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Aliases for CNGA1 Gene

Aliases for CNGA1 Gene

  • Cyclic Nucleotide Gated Channel Alpha 1 2 3 5
  • Rod Photoreceptor CGMP-Gated Channel Subunit Alpha 3 4
  • Cyclic Nucleotide-Gated Channel, Photoreceptor 3 4
  • Cyclic Nucleotide-Gated Cation Channel 1 3 4
  • CGMP-Gated Cation Channel Alpha-1 2 3
  • CNG Channel Alpha-1 3 4
  • CNCG1 3 4
  • CNG-1 3 4
  • CNCG 3 4
  • CNG1 3 4
  • Cyclic Nucleotide-Gated Channel Alpha-1 4
  • Interleukin-1 Homologue 3
  • RCNCalpha 3
  • RCNC1 3
  • RCNCa 3
  • RP49 3

External Ids for CNGA1 Gene

Previous HGNC Symbols for CNGA1 Gene

  • CNCG1
  • CNCG

Previous GeneCards Identifiers for CNGA1 Gene

  • GC04M048014
  • GC04M048247
  • GC04M047787
  • GC04M047778
  • GC04M047632
  • GC04M047257

Summaries for CNGA1 Gene

Entrez Gene Summary for CNGA1 Gene

  • The protein encoded by this gene is involved in phototransduction. Along with another protein, the encoded protein forms a cGMP-gated cation channel in the plasma membrane, allowing depolarization of rod photoreceptors. This represents the last step in the phototransduction pathway. Defects in this gene are a cause of retinitis pigmentosa autosomal recessive (ARRP) disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

GeneCards Summary for CNGA1 Gene

CNGA1 (Cyclic Nucleotide Gated Channel Alpha 1) is a Protein Coding gene. Diseases associated with CNGA1 include Retinitis Pigmentosa 49 and Retinitis Pigmentosa. Among its related pathways are Activation of cAMP-Dependent PKA and Sweet Taste Signaling. Gene Ontology (GO) annotations related to this gene include ion channel activity and cGMP binding. An important paralog of this gene is CNGA3.

UniProtKB/Swiss-Prot for CNGA1 Gene

  • Visual signal transduction is mediated by a G-protein coupled cascade using cGMP as second messenger. This protein can be activated by cyclic GMP which leads to an opening of the cation channel and thereby causing a depolarization of rod photoreceptors.

Gene Wiki entry for CNGA1 Gene

Additional gene information for CNGA1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNGA1 Gene

Genomics for CNGA1 Gene

GeneHancer (GH) Regulatory Elements for CNGA1 Gene

Promoters and enhancers for CNGA1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J048014 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 695.2 -2.5 -2477 8.7 ATF1 FOXA2 SIN3A DMAP1 ZNF48 YY1 GLIS2 FOS ATF7 ZNF202 CNGA1 NIPAL1 NFXL1 RNU6-838P GC04P048104
GH04J047981 Promoter 0.5 EPDnew 650.3 +35.0 35034 0.1 CNGA1 PIR42399 LOC101927157 NIPAL1 NFXL1
GH04J048036 Enhancer 0.9 Ensembl ENCODE 45.3 -20.2 -20230 1.3 HDGF PKNOX1 STAT5A BATF NFATC1 EED ZNF207 ATF7 ETV6 BCLAF1 CNGA1 NIPAL1 RNU6-838P GC04P048104
GH04J047913 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 16.2 +102.4 102426 2.3 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B ZNF766 CBX5 NFXL1 NIPAL1 LOC101927157 CNGA1
GH04J047836 Promoter/Enhancer 1.3 Ensembl ENCODE 24.6 +179.5 179478 1.6 ELF3 PKNOX1 ARID4B SIN3A IRF4 ZNF48 RAD21 ZNF335 GLIS2 ZNF143 CORIN NFXL1 CNGA1 LOC101927179
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNGA1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CNGA1 gene promoter:
  • NF-YC
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • NF-Y
  • NF-YA
  • NF-YB

Genomic Locations for CNGA1 Gene

Genomic Locations for CNGA1 Gene
81,665 bases
Minus strand
80,696 bases
Minus strand

Genomic View for CNGA1 Gene

Genes around CNGA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNGA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNGA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNGA1 Gene

