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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 61
  • EC 2.3.1 61
  • 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

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
GH05G036873 2.4 ENCODE dbSUPER 17.4 +372.5 372463 6.4 CREB3L1 AGO1 DMAP1 FEZF1 YY1 ZNF143 ZNF263 SP3 GLIS1 NBN WDR70 C5orf42 OFD1P17 ENSG00000250155 NIPBL KRT18P31
GH05G036743 1.3 Ensembl ENCODE 25.6 +504.4 504375 2.8 SIN3A ZNF2 YY1 ZNF766 ZNF302 ZNF263 SP3 ZHX2 REST ZNF579 C5orf42 OFD1P17 ENSG00000250155 CAPSL GC05M036752
GH05G036656 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.4 +591.5 591480 2.9 TBP BRCA1 RAD21 RFX5 YY1 SMARCC2 RCOR1 FOS DEK ZHX1 C5orf42 WDR70 SLC1A3 NIPBL ENSG00000279400 ENSG00000274441
GH05G037737 1.5 Ensembl ENCODE dbSUPER 17.4 -490.2 -490236 4.6 PKNOX1 SIN3A FEZF1 FOS JUNB TSHZ1 ZNF623 TBX21 MYNN NBN C5orf42 GDNF-AS1 GDNF WDR70 RNU6-484P GC05M037700
GH05G037667 1.3 Ensembl ENCODE 17.4 -419.3 -419289 2.3 ATF1 FOXA2 SIN3A BRCA1 TCF12 GLIS2 GATA2 FOS SP3 JUNB C5orf42 ENSG00000250155 GC05P037665 GC05M037700 RNU6-484P
- 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 ZNF2 ZNF207 ZNF263 SP3 REST SMARCB1

Genomic Location for C5orf42 Gene

Chromosome:
5
Start:
37,065,171 bp from pter
End:
37,249,428 bp from pter
Size:
184,258 bases
Orientation:
Minus strand

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

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 Gene Families and 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

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

Animal Model Products

CRISPR Products

miRNA for C5orf42 Gene

Inhibitory RNA 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

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:

CRISPR Products

Inhibitory RNA 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

Primer Products

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 34
  • 99.38 (n)
C5orf42 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia C4H5orf42 34
  • 85.47 (n)
C5orf42 35
  • 74 (a)
OneToOne
cow
(Bos Taurus)
Mammalia C20H5orf42 34
  • 85.13 (n)
C5orf42 35
  • 72 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 2410089E03Rik 34 16 35
  • 77.59 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 56 (a)
OneToMany
-- 35
  • 38 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia C5orf42 35
  • 38 (a)
OneToOne
chicken
(Gallus gallus)
Aves CZH5ORF42 34
  • 60.03 (n)
C5orf42 35
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C5orf42 35
  • 39 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii si:ch73-209l12.1 34
  • 47.45 (n)
C10H5orf42 35
  • 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
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 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: 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
joubert syndrome 1
  • joubert syndrome
amyotrophy, monomelic
  • monomelic amyotrophy
- 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 R.R. … Lo C.W. (Hum. Mol. Genet. 2015) 2 3 4 64
  2. Exome sequencing identifies KIAA1377 and C5orf42 as susceptibility genes for monomelic amyotrophy. (PMID: 22264561) Lim Y.M. … Kim K.K. (Neuromuscul. Disord. 2012) 2 3 4 64
  3. Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI. (PMID: 25846457) Bayram Y. … Lupski J.R. (Am. J. Med. Genet. A 2015) 3 4 64
  4. C5orf42 is the major gene responsible for OFD syndrome type VI. (PMID: 24178751) Lopez E. … AttiAc-Bitach T. (Hum. Genet. 2014) 3 4 64
  5. Mutations in C5ORF42 cause Joubert syndrome in the French Canadian population. (PMID: 22425360) Srour M. … Michaud J.L. (Am. J. Hum. Genet. 2012) 3 4 64

Products for C5orf42 Gene

Sources for C5orf42 Gene

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