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 (MRT... See more...

Aliases for CC2D1A Gene

Aliases for CC2D1A Gene

  • Coiled-Coil And C2 Domain Containing 1A 2 3 5
  • Five Prime Repressor Element Under Dual Repression-Binding Protein 1 3 4
  • Coiled-Coil And C2 Domain-Containing Protein 1A 3 4
  • Putative NF-Kappa-B-Activating Protein 023N 3 4
  • FRE Under Dual Repression-Binding Protein 1 3 4
  • Akt Kinase-Interacting Protein 1 3 4
  • Five Repressor Element Under Dual Repression-Binding Protein 1 3
  • Mental Retardation, Nonsyndromic, Autosomal Recessive, 3 2
  • Putative NFkB Activating Protein 3
  • Freud-1/Aki1 3
  • FREUD-1 3
  • Freud-1 4
  • MRT3 3
  • AKI1 4

External Ids for CC2D1A Gene

Previous GeneCards Identifiers for CC2D1A Gene

  • GC19P013865
  • GC19P014016
  • GC19P013588

Summaries for CC2D1A Gene

Entrez Gene Summary for CC2D1A Gene

  • 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]

GeneCards Summary for CC2D1A Gene

CC2D1A (Coiled-Coil And C2 Domain Containing 1A) is a Protein Coding gene. Diseases associated with CC2D1A include Autosomal Recessive Non-Syndromic Intellectual Disability and Non-Syndromic Intellectual Disability. Among its related pathways are Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways. Gene Ontology (GO) annotations related to this gene include obsolete signal transducer activity and DNA-binding transcription factor activity, RNA polymerase II-specific. An important paralog of this gene is CC2D1B.

UniProtKB/Swiss-Prot Summary for CC2D1A Gene

  • Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells. The combination of calcium and ATP specifically inactivates the binding with FRE. May play a role in the altered regulation of HTR1A associated with anxiety and major depression. Mediates HDAC-independent repression of HTR1A promoter in neuronal cell. Performs essential function in controlling functional maturation of synapses (By similarity). Plays distinct roles depending on its localization. When cytoplasmic, acts as a scaffold protein in the PI3K/PDK1/AKT pathway. Repressor of HTR1A when nuclear. In the centrosome, regulates spindle pole localization of the cohesin subunit SCC1/RAD21, thereby mediating centriole cohesion during mitosis.

Gene Wiki entry for CC2D1A Gene

Additional gene information for CC2D1A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CC2D1A Gene

Genomics for CC2D1A Gene

GeneHancer (GH) Regulatory Elements for CC2D1A Gene

Promoters and enhancers for CC2D1A Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CC2D1A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CC2D1A gene promoter:
  • AREB6
  • Elk-1
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • Olf-1
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for CC2D1A Gene

Genomic Locations for CC2D1A Gene
chr19:13,906,143-13,930,880
(GRCh38/hg38)
Size:
24,738 bases
Orientation:
Plus strand
chr19:14,016,956-14,041,693
(GRCh37/hg19)
Size:
24,738 bases
Orientation:
Plus strand

Genomic View for CC2D1A Gene

Genes around CC2D1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CC2D1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CC2D1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CC2D1A Gene

Proteins for CC2D1A Gene

  • Protein details for CC2D1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P1N0-C2D1A_HUMAN
    Recommended name:
    Coiled-coil and C2 domain-containing protein 1A
    Protein Accession:
    Q6P1N0
    Secondary Accessions:
    • Q7Z435
    • Q86XV0
    • Q8NF89
    • Q9H603
    • Q9NXI1

    Protein attributes for CC2D1A Gene

    Size:
    951 amino acids
    Molecular mass:
    104062 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91029.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=BAB15464.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for CC2D1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CC2D1A Gene

Post-translational modifications for CC2D1A Gene

  • Phosphorylation on Ser-208 by CDK1 promotes spindle pole localization and association with SCC1/RAD21.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CC2D1A Gene

Domains & Families for CC2D1A Gene

Gene Families for CC2D1A Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CC2D1A Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CC2D1A Gene

GenScript: Design optimal peptide antigens:
  • Putative NF-kappa-B-activating protein 023N (C2D1A_HUMAN)
  • CC2D1A protein (Q24K25_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6P1N0

