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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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CC2D1A
coiled-coil and C2 domain containing 1A
Chromosome 19 Β· 19p13.12
NCBI Gene: 54862Ensembl: ENSG00000132024.19HGNC: HGNC:30237UniProt: Q6P1N0
113PubMed Papers
1Diseases
0Drugs
63Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA polymerase II cis-regulatory region sequence-specific DNA bindingcadherin bindingpositive regulation of canonical NF-kappaB signal transductionnegative regulation of snRNA transcription by RNA polymerase IIIntellectual developmental disorder, autosomal recessive 3
✦AI Summary

CC2D1A (coiled-coil and C2 domain containing 1A) is a multifunctional scaffold protein that plays critical roles in neurodevelopment and cellular signaling. The protein functions as a transcriptional repressor of the HTR1A (serotonin-1A receptor) gene, binding to specific DNA elements and mediating calcium-dependent regulation of transcription 1. CC2D1A exhibits diverse subcellular localizations with distinct functions: when nuclear, it acts as a transcriptional repressor; when cytoplasmic, it serves as a scaffold in PI3K/AKT signaling pathways; and in centrosomes, it regulates spindle pole organization during mitosis. Recent studies have revealed a crucial role in ciliogenesis, with CC2D1A expression in ciliated tissues including the brain's ventricular zone, kidney, and left-right organizer 2. Loss of CC2D1A function disrupts primary cilia formation and cerebrospinal fluid circulation 2. The protein also regulates NF-ΞΊB signaling homeostasis, with both gain and loss of function increasing NF-ΞΊB activation 3. Proteomic analyses identify CC2D1A as uniquely enriched in postsynaptic compartments, interacting with proteins involved in RNA regulation and synaptic function 4. Biallelic loss-of-function mutations cause autosomal recessive intellectual disability, often accompanied by autism spectrum disorder, seizures, and heterotaxy 35, highlighting its essential role in neurodevelopmental processes.

Sources cited
1
CC2D1A functions as a transcriptional repressor of HTR1A gene and contains conserved domains including C2 calcium-dependent phospholipid binding domain
PMID: 17394259
2
CC2D1A is expressed in ciliated tissues and loss leads to defective ciliogenesis, cardiac heterotaxy, cystic kidneys, and abnormal CSF circulation
PMID: 39168639
3
CC2D1A regulates NF-ΞΊB signaling homeostasis and mutations cause intellectual disability, autism spectrum disorder, and seizures
PMID: 25066123
4
CC2D1A mutations are associated with heterotaxy through loss-of-function mechanism and ciliary dysfunction
PMID: 33196317
5
CC2D1A is enriched in postsynaptic compartments and interacts with proteins involved in RNA regulation and synaptic function
PMID: 40667103
Disease Associationsβ“˜1
Intellectual developmental disorder, autosomal recessive 3UniProt
Pathogenic Variants63
NM_017721.5(CC2D1A):c.2454+1G>ALikely pathogenic
not provided|Intellectual disability, autosomal recessive 3
β˜…β˜…β˜†β˜†2026
NM_017721.5(CC2D1A):c.61-2A>GLikely pathogenic
Inborn genetic diseases|Intellectual disability, autosomal recessive 3|not provided|Clear cell carcinoma of kidney
β˜…β˜…β˜†β˜†2025
NM_017721.5(CC2D1A):c.2693del (p.Gly898fs)Pathogenic
Intellectual disability, autosomal recessive 3|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 898
NM_017721.5(CC2D1A):c.179_180insCA (p.Glu60fs)Pathogenic
not provided|Intellectual disability, autosomal recessive 3
β˜…β˜…β˜†β˜†2024β†’ Residue 60
NM_017721.5(CC2D1A):c.2710+1G>ALikely pathogenic
not provided|Intellectual disability, autosomal recessive 3
β˜…β˜…β˜†β˜†2024
NM_017721.5(CC2D1A):c.1061dup (p.Arg355fs)Pathogenic
not provided|Intellectual disability, autosomal recessive 3
β˜…β˜…β˜†β˜†2024β†’ Residue 355
NM_017721.5(CC2D1A):c.511_513+1delLikely pathogenic
Intellectual disability, autosomal recessive 3|not provided
β˜…β˜…β˜†β˜†2024
NM_017721.5(CC2D1A):c.621C>G (p.Tyr207Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 207
NM_017721.5(CC2D1A):c.2225+1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_017721.5(CC2D1A):c.2012del (p.Pro671fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 671
NM_017721.5(CC2D1A):c.1264C>T (p.Gln422Ter)Likely pathogenic
Ciliopathy
β˜…β˜†β˜†β˜†2024β†’ Residue 422
NM_017721.5(CC2D1A):c.1186C>T (p.Arg396Ter)Likely pathogenic
Ciliopathy
β˜…β˜†β˜†β˜†2024β†’ Residue 396
NM_017721.5(CC2D1A):c.1468+1G>CLikely pathogenic
Intellectual disability, autosomal recessive 3
β˜…β˜†β˜†β˜†2024
NM_017721.5(CC2D1A):c.959dup (p.Asp321fs)Likely pathogenic
Intellectual disability, autosomal recessive 3
β˜…β˜†β˜†β˜†2024β†’ Residue 321
NM_017721.5(CC2D1A):c.1357-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_017721.5(CC2D1A):c.1117_1121dup (p.Lys374fs)Likely pathogenic
Intellectual disability, autosomal recessive 3
β˜…β˜†β˜†β˜†2024β†’ Residue 374
NM_017721.5(CC2D1A):c.1528C>T (p.Arg510Ter)Likely pathogenic
Intellectual disability, autosomal recessive 3
β˜…β˜†β˜†β˜†2024β†’ Residue 510
NM_017721.5(CC2D1A):c.2711-2A>GLikely pathogenic
Intellectual disability, autosomal recessive 3
β˜…β˜†β˜†β˜†2024
NM_017721.5(CC2D1A):c.1048G>T (p.Glu350Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 350
NM_017721.5(CC2D1A):c.313-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
View on ClinVar β†—
Related Genes
CXXC5Shared pathway100%C18orf32Shared pathway100%LURAP1LShared pathway100%TMEM101Shared pathway100%TMEM9BShared pathway100%CHMP6Protein interaction100%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
Click a node to explore
CC2D1ACXXC5C18orf32LURAP1LTMEM101TMEM9BCHMP6
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q6P1N0
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.65LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.53 [0.43–0.65]
RankingsWhere CC2D1A stands among ~20K protein-coding genes
  • #4,182of 20,598
    Most Researched113 Β· top quartile
  • #1,125of 5,498
    Most Pathogenic Variants63 Β· top quartile
  • #4,695of 17,882
    Most Constrained (LOEUF)0.65
Genes detectedCC2D1A
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow.
PMID: 39168639
Life Sci Alliance Β· 2024
1.00
2
CC2D1A regulates human intellectual and social function as well as NF-ΞΊB signaling homeostasis.
PMID: 25066123
Cell Rep Β· 2014
0.90
3
The roles of CC2D1A and HTR1A gene expressions in autism spectrum disorders.
PMID: 26782176
Metab Brain Dis Β· 2016
0.80
4
Monoallelic Mutations in
PMID: 33196317
Circ Genom Precis Med Β· 2020
0.70
5
The Freud-1/CC2D1A family: transcriptional regulators implicated in mental retardation.
PMID: 17394259
J Neurosci Res Β· 2007
0.60