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

    Gene ID: 57545, updated on 28-Oct-2024

    Summary

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    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; AllianceGenome:HGNC:29253
    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; RP93; JBTS9; COACH2
    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
    mouse all
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    Genomic context

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    See CC2D2A in Genome Data Viewer
    Location:
    4p15.32
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (15469865..15601557)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (15451777..15583448)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (15471489..15603180)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene C1QTNF7 antisense RNA 1 Neighboring gene C1q and TNF related 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21339 Neighboring gene uncharacterized LOC107986185 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:15480526-15481176 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:15503443-15503998 Neighboring gene uncharacterized LOC124900672 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:15545311-15545892 Neighboring gene uncharacterized LOC124900671 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:15637196-15637392 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:15648787-15649012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15297 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15298 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:15656873-15657050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21340 Neighboring gene F-box and leucine rich repeat protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21343 Neighboring gene family with sequence similarity 200 member B Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:15696758-15697354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15300 Neighboring gene ribosomal protein L10a pseudogene 7 Neighboring gene bone marrow stromal cell antigen 1

    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 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. New insights into CC2D2A-related Joubert syndrome. Harion M, et al. J Med Genet, 2023 Jun. PMID 36319078
    2. CC2D2A, encoding a coiled-coil and C2 domain protein, causes autosomal-recessive mental retardation with retinitis pigmentosa. Noor A, et al. Am J Hum Genet, 2008 Apr. PMID 18387594, Free PMC Article
    3. Identification of CC2D2A as a Meckel syndrome gene adds an important piece to the ciliopathy puzzle. Tallila J, et al. Am J Hum Genet, 2008 Jun. PMID 18513680, Free PMC Article
    4. Whole exome sequencing identified a novel missense alteration in CC2D2A causing Joubert syndrome 9 in a Pakhtun family. Khan MI, et al. J Gene Med, 2021 Jan. PMID 32989887
    5. CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation. Mougou-Zerelli S, et al. Hum Mutat, 2009 Nov. PMID 19777577, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. New insights into CC2D2A-related Joubert syndrome.
      Title: New insights into CC2D2A-related Joubert syndrome.
    2. Exome Analysis Reveals Novel Missense and Deletion Variants in the CC2D2A Gene as Causative of Joubert Syndrome.
      Title: Exome Analysis Reveals Novel Missense and Deletion Variants in the CC2D2A Gene as Causative of Joubert Syndrome.
    3. Update of genetic variants in CEP120 and CC2D2A-With an emphasis on genotype-phenotype correlations, tissue specific transcripts and exploring mutation specific exon skipping therapies.
      Title: Update of genetic variants in CEP120 and CC2D2A-With an emphasis on genotype-phenotype correlations, tissue specific transcripts and exploring mutation specific exon skipping therapies.
    4. Primary cilia biogenesis and associated retinal ciliopathies.
      Title: Primary cilia biogenesis and associated retinal ciliopathies.
    5. Whole exome sequencing identified a novel missense alteration in CC2D2A causing Joubert syndrome 9 in a Pakhtun family.
      Title: Whole exome sequencing identified a novel missense alteration in CC2D2A causing Joubert syndrome 9 in a Pakhtun family.
    6. Atypical, milder presentation in a child with CC2D2A and KIDINS220 variants.
      Title: Atypical, milder presentation in a child with CC2D2A and KIDINS220 variants.
    7. Our study identifies for the first time CC2D2A mutations in isolated RCD and underlines the power of WES to decipher complex phenotypes.
      Title: Whole exome sequencing resolves complex phenotype and identifies CC2D2A mutations underlying non-syndromic rod-cone dystrophy.
    8. Mutations in CC2D2A were the most common cause of an antenatal cystic kidney disease and a suspected ciliopathy in Saudi Arabian cohort.
      Title: Genetic spectrum of Saudi Arabian patients with antenatal cystic kidney disease and ciliopathy phenotypes using a targeted renal gene panel.
    9. Using a dedicated bioinformatics algorithm for TE detection, we identified an exonic retrotransposon insertion of L1 to the CC2D2A locus in a patient with Meckel-Gruber syndrome, the most severe form of the ciliopathy phenotypes.
      Title: Diagnostic use of computational retrotransposon detection: Successful definition of pathogenetic mechanism in a ciliopathy phenotype.
    10. these data support a model where CC2D2A associates with NINL to provide a docking point for cilia-directed cargo vesicles, suggesting a mechanism by which transition zone proteins can control the protein content of the ciliary compartment.
      Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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

