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Aliases for CPLANE1 Gene

Aliases for CPLANE1 Gene

  • Ciliogenesis And Planar Polarity Effector 1 2 3
  • Chromosome 5 Open Reading Frame 42 2 5
  • C5orf42 3 5
  • JBTS17 3 4
  • Transmembrane Protein ENSP00000382582 3
  • Protein C5orf42 4
  • Protein JBTS17 3
  • OFD6 3
  • Hug 3

External Ids for CPLANE1 Gene

Previous HGNC Symbols for CPLANE1 Gene

  • C5orf42

Summaries for CPLANE1 Gene

Entrez Gene Summary for CPLANE1 Gene

  • The protein encoded by this gene has putative coiled-coil domains and may be a transmembrane protein. Defects in this gene are a cause of Joubert syndrome (JBTS). [provided by RefSeq, May 2012]

GeneCards Summary for CPLANE1 Gene

CPLANE1 (Ciliogenesis And Planar Polarity Effector 1) is a Protein Coding gene. Diseases associated with CPLANE1 include Joubert Syndrome 17 and Orofaciodigital Syndrome Vi.

UniProtKB/Swiss-Prot for CPLANE1 Gene

  • Involved in ciliogenesis (PubMed:25877302). Involved in the establishment of cell polarity required for directional cell migration. Proposed to act in association with the CPLANE (ciliogenesis and planar polarity effectors) complex. Involved in recruitment of peripheral IFT-A proteins to basal bodies (By similarity).

Gene Wiki entry for CPLANE1 Gene

Additional gene information for CPLANE1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CPLANE1 Gene

Genomics for CPLANE1 Gene

GeneHancer (GH) Regulatory Elements for CPLANE1 Gene

Promoters and enhancers for CPLANE1 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
GH05J037248 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 665.4 +0.1 118 2.1 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 ZNF207 SP3 REST WDR70 CPLANE1 LOC105374727 LINC02117 NIPBL NUP155 OFD1P17 ENSG00000250455 GC05M037029
GH05J037378 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 30.5 -130.0 -130002 1.5 PKNOX1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B WDR70 CPLANE1 NIPBL OFD1P17 ENSG00000270558 NUP155 KCTD9P5
GH05J036605 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 17.1 +642.2 642187 2.8 PKNOX1 SIN3A FEZF1 GLI4 ZNF2 BRCA1 YY1 KLF7 FOS KLF13 SLC1A3 CPLANE1 SKP2 NADK2-AS1 NUP155 OFD1P17 WDR70 ENSG00000272103 ENSG00000274441
GH05J036743 Enhancer 1.2 Ensembl ENCODE 25.6 +504.4 504375 2.8 ATF1 NEUROD1 SIN3A GLI4 ZNF2 YY1 ZNF121 ZNF766 GLIS2 ZNF213 CPLANE1 OFD1P17 WDR70 NIPBL NUP155 ENSG00000250155 CAPSL GC05M036752
GH05J037717 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.6 -468.7 -468705 1.9 PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 ZNF213 FOS DEK SP5 CPLANE1 RNU6-484P GC05M037700 GDNF-AS1 WDR70
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CPLANE1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CPLANE1 Gene

Genomic Locations for CPLANE1 Gene
chr5:37,065,171-37,249,428
(GRCh38/hg38)
Size:
184,258 bases
Orientation:
Minus strand
chr5:37,106,330-37,249,530
(GRCh37/hg19)
Size:
143,201 bases
Orientation:
Minus strand

Genomic View for CPLANE1 Gene

Genes around CPLANE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPLANE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPLANE1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPLANE1 Gene

Proteins for CPLANE1 Gene

  • Protein details for CPLANE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H799-CE042_HUMAN
    Recommended name:
    Protein JBTS17
    Protein Accession:
    Q9H799
    Secondary Accessions:
    • A8MUB7
    • B7ZLV7
    • Q4G174
    • Q6DK46
    • Q8N8L4
    • Q9H5T1
    • Q9H8T9

