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Aliases for C5orf42 Gene

Aliases for C5orf42 Gene

  • Chromosome 5 Open Reading Frame 42 2 3 5
  • JBTS17 3 4
  • Transmembrane Protein ENSP00000382582 3
  • Uncharacterized Protein C5orf42 3
  • Protein C5orf42 4
  • Protein JBTS17 3
  • EC 3.6.1 58
  • EC 2.3.1 58
  • OFD6 3
  • Hug 3

External Ids for C5orf42 Gene

Previous GeneCards Identifiers for C5orf42 Gene

  • GC05M037144
  • GC05M037107

Summaries for C5orf42 Gene

Entrez Gene Summary for C5orf42 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 C5orf42 Gene

C5orf42 (Chromosome 5 Open Reading Frame 42) is a Protein Coding gene. Diseases associated with C5orf42 include Orofaciodigital Syndrome Vi and Joubert Syndrome 17.

UniProtKB/Swiss-Prot for C5orf42 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 C5orf42 Gene

Additional gene information for C5orf42 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C5orf42 Gene

Genomics for C5orf42 Gene

Regulatory Elements for C5orf42 Gene

Enhancers for C5orf42 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
GH05H036743 1.3 Ensembl ENCODE 36.9 +504.4 504375 2.8 ATF1 SIN3A GLI4 ZNF2 YY1 ZNF121 ZNF766 GLIS2 ZNF302 GATA2 C5orf42 OFD1P17 WDR70 NIPBL NUP155 ENSG00000250155 CAPSL GC05M036752
GH05H037378 1.1 ENCODE 30.5 -129.9 -129893 1.3 PKNOX1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF416 WDR70 C5orf42 NIPBL OFD1P17 ENSG00000270558 NUP155 KCTD9P5
GH05H036605 1.3 ENCODE dbSUPER 17.1 +642.2 642187 2.8 PKNOX1 FEZF1 GLI4 BRCA1 ZNF2 FOS KLF7 SP3 YY2 JUNB WDR70 NIPBL C5orf42 SKP2 NADK2-AS1 OFD1P17 ENSG00000272103 SLC1A3 ENSG00000274441
GH05H036929 1 ENCODE 21.3 +320.3 320295 0.2 PKNOX1 FEZF1 GLI4 ZNF2 GLIS2 ZNF302 FOS ATF7 RUNX3 SP3 NIPBL C5orf42 OFD1P17 ENSG00000250155 SKP2 WDR70 KRT18P31 GC05P037069
GH05H037369 1.2 ENCODE 13.2 -121.4 -121437 3 HDGF FOXA2 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 NIPBL WDR70 NUP155 C5orf42 ENSG00000250155 GC05P037328
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around C5orf42 on UCSC Golden Path with GeneCards custom track

Promoters for C5orf42 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000179616 228 1601 PKNOX1 ARID4B SIN3A FEZF1 GLI4 ZNF2 GLIS2 ELK1 ZNF207 KLF7

Genomic Locations for C5orf42 Gene

Genomic Locations for C5orf42 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)

Genomic View for C5orf42 Gene

Genes around C5orf42 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C5orf42 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C5orf42 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C5orf42 Gene

Proteins for C5orf42 Gene

  • Protein details for C5orf42 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 C5orf42 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 C5orf42 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for C5orf42 Gene

Selected DME Specific Peptides for C5orf42 Gene

Q9H799:
  • AAILTSL
  • SVAVATP

Post-translational modifications for C5orf42 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for C5orf42 Gene

Gene Families for C5orf42 Gene

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

Protein Domains for C5orf42 Gene

Suggested Antigen Peptide Sequences for C5orf42 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with C5orf42: view

No data available for UniProtKB/Swiss-Prot for C5orf42 Gene

Function for C5orf42 Gene

Molecular function for C5orf42 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).

