)GGTGA upstream-variant-2KB
rs10408974 -- 44,972,926(+) ATCTT(A/C/G)TCTCC intron-variant
rs10415096 -- 44,979,340(+) GTAGA(A/C)ATCTC 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)

Relevant External Links 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

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

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

Relevant External Links for CLPTM1

Genetic Association Database (GAD)
CLPTM1
Human Genome Epidemiology (HuGE) Navigator
CLPTM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLPTM1
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 J.C. (Genomics 1998) 2 3 4 64
  2. Testing reported associations of genetic risk factors for oral clefts in a large Irish study population. (PMID: 19937600) Carter T.C. … Mills J.L. (Birth Defects Res. Part A Clin. Mol. Teratol. 2010) 3 46 64
  3. MTHFR and MSX1 contribute to the risk of nonsyndromic cleft lip/palate. (PMID: 20572854) JagomAogi T. … Metspalu A. (Eur. J. Oral Sci. 2010) 3 46 64
  4. 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 S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  5. 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 J.C. (PLoS ONE 2010) 3 46 64

Products for CLPTM1 Gene

Sources for CLPTM1 Gene

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