    Protein attributes for CPLANE1 Gene

    Size:
    3197 amino acids
    Molecular mass:
    361746 Da
    Quaternary structure:
    • Interacts with FUZ; INTU and WDPCP; the interactors are proposed to form the core CPLANE (ciliogenesis and planar polarity effectors) complex.
    SequenceCaution:
    • Sequence=AAH28410.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence and intronic sequence in 5.; Evidence={ECO:0000305}; Sequence=AAI44070.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI50595.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14513.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14513.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential intronic sequence in 5.; Evidence={ECO:0000305}; Sequence=BAB14999.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14999.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAB15539.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC04822.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for CPLANE1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CPLANE1 Gene

Post-translational modifications for CPLANE1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CPLANE1 Gene

Domains & Families for CPLANE1 Gene

Gene Families for CPLANE1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CPLANE1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CPLANE1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CPLANE1: view

No data available for UniProtKB/Swiss-Prot for CPLANE1 Gene

Function for CPLANE1 Gene

Molecular function for CPLANE1 Gene

UniProtKB/Swiss-Prot Function:
Involved in ciliogenesis (PubMed:25877302). Involved in the establishment of cell polarity required for directional cell migration. Proposed to act in association with the CPLANE (ciliogenesis and planar polarity effectors) complex. Involved in recruitment of peripheral IFT-A proteins to basal bodies (By similarity).

Phenotypes From GWAS Catalog for CPLANE1 Gene

Gene Ontology (GO) - Molecular Function for CPLANE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with CPLANE1: view
genes like me logo Genes that share phenotypes with CPLANE1: view

Human Phenotype Ontology for CPLANE1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for CPLANE1 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for CPLANE1 Gene

Localization for CPLANE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CPLANE1 Gene

Membrane; Multi-pass membrane protein. Cell projection, cilium. Note=Localizes to the ciliary transition zone. {ECO:0000250 UniProtKB:Q8CE72}.

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 CPLANE1 gene
Compartment Confidence
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CPLANE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005929 cilium IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0035869 ciliary transition zone IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with CPLANE1: view

Pathways & Interactions for CPLANE1 Gene

SuperPathways for CPLANE1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CPLANE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001736 establishment of planar polarity IEA --
GO:0001822 kidney development IEA --
GO:0003279 cardiac septum development IEA --
GO:0003281 ventricular septum development IEA --
GO:0007507 heart development IEA --
genes like me logo Genes that share ontologies with CPLANE1: view

No data available for Pathways by source and SIGNOR curated interactions for CPLANE1 Gene

Drugs & Compounds for CPLANE1 Gene

No Compound Related Data Available

Transcripts for CPLANE1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CPLANE1 Gene

No ASD Table

Relevant External Links for CPLANE1 Gene

GeneLoc Exon Structure for
CPLANE1
ECgene alternative splicing isoforms for
CPLANE1

Expression for CPLANE1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CPLANE1 Gene:

CPLANE1

Evidence on tissue expression from TISSUES for CPLANE1 Gene

  • Nervous system(4.3)
  • Lung(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CPLANE1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • hypothalamus
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • nose
  • outer ear
  • pituitary gland
  • skull
  • tongue
  • tooth
Thorax:
  • diaphragm
  • heart
  • lung
  • rib
  • rib cage
Abdomen:
  • biliary tract
  • kidney
  • liver
Pelvis:
  • pelvis
  • penis
  • testicle
  • ureter
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • nail
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
  • white blood cell
No Expression Related Data Available

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for CPLANE1 Gene

Orthologs for CPLANE1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CPLANE1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C5H5orf42 33
  • 99.38 (n)
C5orf42 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia C4H5orf42 33
  • 85.47 (n)
C5orf42 34
  • 74 (a)
OneToOne
cow
(Bos Taurus)
Mammalia C20H5orf42 33
  • 85.13 (n)
C5orf42 34
  • 72 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 2410089E03Rik 34 33
  • 77.59 (n)
OneToOne
Cplane1 16
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 56 (a)
OneToMany
-- 34
  • 38 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia C5orf42 34
  • 38 (a)
OneToOne
chicken
(Gallus gallus)
Aves CZH5ORF42 33
  • 60.03 (n)
C5orf42 34
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C5orf42 34
  • 39 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii si:ch73-209l12.1 33
  • 47.45 (n)
C10H5orf42 34
  • 13 (a)
OneToOne
Species where no ortholog for CPLANE1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CPLANE1 Gene

