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Aliases for C5orf42 Gene

Aliases for C5orf42 Gene

  • Chromosome 5 Open Reading Frame 42 2 3 5
  • Transmembrane Protein ENSP00000382582 3
  • EC 3.6.1 63
  • EC 2.3.1 63
  • JBTS17 3
  • 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 joubert syndrome 17 and orofaciodigital syndrome vi.

Gene Wiki entry for C5orf42 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C5orf42 Gene

Genomics for C5orf42 Gene

Regulatory Elements for C5orf42 Gene

Promoters for C5orf42 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around C5orf42 on UCSC Golden Path with GeneCards custom track

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:
    Uncharacterized protein C5orf42
    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:
    No Data Available
    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

Proteomics data for C5orf42 Gene at MOPED

Selected DME Specific Peptides for C5orf42 Gene

Post-translational modifications for C5orf42 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for C5orf42 Gene

Domains & Families for C5orf42 Gene

Protein Domains for C5orf42 Gene

InterPro:
ProtoNet:

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

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

In Situ Assay Products

Flow Cytometry Products

No data available for Molecular function , 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.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for C5orf42 Gene COMPARTMENTS Subcellular localization image for C5orf42 gene
Compartment Confidence
cytosol 2
nucleus 2

No data available for Gene Ontology (GO) - Cellular Components for C5orf42 Gene

Pathways & Interactions for C5orf42 Gene

SuperPathways for C5orf42 Gene

No Data Available

Interacting Proteins for C5orf42 Gene

STRING Interaction Network Preview (showing 3 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000389014%0d%0a9606.ENSP00000376076%0d%0a9606.ENSP00000278568%0d%0a9606.ENSP00000344818%0d%0a
Selected Interacting proteins: ENSP00000389014 for C5orf42 Gene via STRING

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:

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 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 and MOPED for C5orf42 Gene



SOURCE GeneReport for Unigene cluster for C5orf42 Gene Hs.586199

genes like me logo Genes that share expression patterns with C5orf42: view

Protein tissue co-expression partners for C5orf42 Gene

Primer Products

In Situ Assay 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 35
  • 99.38 (n)
  • 98.94 (a)
C5orf42 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia C5orf42 36
  • 72 (a)
OneToOne
C20H5orf42 35
  • 85.13 (n)
  • 78.44 (a)
dog
(Canis familiaris)
Mammalia C4H5orf42 35
  • 85.47 (n)
  • 78.6 (a)
C5orf42 36
  • 74 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 2410089E03Rik 36
  • 65 (a)
OneToOne
2410089E03Rik 16
2410089E03Rik 35
  • 77.59 (n)
  • 68.8 (a)
oppossum
(Monodelphis domestica)
Mammalia C5orf42 36
  • 38 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 38 (a)
OneToMany
-- 36
  • 56 (a)
OneToMany
chicken
(Gallus gallus)
Aves CZH5ORF42 35
  • 60.03 (n)
  • 49.01 (a)
C5orf42 36
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C5orf42 36
  • 39 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii C10H5orf42 36
  • 13 (a)
OneToOne
si:ch73-209l12.1 35
  • 47.45 (n)
  • 39.22 (a)
Species with no ortholog for C5orf42:
  • 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
rs6859950 - 37,184,959(+) CTTCA(A/G)TTGGT nc-transcript-variant, reference, missense
rs10076911 -, - 37,173,828(+) CCGTG(A/C)ATTCA nc-transcript-variant, reference, missense
rs6884652 - 37,170,076(+) TGGGA(C/T)AGTTC nc-transcript-variant, reference, missense
rs16903518 - 37,158,261(+) ACCAA(A/G)GTTTC nc-transcript-variant, reference, missense, utr-variant-3-prime
rs7702892 - 37,115,014(+) GGCTC(C/T)ACCAG nc-transcript-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv525478 CNV Loss 19592680
nsv881511 CNV Gain 21882294
esv2674155 CNV Deletion 23128226
nsv830265 CNV Loss 17160897
nsv880406 CNV Gain 21882294
dgv6037n71 CNV Gain 21882294
esv2667122 CNV Deletion 23128226
nsv881512 CNV Gain 21882294

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

HapMap Linkage Disequilibrium report
C5orf42
Human Gene Mutation Database (HGMD)
C5orf42

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

Disorders for C5orf42 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
joubert syndrome 17
  • jbts17
orofaciodigital syndrome vi
  • ofd6
joubert syndrome with orofaciodigital defect
  • orofaciodigital syndrome vi
c5orf42-related joubert syndrome
  • joubert syndrome 17
polydactyly cleft lip palate psychomotor retardation
  • joubert syndrome with orofaciodigital defect
- 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}. 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. 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 67
  2. 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
  3. Oral-facial-digital syndrome type VI: is C5orf42 really the major gene? (PMID: 25407461) Romani M. … Valente E.M. (Hum. Genet. 2015) 3
  4. Genome-wide association study identifies variants in casein kinase II (CSNK2A2) to be associated with leukocyte telomere length in a Punjabi Sikh diabetic cohort. (PMID: 24795349) Saxena R. … Sanghera D.K. (Circ Cardiovasc Genet 2014) 3
  5. C5orf42 is the major gene responsible for OFD syndrome type VI. (PMID: 24178751) Lopez E. … AttiAc-Bitach T. (Hum. Genet. 2014) 3

Products for C5orf42 Gene

Sources for C5orf42 Gene

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