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Aliases for CCDC50 Gene

Aliases for CCDC50 Gene

  • Coiled-Coil Domain Containing 50 2 3 5
  • Protein Ymer 3 4
  • C3orf6 3 4
  • Coiled-Coil Domain-Containing Protein 50 3
  • Deafness, Autosomal Dominant 44 2
  • DFNA44 3
  • YMER 3

External Ids for CCDC50 Gene

Previous HGNC Symbols for CCDC50 Gene

  • C3orf6
  • DFNA44

Previous GeneCards Identifiers for CCDC50 Gene

  • GC03P192530
  • GC03P191046
  • GC03P188446

Summaries for CCDC50 Gene

Entrez Gene Summary for CCDC50 Gene

  • This gene encodes a soluble, cytoplasmic, tyrosine-phosphorylated protein with multiple ubiquitin-interacting domains. Mutations in this gene cause nonsyndromic, postlingual, progressive sensorineural DFNA44 hearing loss. In mouse, the protein is expressed in the inner ear during development and postnatal maturation and associates with microtubule-based structures. This protein may also function as a negative regulator of NF-kB signaling and as an effector of epidermal growth factor (EGF)-mediated cell signaling. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]

GeneCards Summary for CCDC50 Gene

CCDC50 (Coiled-Coil Domain Containing 50) is a Protein Coding gene. Diseases associated with CCDC50 include Deafness, Autosomal Dominant 44 and Autosomal Dominant Non-Syndromic Sensorineural Deafness Type Dfna. Gene Ontology (GO) annotations related to this gene include ubiquitin protein ligase binding.

UniProtKB/Swiss-Prot for CCDC50 Gene

  • Involved in EGFR signaling.

Gene Wiki entry for CCDC50 Gene

Additional gene information for CCDC50 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCDC50 Gene

Genomics for CCDC50 Gene

GeneHancer (GH) Regulatory Elements for CCDC50 Gene

Promoters and enhancers for CCDC50 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
GH03J191328 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 691 +1.6 1602 5.2 HDGF FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 CCDC50 UTS2B GC03P191372
GH03J191355 Enhancer 1.1 Ensembl ENCODE dbSUPER 53 +27.9 27913 2.6 INSM2 RAD21 RELA HIC1 ATF7 ETV6 RUNX3 NR2F1 TRIM22 JUNB CCDC50 UTS2B GC03P191372
GH03J191375 Enhancer 1.1 Ensembl ENCODE dbSUPER 50.2 +47.8 47773 1.8 KLF1 ZBTB6 JUN INSM2 FEZF1 ZFHX2 ZNF316 PRDM10 ZNF600 NFE2 CCDC50 UTS2B GC03P191372 GC03P191395
GH03J191364 Enhancer 0.6 dbSUPER 52.1 +39.7 39695 8.9 NANOG JUN MAFG CBFA2T3 DPF2 ZBTB40 ATF4 ZNF316 POU5F1 HMBOX1 CCDC50 UTS2B OSTN GC03P191372
GH03J191382 Enhancer 0.7 ENCODE dbSUPER 33.7 +54.1 54101 2.2 NR2F1 IKZF1 IKZF2 SPI1 CCDC50 UTS2B GC03P191372 GC03P191395
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CCDC50 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CCDC50 gene promoter:

Genomic Locations for CCDC50 Gene

Genomic Locations for CCDC50 Gene
chr3:191,329,077-191,398,670
(GRCh38/hg38)
Size:
69,594 bases
Orientation:
Plus strand
chr3:191,046,866-191,116,459
(GRCh37/hg19)

Genomic View for CCDC50 Gene

Genes around CCDC50 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC50 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC50 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC50 Gene

Proteins for CCDC50 Gene

  • Protein details for CCDC50 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IVM0-CCD50_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 50
    Protein Accession:
    Q8IVM0
    Secondary Accessions:
    • Q86VH7

    Protein attributes for CCDC50 Gene

    Size:
    306 amino acids
    Molecular mass:
    35822 Da
    Quaternary structure:
    • Interacts with RNF126.
    Miscellaneous:
    • Found in a critical region of hereditary spastic paraplegia (HSP) SPG14 locus. No causative CCDC50 mutations were found in HSP families.

