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

Gene ID: 152137, updated on 7-Apr-2024

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; 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
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Genomic context

See CCDC50 in Genome Data Viewer
Location:
3q28
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (191329394..191398659)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (194145445..194207797)
105.20220307 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

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 Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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

NCBI Reference Sequences (RefSeq)

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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_174908.4NP_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: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, ENST00000392455.9
    Conserved Domains (1) summary
    pfam15295
    Location:7126
    CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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_011512460.2XP_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

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_054345382.1XP_054201357.1  coiled-coil domain-containing protein 50 isoform X1