UniProtKB/Swiss-Prot:

C2D1A_HUMAN :
  • The C2 domain is required for the repression.
  • Belongs to the CC2D1 family.
Domain:
  • The C2 domain is required for the repression.
Family:
  • Belongs to the CC2D1 family.
genes like me logo Genes that share domains with CC2D1A: view

Function for CC2D1A Gene

Molecular function for CC2D1A Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells. The combination of calcium and ATP specifically inactivates the binding with FRE. May play a role in the altered regulation of HTR1A associated with anxiety and major depression. Mediates HDAC-independent repression of HTR1A promoter in neuronal cell. Performs essential function in controlling functional maturation of synapses (By similarity). Plays distinct roles depending on its localization. When cytoplasmic, acts as a scaffold protein in the PI3K/PDK1/AKT pathway. Repressor of HTR1A when nuclear. In the centrosome, regulates spindle pole localization of the cohesin subunit SCC1/RAD21, thereby mediating centriole cohesion during mitosis.

Phenotypes From GWAS Catalog for CC2D1A Gene

Gene Ontology (GO) - Molecular Function for CC2D1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 16730941
GO:0045296 cadherin binding HDA 25468996
genes like me logo Genes that share ontologies with CC2D1A: view
genes like me logo Genes that share phenotypes with CC2D1A: view

Human Phenotype Ontology for CC2D1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CC2D1A Gene

MGI Knock Outs for CC2D1A:

Animal Model Products

CRISPR Products

miRNA for CC2D1A Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CC2D1A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CC2D1A Gene

Localization for CC2D1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CC2D1A Gene

Cytoplasm. Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CC2D1A gene
Compartment Confidence
nucleus 5
plasma membrane 4
cytosol 4
cytoskeleton 3
mitochondrion 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli fibrillar center (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CC2D1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005815 microtubule organizing center IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with CC2D1A: view

Pathways & Interactions for CC2D1A Gene

genes like me logo Genes that share pathways with CC2D1A: view

Pathways by source for CC2D1A Gene

Gene Ontology (GO) - Biological Process for CC2D1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA 21873635
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling HMP 12761501
genes like me logo Genes that share ontologies with CC2D1A: view

No data available for SIGNOR curated interactions for CC2D1A Gene

Drugs & Compounds for CC2D1A Gene

(1) Drugs for CC2D1A Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7773
genes like me logo Genes that share compounds with CC2D1A: view

Transcripts for CC2D1A Gene

mRNA/cDNA for CC2D1A Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CC2D1A

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CC2D1A Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b · 12c ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c ^ 16 ^ 17a ·
SP1: - - -
SP2: - - - -
SP3: - - - - - - - - - - -
SP4: - - -
SP5:
SP6: - - -
SP7:
SP8: - -
SP9:

ExUns: 17b ^ 18 ^ 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29
SP1: - -
SP2: - -
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for CC2D1A Gene

GeneLoc Exon Structure for
CC2D1A
ECgene alternative splicing isoforms for
CC2D1A

Expression for CC2D1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CC2D1A Gene

Protein differential expression in normal tissues from HIPED for CC2D1A Gene

This gene is overexpressed in Brain (7.9) and Pancreas (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CC2D1A Gene



Protein tissue co-expression partners for CC2D1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CC2D1A Gene:

CC2D1A

SOURCE GeneReport for Unigene cluster for CC2D1A Gene:

Hs.269592

Evidence on tissue expression from TISSUES for CC2D1A Gene

  • Nervous system(4.8)
  • Kidney(4.5)
  • Lung(4.3)
  • Liver(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CC2D1A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
Thorax:
  • chest wall
  • heart
Abdomen:
  • abdominal wall
Limb:
  • foot
  • lower limb
General:
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
genes like me logo Genes that share expression patterns with CC2D1A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CC2D1A Gene

Orthologs for CC2D1A Gene

This gene was present in the common ancestor of animals.

