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CC2D1A coiled-coil and C2 domain containing 1A [ Homo sapiens (human) ]

Gene ID: 54862, updated on 2-Nov-2024

Summary

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Official Symbol
CC2D1Aprovided by HGNC
Official Full Name
coiled-coil and C2 domain containing 1Aprovided by HGNC
Primary source
HGNC:HGNC:30237
See related
Ensembl:ENSG00000132024 MIM:610055; AllianceGenome:HGNC:30237
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
Lgd2; MRT3; TAPE; Aki-1; FREUD-1; Freud-1/Aki1
Summary
This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5'-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities of the protein are inhibited by calcium. A mutation in this gene results in a nonsyndromic form of cognitive disability (MRT3). [provided by RefSeq, Jul 2017]
Expression
Ubiquitous expression in duodenum (RPKM 16.8), small intestine (RPKM 12.5) and 25 other tissues See more
Orthologs
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Genomic context

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See CC2D1A in Genome Data Viewer
Location:
19p13.12
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13906201..13930879)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14032358..14057039)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14017014..14041692)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene nanos C2HC-type zinc finger 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13993737-13994582 Neighboring gene microRNA 181d Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14000391-14000892 Neighboring gene break repair meiotic recombinase recruitment factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10218 Neighboring gene MPRA-validated peak3378 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14046993-14047750 Neighboring gene podocan like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14069830-14070403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14070404-14070976 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene regulatory factor X1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090312-14090838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090839-14091365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14091366-14091891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14093768-14094294 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14096053-14096944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14097836-14098726 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116358-14116886 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116887-14117414 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14117415-14117942

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. 5-HT1A receptors, gene repression, and depression: guilt by association. Albert PR, et al. Neuroscientist, 2004 Dec. PMID 15534042
  2. Expression of Akt kinase-interacting protein 1, a scaffold protein of the PI3K/PDK1/Akt pathway, in pancreatic cancer. Ohtsubo K, et al. Pancreas, 2014 Oct. PMID 25036909
  3. CC2D1A regulates human intellectual and social function as well as NF-κB signaling homeostasis. Manzini MC, et al. Cell Rep, 2014 Aug 7. PMID 25066123, Free PMC Article
  4. The mental retardation gene CC2D1A/Freud-1 encodes a long isoform that binds conserved DNA elements to repress gene transcription. Rogaeva A, et al. Eur J Neurosci, 2007 Aug. PMID 17714190
  5. Novel alterations of CC2D1A as a candidate gene in a Turkish sample of patients with autism spectrum disorder. Sener EF, et al. Int J Neurosci, 2022 Nov. PMID 33287601

See all (105) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow.
    Title: CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow.
  2. Effects of the Cc2d1a/Freud-1 Knockdown in the Hippocampus of BTBR Mice on the Autistic-Like Behavior, Expression of Serotonin 5-HT1A and D2 Dopamine Receptors, and CREB and NF-kB Intracellular Signaling.
    Title: Effects of the Cc2d1a/Freud-1 Knockdown in the Hippocampus of BTBR Mice on the Autistic-Like Behavior, Expression of Serotonin 5-HT(1A) and D2 Dopamine Receptors, and CREB and NF-kB Intracellular Signaling.
  3. Novel alterations of CC2D1A as a candidate gene in a Turkish sample of patients with autism spectrum disorder.
    Title: Novel alterations of CC2D1A as a candidate gene in a Turkish sample of patients with autism spectrum disorder.
  4. Monoallelic Mutations in CC2D1A Suggest a Novel Role in Human Heterotaxy and Ciliary Dysfunction.
    Title: Monoallelic Mutations in CC2D1A Suggest a Novel Role in Human Heterotaxy and Ciliary Dysfunction.
  5. Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer.
    Title: Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer.
  6. Both expressions of CC2D1A and HTR1A genes studied on autism spectrum disorder cases and controls were significantly different
    Title: The roles of CC2D1A and HTR1A gene expressions in autism spectrum disorders.
  7. CC2D1A binds to CHMP4B polymers formed on endosomes to regulate the endosomal sorting pathway.CC2D1A regulates degradation and signaling of EGFR and TLR4.
    Title: CC2D1A and CC2D1B regulate degradation and signaling of EGFR and TLR4.
  8. Aki1 was expressed in human diffuse malignant mesothelioma specimens. Expression correlated with phosphorylated CREB1. Aki1 regulates CREB by modulating protein kinase A activity. The Aki1-CREB axis plays an important role in DMM pathogenesis.
    Title: Akt Kinase-Interacting Protein 1 Signals through CREB to Drive Diffuse Malignant Mesothelioma.
  9. Null mutations in CC2D1A consistently cause a variable spectrum of presentations including ID, ASD, and seizures. CC2D1A regulates NF-kappaB signaling.
    Title: CC2D1A regulates human intellectual and social function as well as NF-κB signaling homeostasis.
  10. All of the pancreatic cancer cell lines expressed Aki1. Silencing of Aki1 in Panc1 cells reduced the phosphorylation of Akt and increased the phosphorylation of cleaved PARP.
    Title: Expression of Akt kinase-interacting protein 1, a scaffold protein of the PI3K/PDK1/Akt pathway, in pancreatic cancer.
Submit: New GeneRIF Correction See all GeneRIFs (32)