ENSEMBL:
Gene Tree for CPLANE1 (if available)
TreeFam:
Gene Tree for CPLANE1 (if available)

Paralogs for CPLANE1 Gene

No data available for Paralogs for CPLANE1 Gene

Variants for CPLANE1 Gene

Sequence variations from dbSNP and Humsavar for CPLANE1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs10076911 conflicting-interpretations-of-pathogenicity, benign, not specified, Joubert syndrome 37,173,828(-) A/C coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs10805625 conflicting-interpretations-of-pathogenicity, likely-benign, not specified, Joubert syndrome 37,175,989(-) A/G intron_variant
rs111294855 conflicting-interpretations-of-pathogenicity, Joubert syndrome 17 37,157,382(-) C/T coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs111508546 benign, likely-benign, not specified, Joubert syndrome, Joubert syndrome 17, Orofaciodigital syndrome 6 37,185,088(-) AAAA/AA/AAA genic_upstream_transcript_variant, intron_variant
rs114126795 conflicting-interpretations-of-pathogenicity, uncertain-significance, not specified, Joubert syndrome 37,153,827(-) G/A coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for CPLANE1 Gene

Variant ID Type Subtype PubMed ID
dgv9722n54 CNV loss 21841781
esv2667122 CNV deletion 23128226
esv2674155 CNV deletion 23128226
esv3604728 CNV gain 21293372
esv3604729 CNV gain 21293372
esv3604730 CNV loss 21293372
esv3604731 CNV gain 21293372
nsv525478 CNV loss 19592680
nsv597822 CNV loss 21841781
nsv597823 CNV gain 21841781
nsv830265 CNV loss 17160897
nsv964844 CNV duplication 23825009

Variation tolerance for CPLANE1 Gene

Residual Variation Intolerance Score: 75.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.33; 88.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CPLANE1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CPLANE1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPLANE1 Gene

Disorders for CPLANE1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for CPLANE1 Gene - From: OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CE042_HUMAN
  • Joubert syndrome 17 (JBTS17) [MIM:614615]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. {ECO:0000269 PubMed:22425360, ECO:0000269 PubMed:23012439, ECO:0000269 PubMed:26477546}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Orofaciodigital syndrome 6 (OFD6) [MIM:277170]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD6 is characterized by metacarpal abnormalities with central polydactyly, cerebellar abnormalities including the molar tooth sign, tongue hamartomas, additional frenula, and upper lip notch. {ECO:0000269 PubMed:24178751, ECO:0000269 PubMed:25846457, ECO:0000269 PubMed:27081551}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CPLANE1

genes like me logo Genes that share disorders with CPLANE1: view

No data available for Genatlas for CPLANE1 Gene

Publications for CPLANE1 Gene

  1. Novel Jbts17 mutant mouse model of Joubert syndrome with cilia transition zone defects and cerebellar and other ciliopathy related anomalies. (PMID: 25877302) Damerla RR … Lo CW (Human molecular genetics 2015) 2 3 4 58
  2. Exome sequencing identifies KIAA1377 and C5orf42 as susceptibility genes for monomelic amyotrophy. (PMID: 22264561) Lim YM … Kim KK (Neuromuscular disorders : NMD 2012) 2 3 4 58
  3. Novel mutations in the ciliopathy-associated gene CPLANE1 (C5orf42) cause OFD syndrome type VI rather than Joubert syndrome. (PMID: 29605658) Bonnard C … Kariminejad A (European journal of medical genetics 2018) 2 3 58
  4. Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI. (PMID: 25846457) Bayram Y … Lupski JR (American journal of medical genetics. Part A 2015) 3 4 58
  5. C5orf42 is the major gene responsible for OFD syndrome type VI. (PMID: 24178751) Lopez E … Attié-Bitach T (Human genetics 2014) 3 4 58

Products for CPLANE1 Gene

Sources for CPLANE1 Gene

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