Orthologs for CC2D1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CC2D1A 33 32
  • 98.84 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CC2D1A 33 32
  • 88.22 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CC2D1A 33 32
  • 87.73 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cc2d1a 32
  • 81.47 (n)
mouse
(Mus musculus)
Mammalia Cc2d1a 17 33 32
  • 81.27 (n)
oppossum
(Monodelphis domestica)
Mammalia CC2D1A 33
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CC2D1A 33
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 33
  • 63 (a)
OneToMany
-- 33
  • 56 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia cc2d1a 32
  • 58.09 (n)
zebrafish
(Danio rerio)
Actinopterygii CC2D1A 33
  • 47 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta l(2)gd1 33 32
  • 48.92 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010539 32
  • 48.58 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_Y37H9A.3 32
  • 43.35 (n)
Y37H9A.3 33
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 40 (a)
ManyToMany
-- 33
  • 32 (a)
ManyToMany
-- 33
  • 31 (a)
ManyToMany
Species where no ortholog for CC2D1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CC2D1A Gene

ENSEMBL:
Gene Tree for CC2D1A (if available)
TreeFam:
Gene Tree for CC2D1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CC2D1A: view image

Paralogs for CC2D1A Gene

Paralogs for CC2D1A Gene

(1) SIMAP similar genes for CC2D1A Gene using alignment to 4 proteins:

  • C2D1A_HUMAN
  • K7EJY5_HUMAN
  • K7EMP1_HUMAN
  • Q24K25_HUMAN
genes like me logo Genes that share paralogs with CC2D1A: view

Variants for CC2D1A Gene

Sequence variations from dbSNP and Humsavar for CC2D1A Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1011061003 uncertain-significance, History of neurodevelopmental disorder 13,906,457(+) G/A coding_sequence_variant, missense_variant
rs10410239 likely-benign, benign, not specified, History of neurodevelopmental disorder 13,919,876(+) T/C coding_sequence_variant, synonymous_variant
rs11669628 likely-benign, benign, not specified, History of neurodevelopmental disorder 13,930,083(+) G/A/C coding_sequence_variant, missense_variant
rs11883041 likely-benign, benign, not specified, History of neurodevelopmental disorder, - 13,918,814(+) A/C coding_sequence_variant, missense_variant
rs1394531439 uncertain-significance, History of neurodevelopmental disorder 13,913,557(+) G/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CC2D1A Gene

Variant ID Type Subtype PubMed ID
nsv833757 CNV loss 17160897
nsv833760 CNV loss 17160897
nsv953979 CNV deletion 24416366

Variation tolerance for CC2D1A Gene

Residual Variation Intolerance Score: 97.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.58; 86.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CC2D1A Gene

Human Gene Mutation Database (HGMD)
CC2D1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CC2D1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CC2D1A Gene

Disorders for CC2D1A Gene

MalaCards: The human disease database

(2) MalaCards diseases for CC2D1A Gene - From: HGMD, ClinVar, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
autosomal recessive non-syndromic intellectual disability
  • autosomal recessive mental retardation
non-syndromic intellectual disability
  • intellectual disability, non syndromic
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

C2D1A_HUMAN
  • Mental retardation, autosomal recessive 3 (MRT3) [MIM:608443]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Non-syndromic mental retardation patients do not manifest other clinical signs. {ECO:0000269 PubMed:16033914}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CC2D1A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CC2D1A: view

No data available for Genatlas for CC2D1A Gene

Publications for CC2D1A Gene

  1. The CC2D1A, a member of a new gene family with C2 domains, is involved in autosomal recessive non-syndromic mental retardation. (PMID: 16033914) Basel-Vanagaite L … Shohat M (Journal of medical genetics 2006) 2 3 4 56
  2. Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK signaling pathways. (PMID: 12761501) Matsuda A … Sugano S (Oncogene 2003) 2 3 4 56
  3. Mitotic phosphorylation of Aki1 at Ser208 by cyclin B1-Cdk1 complex. (PMID: 20171170) Nakamura A … Fujita N (Biochemical and biophysical research communications 2010) 3 4 56
  4. Further assessment of the complement component 2 and factor B region associated with age-related macular degeneration. (PMID: 18806297) McKay GJ … Hughes AE (Investigative ophthalmology & visual science 2009) 3 43 56
  5. The Freud-1/CC2D1A family: transcriptional regulators implicated in mental retardation. (PMID: 17394259) Rogaeva A … Albert PR (Journal of neuroscience research 2007) 3 23 56

Products for CC2D1A Gene

Sources for CC2D1A Gene