    Alternative splice isoforms for CCDC50 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCDC50 Gene

Post-translational modifications for CCDC50 Gene

  • Phosphorylated on tyrosine residues.
  • Ubiquitination at Lys232, posLast=181181, Lys157, posLast=152152, posLast=129129, and Lys119
  • Modification sites at PhosphoSitePlus

Other Protein References for CCDC50 Gene

No data available for DME Specific Peptides for CCDC50 Gene

Domains & Families for CCDC50 Gene

Gene Families for CCDC50 Gene

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

Protein Domains for CCDC50 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCDC50 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CCDC50: view

No data available for UniProtKB/Swiss-Prot for CCDC50 Gene

Function for CCDC50 Gene

Molecular function for CCDC50 Gene

UniProtKB/Swiss-Prot Function:
Involved in EGFR signaling.

Phenotypes From GWAS Catalog for CCDC50 Gene

Gene Ontology (GO) - Molecular Function for CCDC50 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18029035
GO:0031625 ubiquitin protein ligase binding IPI 23418353
genes like me logo Genes that share ontologies with CCDC50: view
genes like me logo Genes that share phenotypes with CCDC50: view

Human Phenotype Ontology for CCDC50 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC50

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for CCDC50 Gene

Localization for CCDC50 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC50 Gene

Cytoplasm. Note=Associated with microtubules of the cytoskeleton and mitotic apparatus. {ECO:0000250}.

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 CCDC50 gene
Compartment Confidence
cytosol 5
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CCDC50 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with CCDC50: view

Pathways & Interactions for CCDC50 Gene

SuperPathways for CCDC50 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CCDC50 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007605 sensory perception of sound IMP 17503326
genes like me logo Genes that share ontologies with CCDC50: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC50 Gene

Drugs & Compounds for CCDC50 Gene

No Compound Related Data Available

Transcripts for CCDC50 Gene

mRNA/cDNA for CCDC50 Gene

Unigene Clusters for CCDC50 Gene

Coiled-coil domain containing 50:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC50

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC50 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1:
SP2: -

Relevant External Links for CCDC50 Gene

GeneLoc Exon Structure for
CCDC50
ECgene alternative splicing isoforms for
CCDC50

Expression for CCDC50 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCDC50 Gene

Protein differential expression in normal tissues from HIPED for CCDC50 Gene

This gene is overexpressed in Heart (12.2), Breast (10.6), Lymph node (7.2), and Fetal Brain (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CCDC50 Gene



Protein tissue co-expression partners for CCDC50 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CCDC50 Gene:

CCDC50

SOURCE GeneReport for Unigene cluster for CCDC50 Gene:

Hs.478682

mRNA Expression by UniProt/SwissProt for CCDC50 Gene:

Q8IVM0-CCD50_HUMAN
Tissue specificity: Isoform 1 and isoform 2 are coexpressed in placenta, liver, lung, kidney and pancreas. Only isoform 1 is detected in skeletal muscle, brain and heart.

Evidence on tissue expression from TISSUES for CCDC50 Gene

  • Skin(4.3)
  • Nervous system(3.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC50 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • head
  • inner ear
  • middle ear
  • outer ear
Thorax:
  • heart
  • heart valve
Limb:
  • forearm
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CCDC50: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for CCDC50 Gene

Orthologs for CCDC50 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CCDC50 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CCDC50 34 33
  • 99.24 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CCDC50 34
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CCDC50 34 33
  • 88.84 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ccdc50 34
  • 84 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CCDC50 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CCDC50 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves CCDC50 34 33
  • 67.8 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CCDC50 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17651 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.14896 33
zebrafish
(Danio rerio)
Actinopterygii AL929204.1 34
  • 27 (a)
OneToMany
CCDC50 (2 of 4) 34
  • 24 (a)
OneToMany
CCDC50 (4 of 4) 34
  • 19 (a)
OneToMany
CCDC50 (1 of 4) 34
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 14 (a)
OneToOne
Species where no ortholog for CCDC50 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CCDC50 Gene

ENSEMBL:
Gene Tree for CCDC50 (if available)
TreeFam:
Gene Tree for CCDC50 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC50: view image

Paralogs for CCDC50 Gene

No data available for Paralogs for CCDC50 Gene

Variants for CCDC50 Gene

Sequence variations from dbSNP and Humsavar for CCDC50 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs138153104 conflicting-interpretations-of-pathogenicity, not specified 191,375,230(+) C/T coding_sequence_variant, intron_variant, missense_variant
rs114146378 likely-benign, not specified 191,382,779(+) A/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs138707536 likely-benign, not specified 191,380,921(+) C/A/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs201015131 likely-benign, not specified 191,358,038(+) G/A coding_sequence_variant, synonymous_variant
rs727502916 likely-benign, not specified 191,375,362(+) A/G coding_sequence_variant, intron_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CCDC50 Gene