Enzyme Numbers (IUBMB) for C5orf42 Gene

Phenotypes From GWAS Catalog for C5orf42 Gene

genes like me logo Genes that share phenotypes with C5orf42: view

Human Phenotype Ontology for C5orf42 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for C5orf42 Gene

Clone Products

No data available for Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for C5orf42 Gene

Localization for C5orf42 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C5orf42 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 C5orf42 gene
Compartment Confidence
nucleus 2
cytosol 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for C5orf42 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 C5orf42: view

Pathways & Interactions for C5orf42 Gene

SuperPathways for C5orf42 Gene

No Data Available

Interacting Proteins for C5orf42 Gene

Gene Ontology (GO) - Biological Process for C5orf42 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 C5orf42: view

No data available for Pathways by source and SIGNOR curated interactions for C5orf42 Gene

Drugs & Compounds for C5orf42 Gene

No Compound Related Data Available

Transcripts for C5orf42 Gene

Unigene Clusters for C5orf42 Gene

Chromosome 5 open reading frame 42:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for C5orf42 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b · 15c ^ 16 ^ 17a · 17b · 17c ^ 18 ^
SP1: -
SP2: -
SP3:
SP4: -
SP5: - -
SP6:
SP7:
SP8:
SP9: -

ExUns: 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26 ^ 27
SP1:
SP2:
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for C5orf42 Gene

GeneLoc Exon Structure for
C5orf42
ECgene alternative splicing isoforms for
C5orf42

Expression for C5orf42 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for C5orf42 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for C5orf42 Gene

This gene is overexpressed in Urinary Bladder (35.0), Plasma (16.1), and Platelet (11.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for C5orf42 Gene



Protein tissue co-expression partners for C5orf42 Gene

NURSA nuclear receptor signaling pathways regulating expression of C5orf42 Gene:

C5orf42

SOURCE GeneReport for Unigene cluster for C5orf42 Gene:

Hs.586199

Evidence on tissue expression from TISSUES for C5orf42 Gene

  • Nervous system(4.4)
  • Lung(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for C5orf42 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
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
genes like me logo Genes that share expression patterns with C5orf42: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for C5orf42 Gene

Orthologs for C5orf42 Gene

This gene was present in the common ancestor of chordates.

Orthologs for C5orf42 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 33 16 34
  • 77.59 (n)
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 C5orf42 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 C5orf42 Gene

ENSEMBL:
Gene Tree for C5orf42 (if available)
TreeFam:
Gene Tree for C5orf42 (if available)

Paralogs for C5orf42 Gene

No data available for Paralogs for C5orf42 Gene

Variants for C5orf42 Gene

Sequence variations from dbSNP and Humsavar for C5orf42 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs141153181 Pathogenic, Orofaciodigital syndrome 6 (OFD6) [MIM:277170] 37,198,775(+) GAGCC(A/G/T)CCCGG nc-transcript-variant, reference, missense
rs149170427 Likely pathogenic, Orofaciodigital syndrome 6 (OFD6) [MIM:277170] 37,198,797(+) AACAC(A/G)CTGAA nc-transcript-variant, reference, missense
rs367543061 Pathogenic, Joubert syndrome 17 (JBTS17) [MIM:614615] 37,187,488(-) TCTCT(C/T)GGTTT nc-transcript-variant, reference, missense
rs375009168 Pathogenic, Orofaciodigital syndrome 6 (OFD6) [MIM:277170] 37,201,718(+) TCTCC(A/G/T)AAAGA nc-transcript-variant, reference, missense, stop-gained
rs606231261 Pathogenic, Orofaciodigital syndrome 6 (OFD6) [MIM:277170] 37,187,795(-) TCCGT(C/G)ATAAG nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for C5orf42 Gene

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

Variation tolerance for C5orf42 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)

Relevant External Links for C5orf42 Gene

Human Gene Mutation Database (HGMD)
C5orf42
SNPedia medical, phenotypic, and genealogical associations of SNPs for
C5orf42

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C5orf42 Gene

Disorders for C5orf42 Gene

MalaCards: The human disease database

(8) MalaCards diseases for C5orf42 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
orofaciodigital syndrome vi
  • joubert syndrome with orofaciodigital defect
joubert syndrome 17
  • jbts17
c5orf42-related joubert syndrome
  • joubert syndrome 17
polydactyly cleft lip palate psychomotor retardation
  • orofaciodigital syndrome vi
joubert syndrome 1
  • joubert syndrome
- 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.

Relevant External Links for C5orf42

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
C5orf42
genes like me logo Genes that share disorders with C5orf42: view

No data available for Genatlas for C5orf42 Gene

Publications for C5orf42 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 60
  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 60
  3. 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 60
  4. C5orf42 is the major gene responsible for OFD syndrome type VI. (PMID: 24178751) Lopez E … Attié-Bitach T (Human genetics 2014) 3 4 60
  5. Mutations in C5ORF42 cause Joubert syndrome in the French Canadian population. (PMID: 22425360) Srour M … Michaud JL (American journal of human genetics 2012) 3 4 60

Products for C5orf42 Gene

Sources for C5orf42 Gene

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