    Associated conditions

    Description Tests
    COACH syndrome 2
    MedGen: C5436837 OMIM: 619111 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
    Retinitis pigmentosa 93
    MedGen: C5676970 OMIM: 619845 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1345

    Gene Ontology Provided by GOA

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

    General protein information

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

    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_013035.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001080522.2 → NP_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
      A6ND97, B3FW08, D6RB72, E7EP21, E9PEV5, Q3SYP3, Q9H8A7, Q9P2K1
      UniProtKB/TrEMBL
      A0A140T8Y7
      Related
      ENSP00000421809.1, ENST00000503292.6
      Conserved Domains (5) summary
      COG1340
      Location:427 → 549
      COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]
      pfam10172
      Location:1066 → 1099
      DDA1; Det1 complexing ubiquitin ligase
      pfam15625
      Location:645 → 819
      CC2D2AN-C2; CC2D2A N-terminal C2 domain
      pfam17661
      Location:131 → 383
      DUF5523; Family of unknown function (DUF5523)
      cl14603
      Location:1097 → 1135
      C2; C2 domain

    2. NM_001164720.3 → NP_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, ENST00000515124.6

    3. NM_001378615.1 → NP_001365544.1  coiled-coil and C2 domain-containing protein 2A isoform a

      Status: REVIEWED

      Source sequence(s)
      AC007016, AC116651
      Consensus CDS
      CCDS47026.1
      UniProtKB/Swiss-Prot
      A6ND97, B3FW08, D6RB72, E7EP21, E9PEV5, Q3SYP3, Q9H8A7, Q9P2K1
      UniProtKB/TrEMBL
      A0A140T8Y7
      Related
      ENSP00000403465.1, ENST00000424120.6
      Conserved Domains (5) summary
      COG1340
      Location:427 → 549
      COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]
      pfam10172
      Location:1066 → 1099
      DDA1; Det1 complexing ubiquitin ligase
      pfam15625
      Location:645 → 819
      CC2D2AN-C2; CC2D2A N-terminal C2 domain
      pfam17661
      Location:131 → 383
      DUF5523; Family of unknown function (DUF5523)
      cl14603
      Location:1097 → 1135
      C2; C2 domain

    4. NM_001378617.1 → NP_001365546.1  coiled-coil and C2 domain-containing protein 2A isoform d

      Status: REVIEWED

      Source sequence(s)
      AC007016, AC116651
      Consensus CDS
      CCDS93481.1
      UniProtKB/TrEMBL
      A0A140T8Y7, H0Y941
      Related
      ENSP00000422931.2, ENST00000506643.5
      Conserved Domains (5) summary
      COG1340
      Location:378 → 500
      COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]
      pfam10172
      Location:1017 → 1050
      DDA1; Det1 complexing ubiquitin ligase
      pfam15625
      Location:596 → 770
      CC2D2AN-C2; CC2D2A N-terminal C2 domain
      pfam17661
      Location:82 → 334
      DUF5523; Family of unknown function (DUF5523)
      cl14603
      Location:1048 → 1086
      C2; C2 domain

    5. NM_020785.2 → NP_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, ENST00000503658.2

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      15469865..15601557
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416010.1 → XP_047271966.1  coiled-coil and C2 domain-containing protein 2A isoform X2

      Related
      ENSP00000501728.1, ENST00000676337.1

    2. XM_011513872.4 → XP_011512174.1  coiled-coil and C2 domain-containing protein 2A isoform X1

      UniProtKB/TrEMBL
      A0A494C0X1
      Conserved Domains (1) summary
      pfam15625
      Location:645 → 816
      CC2D2AN-C2; CC2D2A N-terminal C2 domain

    3. XM_011513874.3 → XP_011512176.1  coiled-coil and C2 domain-containing protein 2A isoform X3

      See identical proteins and their annotated locations for XP_011512176.1

      UniProtKB/Swiss-Prot
      Q9P2K1
      Related
      ENSP00000427221.1, ENST00000507954.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      15451777..15583448
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350591.1 → XP_054206566.1  coiled-coil and C2 domain-containing protein 2A isoform X2

    2. XM_054350590.1 → XP_054206565.1  coiled-coil and C2 domain-containing protein 2A isoform X1

    3. XM_054350592.1 → XP_054206567.1  coiled-coil and C2 domain-containing protein 2A isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P2K1.3 GenPept UniProtKB/Swiss-Prot:Q9P2K1

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