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    CCDC93 coiled-coil domain containing 93 [ Homo sapiens (human) ]

    Gene ID: 54520, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CCDC93provided by HGNC
    Official Full Name
    coiled-coil domain containing 93provided by HGNC
    Primary source
    HGNC:HGNC:25611
    See related
    Ensembl:ENSG00000125633 MIM:620553; AllianceGenome:HGNC:25611
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Involved in Golgi to plasma membrane transport and endocytic recycling. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 7.7), testis (RPKM 7.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC93 in Genome Data Viewer
    Location:
    2q14.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (117915481..118014070, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (118348803..118447355, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (118673057..118771646, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:118615796-118616748 Neighboring gene 5-hydroxytryptamine receptor 5B, pseudogene Neighboring gene uncharacterized LOC101929908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11895 Neighboring gene RNA, 7SL, cytoplasmic 111, pseudogene Neighboring gene uncharacterized LOC102723413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16438

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. A common variant in CCDC93 protects against myocardial infarction and cardiovascular mortality by regulating endosomal trafficking of low-density lipoprotein receptor. Rimbert A, et al. Eur Heart J, 2020 Mar 1. PMID 31630160
    2. Genetic variation in CCDC93 is associated with elevated central systolic blood pressure, impaired arterial relaxation, and mitochondrial dysfunction. Kumar N, et al. PLoS Genet, 2024 Sep. PMID 39250516, Free PMC Article
    3. The landscape of recombination in African Americans. Hinch AG, et al. Nature, 2011 Jul 20. PMID 21775986, Free PMC Article
    4. Recruitment of the endosomal WASH complex is mediated by the extended 'tail' of Fam21 binding to the retromer protein Vps35. Harbour ME, et al. Biochem J, 2012 Feb 15. PMID 22070227
    5. Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Healy MD, et al. Cell, 2023 May 11. PMID 37172566, Free PMC Article

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic variation in CCDC93 is associated with elevated central systolic blood pressure, impaired arterial relaxation, and mitochondrial dysfunction.
      Title: Genetic variation in CCDC93 is associated with elevated central systolic blood pressure, impaired arterial relaxation, and mitochondrial dysfunction.
    2. A common variant in CCDC93 protects against myocardial infarction and cardiovascular mortality by regulating endosomal trafficking of low-density lipoprotein receptor.
      Title: A common variant in CCDC93 protects against myocardial infarction and cardiovascular mortality by regulating endosomal trafficking of low-density lipoprotein receptor.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    The landscape of recombination in African Americans.
    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

    Clone Names

    • FLJ10996, FLJ25197, MGC13033

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to plasma membrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Golgi to plasma membrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 93

    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.

    mRNA and Protein(s)

    1. NM_019044.5 → NP_061917.3  coiled-coil domain-containing protein 93

      See identical proteins and their annotated locations for NP_061917.3

      Status: VALIDATED

      Source sequence(s)
      AC009404, AY726577, BC012052, BC028609, BU621185
      Consensus CDS
      CCDS2121.2
      UniProtKB/Swiss-Prot
      A8K3V7, Q4LE78, Q53TJ2, Q567U6, Q8TBX5, Q9H6R5, Q9NV15
      UniProtKB/TrEMBL
      F8W9X7
      Related
      ENSP00000365477.2, ENST00000376300.7
      Conserved Domains (2) summary
      pfam08202
      Location:212 → 398
      MIS13; Mis12-Mtw1 protein family
      pfam09762
      Location:29 → 206
      KOG2701; Coiled-coil domain-containing protein (DUF2037)

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      117915481..118014070 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011511359.2 → XP_011509661.2  coiled-coil domain-containing protein 93 isoform X1

      UniProtKB/TrEMBL
      F8W9X7

    2. XM_011511361.1 → XP_011509663.1  coiled-coil domain-containing protein 93 isoform X2

      UniProtKB/TrEMBL
      F8W9X7
      Conserved Domains (1) summary
      pfam09762
      Location:1 → 110
      KOG2701; Coiled-coil domain-containing protein (DUF2037)

    3. XM_047444816.1 → XP_047300772.1  coiled-coil domain-containing protein 93 isoform X3

    4. XM_006712600.3 → XP_006712663.2  coiled-coil domain-containing protein 93 isoform X5

    5. XM_011511363.3 → XP_011509665.2  coiled-coil domain-containing protein 93 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      118348803..118447355 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342645.1 → XP_054198620.1  coiled-coil domain-containing protein 93 isoform X1

      UniProtKB/TrEMBL
      F8W9X7

    2. XM_054342646.1 → XP_054198621.1  coiled-coil domain-containing protein 93 isoform X2

      UniProtKB/TrEMBL
      F8W9X7

    3. XM_054342647.1 → XP_054198622.1  coiled-coil domain-containing protein 93 isoform X3

    4. XM_054342649.1 → XP_054198624.1  coiled-coil domain-containing protein 93 isoform X5

    5. XM_054342648.1 → XP_054198623.1  coiled-coil domain-containing protein 93 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q567U6.2 GenPept UniProtKB/Swiss-Prot:Q567U6

    Gene LinkOut

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

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