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CC2D2A coiled-coil and C2 domain containing 2A [ Homo sapiens (human) ]

Gene ID: 57545, updated on 5-Aug-2018

Summary

Official Symbol
CC2D2Aprovided by HGNC
Official Full Name
coiled-coil and C2 domain containing 2Aprovided by HGNC
Primary source
HGNC:HGNC:29253
See related
Ensembl:ENSG00000048342 MIM:612013; Vega:OTTHUMG00000160255
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
MKS6; JBTS9
Summary
This gene encodes a coiled-coil and calcium binding domain protein that appears to play a critical role in cilia formation. Mutations in this gene cause Meckel syndrome type 6, as well as Joubert syndrome type 9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
Expression
Ubiquitous expression in kidney (RPKM 3.7), endometrium (RPKM 3.2) and 23 other tissues See more
Orthologs

Genomic context

See CC2D2A in Genome Data Viewer
Location:
4p15.32
Exon count:
40
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (15468660..15601971)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (15471489..15603594)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929095 Neighboring gene C1q and TNF related 7 Neighboring gene uncharacterized LOC107986185 Neighboring gene F-box and leucine rich repeat protein 5 Neighboring gene family with sequence similarity 200 member B Neighboring gene ribosomal protein L10a pseudogene 7 Neighboring gene bone marrow stromal cell antigen 1

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
COACH syndrome
MedGen: C1857662 OMIM: 216360 GeneReviews: Not available
Compare labs
Joubert syndrome 9
MedGen: C2676788 OMIM: 612285 GeneReviews: Joubert Syndrome
Compare labs
Meckel syndrome type 6
MedGen: C2676790 OMIM: 612284 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of conduct disorder symptomatology.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from BioSystems

  • Anchoring of the basal body to the plasma membrane, organism-specific biosystem (from REACTOME)
    Anchoring of the basal body to the plasma membrane, organism-specific biosystemCilium biogenesis is initiated by the docking of basal bodies, a centriole-derived organelle, to the plasma membrane (reviewed in Reiter et al, 2012). The centriole consists of a multiprotein core su...
  • Cilium Assembly, organism-specific biosystem (from REACTOME)
    Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1345

Gene Ontology Provided by GOA

Process Evidence Code Pubs
axoneme assembly IEA
Inferred from Electronic Annotation
more info
 
camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
ciliary basal body-plasma membrane docking TAS
Traceable Author Statement
more info
 
cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
determination of left/right symmetry IEA
Inferred from Electronic Annotation
more info
 
embryonic brain development IEA
Inferred from Electronic Annotation
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
motile cilium assembly IEA
Inferred from Electronic Annotation
more info
 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
non-motile cilium assembly IEA
Inferred from Electronic Annotation
more info
 
protein localization to ciliary transition zone IEA
Inferred from Electronic Annotation
more info
 
smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
MKS complex ISS
Inferred from Sequence or Structural Similarity
more info
 
ciliary transition zone ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
coiled-coil and C2 domain-containing protein 2A

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_013035.1 RefSeqGene

    Range
    5001..136692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_697

mRNA and Protein(s)

  1. NM_001080522.2NP_001073991.2  coiled-coil and C2 domain-containing protein 2A isoform a

    See identical proteins and their annotated locations for NP_001073991.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    BX647334, CF528984, EU450799, N35522
    Consensus CDS
    CCDS47026.1
    UniProtKB/Swiss-Prot
    Q9P2K1
    Related
    ENSP00000421809.1, OTTHUMP00000217873, ENST00000503292.5, OTTHUMT00000359906
    Conserved Domains (4) summary
    pfam10172
    Location:10661099
    DDA1; Det1 complexing ubiquitin ligase
    pfam13863
    Location:474580
    DUF4200; Domain of unknown function (DUF4200)
    pfam15625
    Location:645816
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    cl14603
    Location:10971135
    C2; C2 domain
  2. NM_001164720.1NP_001158192.1  coiled-coil and C2 domain-containing protein 2A isoform c

    See identical proteins and their annotated locations for NP_001158192.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the presence and absence of exons at its 3' end, compared to variant 1. The encoded isoform (c) has a distinct and significantly shorter C-terminus, compared to isoform a.
    Source sequence(s)
    AI376394, BC053865, N35522
    Consensus CDS
    CCDS54744.1
    UniProtKB/Swiss-Prot
    Q9P2K1
    Related
    ENSP00000424368.1, OTTHUMP00000217876, ENST00000515124.5, OTTHUMT00000359909
  3. NM_020785.2NP_065836.2  coiled-coil and C2 domain-containing protein 2A isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region that results in a frameshift, and differs in the presence and absence of exons at its 3' end, compared to variant 1. The encoded isoform (b) has a distinct and significantly shorter C-terminus, compared to isoform a.
    Source sequence(s)
    AI376394, BC053865, BC070395, DA860072, N35522
    Consensus CDS
    CCDS47027.2
    UniProtKB/Swiss-Prot
    Q9P2K1
    Related
    ENSP00000426846.1, OTTHUMP00000217877, ENST00000503658.2, OTTHUMT00000359910

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    15468660..15601971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513874.2XP_011512176.1  coiled-coil and C2 domain-containing protein 2A isoform X4

    See identical proteins and their annotated locations for XP_011512176.1

    UniProtKB/Swiss-Prot
    Q9P2K1
    Related
    ENSP00000427221.1, OTTHUMP00000217881, ENST00000507954.5, OTTHUMT00000359917
  2. XM_005248177.1XP_005248234.1  coiled-coil and C2 domain-containing protein 2A isoform X1

    See identical proteins and their annotated locations for XP_005248234.1

    UniProtKB/Swiss-Prot
    Q9P2K1
    Conserved Domains (4) summary
    pfam10172
    Location:10661099
    DDA1; Det1 complexing ubiquitin ligase
    pfam13863
    Location:474580
    DUF4200; Domain of unknown function (DUF4200)
    pfam15625
    Location:645816
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
    cl14603
    Location:10971135
    C2; C2 domain
  3. XM_011513872.3XP_011512174.1  coiled-coil and C2 domain-containing protein 2A isoform X3

    Conserved Domains (1) summary
    pfam15625
    Location:645816
    CC2D2AN-C2; CC2D2A N-terminal C2 domain
  4. XM_017008482.1XP_016863971.1  coiled-coil and C2 domain-containing protein 2A isoform X2

    Related
    ENSP00000374303.6, OTTHUMP00000281051, ENST00000389652.9, OTTHUMT00000487863

RNA

  1. XR_001741296.1 RNA Sequence

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