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

Gene ID: 152137, updated on 13-Feb-2019

Summary

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
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

Genomic context

See CCDC50 in Genome Data Viewer
Location:
3q28
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (191329082..191398670)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (191046874..191116459)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986171 Neighboring gene OSTN antisense RNA 1 Neighboring gene osteocrin Neighboring gene urotensin 2B Neighboring gene uncharacterized LincR-0002 Neighboring gene pyrin domain containing 2 Neighboring gene uncharacterized LOC105374275

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Deafness, autosomal dominant 44 Compare labs

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5001..74586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_174908.3NP_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
    Q8IVM0
    Related
    ENSP00000376250.4, ENST00000392456.4
    Conserved Domains (2) summary
    pfam15295
    Location:7126
    CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus
    cl25732
    Location:63233
    SMC_N; RecF/RecN/SMC N terminal domain
  2. NM_178335.3NP_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, ENST00000392455.8
    Conserved Domains (1) summary
    pfam15295
    Location:7126
    CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    191329082..191398670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    pfam15295
    Location:7126
    CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus
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