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    CCDC50 coiled-coil domain containing 50 [ Homo sapiens (human) ]

    Gene ID: 152137, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CCDC50provided by HGNC
    Official Full Name
    coiled-coil domain containing 50provided by HGNC
    Primary source
    HGNC:HGNC:18111
    See related
    Ensembl:ENSG00000152492 MIM:611051; AllianceGenome:HGNC:18111
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    YMER; C3orf6; DFNA44
    Summary
    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]
    Expression
    Ubiquitous expression in fat (RPKM 19.1), ovary (RPKM 13.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC50 in Genome Data Viewer
    Location:
    3q28
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (191329394..191398659)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (194145445..194207797)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (191047183..191116448)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986171 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:190875631-190876830 Neighboring gene NANOG hESC enhancer GRCh37_chr3:190909180-190909700 Neighboring gene OSTN antisense RNA 1 Neighboring gene osteocrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20990 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:191019724-191020249 Neighboring gene urotensin 2B Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:191046750-191047351 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:191047352-191047952 Neighboring gene Sharpr-MPRA regulatory region 6572 Neighboring gene PYDC2 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67093 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:191217087-191217641 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:191217642-191218195 Neighboring gene pyrin domain containing 2 Neighboring gene uncharacterized LOC124909472

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Blagoev B, et al. Nat Biotechnol, 2004 Sep. PMID 15314609
    2. Ymer acts as a multifunctional regulator in nuclear factor-κB and Fas signaling pathways. Tsukiyama T, et al. Mol Med, 2012 May 9. PMID 22331027, Free PMC Article
    3. CCDC50 promotes tumor growth through regulation of lysosome homeostasis. Jia P, et al. EMBO Rep, 2023 Oct 9. PMID 37672005, Free PMC Article
    4. Inhibition of NF-kappaB signaling via tyrosine phosphorylation of Ymer. Kameda H, et al. Biochem Biophys Res Commun, 2009 Jan 23. PMID 19059208
    5. A novel locus for autosomal dominant nonsyndromic hearing loss (DFNA44) maps to chromosome 3q28-29. Modamio-Høybjør S, et al. Hum Genet, 2003 Jan. PMID 12483295

    See all (66) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CCDC50 promotes tumor growth through regulation of lysosome homeostasis.
      Title: CCDC50 promotes tumor growth through regulation of lysosome homeostasis.
    2. Molecular profiling of clinical remission in psoriatic arthritis reveals dysregulation of FOS and CCDC50 genes: a gene expression study.
      Title: Molecular profiling of clinical remission in psoriatic arthritis reveals dysregulation of FOS and CCDC50 genes: a gene expression study.
    3. Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases.
      Title: Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases.
    4. A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection.
      Title: A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection.
    5. Coiled-coil domain containing 50-V2 protein positively regulates neurite outgrowth.
      Title: Coiled-coil domain containing 50-V2 protein positively regulates neurite outgrowth.
    6. Up to now, merely 7 loci have been linked to mid-frequency hearing loss. Only four genetic mid-frequency deafness genes, namely, DFNA10 (EYA4), DFNA8/12 (TECTA), DFNA13 (COL11A2), DFNA44 (CCDC50), have been reported to date. [review]
      Title: Research progress in pathogenic genes of hereditary non-syndromic mid-frequency deafness.
    7. Ymer acts as a regulator downstream of several receptors and that Ymer functions as a positive or negative regulator in a signaling pathway-dependent manner.
      Title: Ymer acts as a multifunctional regulator in nuclear factor-κB and Fas signaling pathways.
    8. CCDC50 is required for survival in mantle cell lymphoma and chronic lymphocytic leukemia cells and controls NFkappaB signaling
      Title: Gene knockdown studies revealed CCDC50 as a candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia.
    9. These findings demonstrate that Ymer is likely to be a negative regulator for the NF-kappaB signaling pathway.
      Title: Inhibition of NF-kappaB signaling via tyrosine phosphorylation of Ymer.
    10. Ymer functions as a novel inhibitor for the down-regulation of the EGF receptor and plays a crucial role for regulating the amount of the EGF receptor on the cell surface membrane
      Title: Suppression of the ligand-mediated down-regulation of epidermal growth factor receptor by Ymer, a novel tyrosine-phosphorylated and ubiquitinated protein.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Autosomal dominant nonsyndromic hearing loss 44
    MedGen: C1843895 OMIM: 607453 GeneReviews: Genetic Hearing Loss Overview
    		not available

    EBI GWAS Catalog

    Description
    GWAS of cerebrospinal fluid tau levels identifies risk variants for Alzheimer's disease.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 50
    Names
    protein Ymer

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008994.1 RefSeqGene

      Range
      5310..74575
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1382

    mRNA and Protein(s)

    1. NM_174908.4 → NP_777568.1  coiled-coil domain-containing protein 50 short isoform

      See identical proteins and their annotated locations for NP_777568.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an in-frame exon in the coding region, compared to variant 2, and encodes the short isoform.
      Source sequence(s)
      AC073365, AJ416916
      Consensus CDS
      CCDS33913.1
      UniProtKB/Swiss-Prot
      Q86VH7, Q8IVM0
      Related
      ENSP00000376250.4, ENST00000392456.4
      Conserved Domains (2) summary
      pfam15295
      Location:7 → 126
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus
      cl25732
      Location:63 → 233
      SMC_N; RecF/RecN/SMC N terminal domain

    2. NM_178335.3 → NP_848018.1  coiled-coil domain-containing protein 50 long isoform

      See identical proteins and their annotated locations for NP_848018.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longer transcript and encodes the long isoform.
      Source sequence(s)
      AC073365, AJ557013
      Consensus CDS
      CCDS33912.1
      UniProtKB/Swiss-Prot
      Q8IVM0
      Related
      ENSP00000376249.4, ENST00000392455.9
      Conserved Domains (1) summary
      pfam15295
      Location:7 → 126
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      191329394..191398659
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011512460.2 → XP_011510762.1  coiled-coil domain-containing protein 50 isoform X1

      Conserved Domains (1) summary
      pfam15295
      Location:7 → 126
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      194145445..194207797
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345382.1 → XP_054201357.1  coiled-coil domain-containing protein 50 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IVM0.1 GenPept UniProtKB/Swiss-Prot:Q8IVM0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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