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

Gene ID: 57545, updated on 3-Apr-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
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Genomic context

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Location:
4p15.32
Exon count:
40
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (15469865..15601557)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (15451777..15583448)
105.20220307 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
  • 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. Exome Analysis Reveals Novel Missense and Deletion Variants in the CC2D2A Gene as Causative of Joubert Syndrome. Cabrita Pinto RL, et al. Genes (Basel), 2023 Mar 28. PMID 37107568, Free PMC Article
  2. New insights into CC2D2A-related Joubert syndrome. Harion M, et al. J Med Genet, 2023 Jun. PMID 36319078
  3. 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
  4. Whole exome sequencing resolves complex phenotype and identifies CC2D2A mutations underlying non-syndromic rod-cone dystrophy. Méjécase C, et al. Clin Genet, 2019 Feb. PMID 30267408
  5. Diagnostic use of computational retrotransposon detection: Successful definition of pathogenetic mechanism in a ciliopathy phenotype. Takenouchi T, et al. Am J Med Genet A, 2017 May. PMID 28374938

See all (32) 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_2023_10

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

Gene LinkOut

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