Proteins for CNGA1 Gene

  • Protein details for CNGA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    cGMP-gated cation channel alpha-1
    Protein Accession:
    Secondary Accessions:
    • A8K7K6
    • J3KPZ2
    • Q16279
    • Q16485
    • Q4W5E3

    Protein attributes for CNGA1 Gene

    690 amino acids
    Molecular mass:
    79586 Da
    Quaternary structure:
    • Tetramer formed of three CNGA1 and one CNGB1 modulatory subunits.
    • Sequence=AAB22778.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for CNGA1 Gene


neXtProt entry for CNGA1 Gene

Post-translational modifications for CNGA1 Gene

  • Glycosylation at posLast=425425
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CNGA1 Gene

Domains & Families for CNGA1 Gene

Gene Families for CNGA1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters
  • Voltage-gated ion channels

Suggested Antigen Peptide Sequences for CNGA1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The C-terminal coiled-coil domain mediates homotrimerization of CNGA subunits.
  • Belongs to the cyclic nucleotide-gated cation channel (TC 1.A.1.5) family. CNGA1 subfamily.
  • The C-terminal coiled-coil domain mediates homotrimerization of CNGA subunits.
  • Belongs to the cyclic nucleotide-gated cation channel (TC 1.A.1.5) family. CNGA1 subfamily.
genes like me logo Genes that share domains with CNGA1: view

Function for CNGA1 Gene

Molecular function for CNGA1 Gene

UniProtKB/Swiss-Prot Function:
Visual signal transduction is mediated by a G-protein coupled cascade using cGMP as second messenger. This protein can be activated by cyclic GMP which leads to an opening of the cation channel and thereby causing a depolarization of rod photoreceptors.
GENATLAS Biochemistry:
cyclic guanine nucleotide gated channel (cGMP),rod photoreceptor,expressed in the rod outer segment alpha 1 subunit,heterodimerizing with CNGB4

Gene Ontology (GO) - Molecular Function for CNGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity IEA --
GO:0005221 intracellular cyclic nucleotide activated cation channel activity IEA --
GO:0005222 intracellular cAMP activated cation channel activity IBA --
GO:0005223 intracellular cGMP activated cation channel activity IBA --
GO:0005249 voltage-gated potassium channel activity IBA --
genes like me logo Genes that share ontologies with CNGA1: view
genes like me logo Genes that share phenotypes with CNGA1: view

Human Phenotype Ontology for CNGA1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNGA1

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CNGA1 Gene

Localization for CNGA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNGA1 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

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 CNGA1 gene
Compartment Confidence
plasma membrane 5
cytosol 1

Gene Ontology (GO) - Cellular Components for CNGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 7479749
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CNGA1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CNGA1 Gene

Pathways & Interactions for CNGA1 Gene

genes like me logo Genes that share pathways with CNGA1: view

Gene Ontology (GO) - Biological Process for CNGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0007165 signal transduction IEA --
GO:0007601 visual perception IEA,TAS --
GO:0016056 rhodopsin mediated signaling pathway TAS --
GO:0022400 regulation of rhodopsin mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with CNGA1: view

No data available for SIGNOR curated interactions for CNGA1 Gene

Drugs & Compounds for CNGA1 Gene

(4) Drugs for CNGA1 Gene - From: DrugBank, DGIdb, IUPHAR, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dequalinium Approved, Investigational Pharma Target, blocker 2
Cyclic GMP Experimental Pharma 0
cgmp Pharma Activator, Agonist, Inhibition, Inhibitor, Activation 0
L-(cis)-diltiazem Pharma Antagonist, Pore Blocker, Inhibitor 0
genes like me logo Genes that share compounds with CNGA1: view

Transcripts for CNGA1 Gene

mRNA/cDNA for CNGA1 Gene

Unigene Clusters for CNGA1 Gene

Cyclic nucleotide gated channel alpha 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNGA1

Alternative Splicing Database (ASD) splice patterns (SP) for CNGA1 Gene

No ASD Table

Relevant External Links for CNGA1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNGA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CNGA1 Gene

mRNA differential expression in normal tissues according to GTEx for CNGA1 Gene

This gene is overexpressed in Liver (x8.0) and Esophagus - Mucosa (x4.1).

Protein differential expression in normal tissues from HIPED for CNGA1 Gene

This gene is overexpressed in Retina (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CNGA1 Gene

Protein tissue co-expression partners for CNGA1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CNGA1 Gene:


SOURCE GeneReport for Unigene cluster for CNGA1 Gene:


mRNA Expression by UniProt/SwissProt for CNGA1 Gene:

Tissue specificity: Rod cells in the retina.