Variant ID Type Subtype PubMed ID
dgv114e180 CNV gain 20482838
dgv132n73 CNV deletion 24416366
dgv632n27 CNV loss 19166990
dgv633n27 CNV loss 19166990
dgv634n27 CNV loss 19166990
dgv79n17 CNV loss 16327808
dgv8792n54 CNV loss 21841781
dgv8793n54 CNV loss 21841781
dgv8794n54 CNV loss 21841781
dgv8795n54 CNV loss 21841781
dgv8796n54 CNV loss 21841781
dgv8797n54 CNV loss 21841781
dgv8798n54 CNV loss 21841781
dgv8799n54 CNV loss 21841781
dgv903e199 CNV deletion 23128226
esv1000145 CNV insertion 20482838
esv1041065 CNV insertion 17803354
esv2421497 CNV deletion 20811451
esv24246 CNV gain 19812545
esv2726395 CNV deletion 23290073
esv2759209 CNV gain+loss 17122850
esv3377157 CNV insertion 20981092
esv3379331 CNV insertion 20981092
esv3563095 CNV deletion 23714750
esv3569192 CNV loss 25503493
esv3599095 CNV loss 21293372
esv3599096 CNV gain 21293372
esv3599102 CNV loss 21293372
esv3599103 CNV gain 21293372
esv3599104 CNV loss 21293372
nsv10370 CNV loss 18304495
nsv10371 CNV gain+loss 18304495
nsv10373 CNV gain 18304495
nsv4169 CNV deletion 18451855
nsv428428 CNV gain 18775914
nsv435761 CNV deletion 17901297
nsv437905 CNV loss 16468122
nsv461056 CNV gain 19166990
nsv461060 CNV loss 19166990
nsv508266 CNV deletion 20534489
nsv514193 CNV loss 21397061
nsv516440 CNV gain+loss 19592680
nsv592822 CNV loss 21841781
nsv592824 CNV gain+loss 21841781
nsv592851 CNV loss 21841781
nsv818199 CNV loss 17921354
nsv818201 CNV loss 17921354
nsv818202 CNV gain+loss 17921354
nsv818203 CNV loss 17921354
nsv818204 CNV loss 17921354
nsv819154 CNV gain 19587683
nsv821209 CNV deletion 20802225
nsv822381 CNV loss 20364138
nsv965411 CNV deletion 23825009
nsv998208 CNV gain 25217958

Variation tolerance for CCDC50 Gene

Residual Variation Intolerance Score: 63.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.51; 55.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC50 Gene

Human Gene Mutation Database (HGMD)
CCDC50
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC50

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC50 Gene

Disorders for CCDC50 Gene

MalaCards: The human disease database

(9) MalaCards diseases for CCDC50 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal dominant 44
  • dfna44
autosomal dominant non-syndromic sensorineural deafness type dfna
  • autosomal dominant isolated neurosensory deafness type dfna
spastic paraplegia 14, autosomal recessive
  • spg14
chromosome 3q29 deletion syndrome
  • microdeletion 3q29 syndrome
deafness, autosomal dominant 10
  • dfna10
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CCD50_HUMAN
  • Deafness, autosomal dominant, 44 (DFNA44) [MIM:607453]: A form of non-syndromic deafness characterized by initially moderate hearing loss that affects mainly low to mid frequencies. Later, it progresses to involve all the frequencies and leads to a profound hearing loss by the 6th decade. {ECO:0000269 PubMed:17503326}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CCDC50

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CCDC50: view

No data available for Genatlas for CCDC50 Gene

Publications for CCDC50 Gene

  1. A mutation in CCDC50, a gene encoding an effector of epidermal growth factor-mediated cell signaling, causes progressive hearing loss. (PMID: 17503326) Modamio-Hoybjor S … Moreno-Pelayo MA (American journal of human genetics 2007) 2 3 4 58
  2. Identification and characterization of C3orf6, a new conserved human gene mapping to chromosome 3q28. (PMID: 14527723) Vazza G … Mostacciuolo ML (Gene 2003) 3 4 22 58
  3. The E3 ubiquitin ligases RNF126 and Rabring7 regulate endosomal sorting of the epidermal growth factor receptor. (PMID: 23418353) Smith CJ … McGlade CJ (Journal of cell science 2013) 3 4 58
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  5. Suppression of the ligand-mediated down-regulation of epidermal growth factor receptor by Ymer, a novel tyrosine-phosphorylated and ubiquitinated protein. (PMID: 16803894) Tashiro K … Taniguchi H (The Journal of biological chemistry 2006) 2 3 58

Products for CCDC50 Gene

Sources for CCDC50 Gene

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