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

Gene ID: 54520, updated on 7-Apr-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, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 7.7), testis (RPKM 7.6) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (117915481..118014070, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (118348803..118447355, complement)
105.20220307 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. The landscape of recombination in African Americans. Hinch AG, et al. Nature, 2011 Jul 20. PMID 21775986, Free PMC Article
  3. 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
  4. COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Phillips-Krawczak CA, et al. Mol Biol Cell, 2015 Jan 1. PMID 25355947, Free PMC Article
  5. Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling. McNally KE, et al. Nat Cell Biol, 2017 Oct. PMID 28892079, Free PMC Article

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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)

Genotypes

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_2023_10

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

  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

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

  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

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