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
Intellectual disability, autosomal recessive 3
MedGen: C1838023 OMIM: 608443 GeneReviews: Not available
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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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human coiled-coil and C2 domain containing 1A (CC2D1A) at amino acid residues 783-784 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

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

  • FLJ20241, FLJ41160

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables cadherin binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in apical dendrite arborization IEA
Inferred from Electronic Annotation
more info
  
involved_in endosome organization IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of snRNA transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of canonical NF-kappaB signal transduction HMP PubMed 
involved_in regulation of postsynapse assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of respiratory gaseous exchange by nervous system process IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in centrosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
coiled-coil and C2 domain-containing protein 1A
Names
Akt kinase-interacting protein 1
FRE under dual repression-binding protein 1
TBK1-associated protein in endolysosomes
five prime repressor element under dual repression-binding protein 1
five repressor element under dual repression-binding protein 1
lethal (2) giant discs homolog 2
putative NF-kappa-B-activating protein 023N
putative NFkB activating protein

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_013089.1 RefSeqGene

    Range
    5059..29737
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001411138.1 → NP_001398067.1  coiled-coil and C2 domain-containing protein 1A isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC020916
    Consensus CDS
    CCDS92537.1
    Related
    ENSP00000467526.1, ENST00000589606.5

  2. NM_017721.5 → NP_060191.3  coiled-coil and C2 domain-containing protein 1A isoform 1

    See identical proteins and their annotated locations for NP_060191.3

    Status: REVIEWED

    Source sequence(s)
    BC064981, DB065701
    Consensus CDS
    CCDS42512.1
    UniProtKB/Swiss-Prot
    Q6P1N0, Q7Z435, Q86XV0, Q8NF89, Q9H603, Q9NXI1
    Related
    ENSP00000313601.6, ENST00000318003.11
    Conserved Domains (2) summary
    smart00685
    Location:349 → 407
    DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241
    cd08690
    Location:652 → 809
    C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    13906201..13930879
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439012.1 → XP_047294968.1  coiled-coil and C2 domain-containing protein 1A isoform X1

  2. XM_047439014.1 → XP_047294970.1  coiled-coil and C2 domain-containing protein 1A isoform X2

  3. XM_047439015.1 → XP_047294971.1  coiled-coil and C2 domain-containing protein 1A isoform X3

  4. XM_047439017.1 → XP_047294973.1  coiled-coil and C2 domain-containing protein 1A isoform X5

  5. XM_047439016.1 → XP_047294972.1  coiled-coil and C2 domain-containing protein 1A isoform X4

  6. XM_047439018.1 → XP_047294974.1  coiled-coil and C2 domain-containing protein 1A isoform X6

  7. XM_047439019.1 → XP_047294975.1  coiled-coil and C2 domain-containing protein 1A isoform X7

  8. XM_047439020.1 → XP_047294976.1  coiled-coil and C2 domain-containing protein 1A isoform X8

    Related
    ENSP00000506358.1, ENST00000680977.1

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160022.1 Reference GRCh38.p14 PATCHES

    Range
    118042..142720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332691.1 → XP_054188666.1  coiled-coil and C2 domain-containing protein 1A isoform X1

  2. XM_054332692.1 → XP_054188667.1  coiled-coil and C2 domain-containing protein 1A isoform X2

  3. XM_054332693.1 → XP_054188668.1  coiled-coil and C2 domain-containing protein 1A isoform X3

  4. XM_054332695.1 → XP_054188670.1  coiled-coil and C2 domain-containing protein 1A isoform X5

  5. XM_054332694.1 → XP_054188669.1  coiled-coil and C2 domain-containing protein 1A isoform X4

  6. XM_054332696.1 → XP_054188671.1  coiled-coil and C2 domain-containing protein 1A isoform X6

  7. XM_054332697.1 → XP_054188672.1  coiled-coil and C2 domain-containing protein 1A isoform X7

  8. XM_054332698.1 → XP_054188673.1  coiled-coil and C2 domain-containing protein 1A isoform X8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    14032358..14057039
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321331.1 → XP_054177306.1  coiled-coil and C2 domain-containing protein 1A isoform X1

  2. XM_054321332.1 → XP_054177307.1  coiled-coil and C2 domain-containing protein 1A isoform X2

  3. XM_054321333.1 → XP_054177308.1  coiled-coil and C2 domain-containing protein 1A isoform X3

  4. XM_054321335.1 → XP_054177310.1  coiled-coil and C2 domain-containing protein 1A isoform X5

  5. XM_054321334.1 → XP_054177309.1  coiled-coil and C2 domain-containing protein 1A isoform X4

  6. XM_054321336.1 → XP_054177311.1  coiled-coil and C2 domain-containing protein 1A isoform X6

  7. XM_054321337.1 → XP_054177312.1  coiled-coil and C2 domain-containing protein 1A isoform X7

  8. XM_054321338.1 → XP_054177313.1  coiled-coil and C2 domain-containing protein 1A isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P1N0.1 GenPept UniProtKB/Swiss-Prot:Q6P1N0

Gene LinkOut

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