Evidence on tissue expression from TISSUES for CNGA1 Gene

  • Eye(4.4)
  • Spleen(4)
  • Lung(3.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CNGA1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
  • penis
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with CNGA1: view

Orthologs for CNGA1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CNGA1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNGA1 34 33
  • 99.43 (n)
(Canis familiaris)
Mammalia CNGA1 34 33
  • 89.34 (n)
(Bos Taurus)
Mammalia CNGA1 34 33
  • 88.29 (n)
(Mus musculus)
Mammalia Cnga1 16 34 33
  • 85.88 (n)
(Rattus norvegicus)
Mammalia Cnga1 33
  • 85.49 (n)
(Ornithorhynchus anatinus)
Mammalia CNGA1 34
  • 83 (a)
(Monodelphis domestica)
Mammalia CNGA1 34
  • 80 (a)
(Gallus gallus)
Aves CNGA1 34 33
  • 76.08 (n)
(Anolis carolinensis)
Reptilia CNGA1 34
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cnga1 33
  • 72.22 (n)
(Danio rerio)
Actinopterygii cnga1 34 33
  • 68.66 (n)
CNGA1 (2 of 2) 34
  • 60 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3536 35
  • 59 (a)
cngl 35
  • 43 (a)
Cng 34 35
  • 36 (a)
(Caenorhabditis elegans)
Secernentea tax-4 34 35
  • 41 (a)
F14H8.6 35
  • 34 (a)
cng-1 34
  • 31 (a)
C23H5.7 35
  • 30 (a)
Y76B12C.1 35
  • 29 (a)
che-6 34
  • 27 (a)
wrt-3 35
  • 24 (a)
cng-3 34
  • 23 (a)
cng-2 34
  • 22 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 58 (a)
Species where no ortholog for CNGA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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 CNGA1 Gene

Gene Tree for CNGA1 (if available)
Gene Tree for CNGA1 (if available)
Evolutionary constrained regions (ECRs) for CNGA1: view image

Paralogs for CNGA1 Gene

Paralogs for CNGA1 Gene

(4) SIMAP similar genes for CNGA1 Gene using alignment to 3 proteins:

  • D6R978_HUMAN
  • D6RCF1_HUMAN Pseudogenes for CNGA1 Gene

genes like me logo Genes that share paralogs with CNGA1: view

Variants for CNGA1 Gene

Sequence variations from dbSNP and Humsavar for CNGA1 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs121909599 pathogenic, Retinitis pigmentosa 49 47,949,894(-) C/A/T coding_sequence_variant, missense_variant, stop_gained
rs121909600 pathogenic, Retinitis pigmentosa 49 47,943,203(-) T/A coding_sequence_variant, stop_gained
rs141978020 uncertain-significance, Retinitis Pigmentosa, Recessive 47,936,147(-) G/A/C 3_prime_UTR_variant
rs17573673 likely-benign, Retinitis Pigmentosa, Recessive 47,936,862(-) G/A coding_sequence_variant, synonymous_variant
rs192912733 uncertain-significance, Retinitis pigmentosa 49 47,937,223(-) C/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CNGA1 Gene

Variant ID Type Subtype PubMed ID
esv2174980 CNV deletion 18987734
esv2498611 CNV deletion 19546169
esv2663876 CNV deletion 23128226
esv2727534 CNV deletion 23290073
esv2727535 CNV deletion 23290073
esv2727536 CNV deletion 23290073
esv3600456 CNV gain 21293372
esv3600457 CNV loss 21293372
nsv290106 CNV deletion 16902084
nsv478149 CNV novel sequence insertion 20440878
nsv509895 OTHER sequence alteration 20534489

Variation tolerance for CNGA1 Gene

Residual Variation Intolerance Score: 31.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.47; 82.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNGA1 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNGA1 Gene

Disorders for CNGA1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CNGA1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 49
  • rp49
retinitis pigmentosa
  • retinitis pigmentosa 1
retinitis pigmentosa 19
  • rp19
fundus dystrophy
  • retinal dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search CNGA1 in MalaCards View complete list of genes associated with diseases


  • Retinitis pigmentosa 49 (RP49) [MIM:613756]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:15570217, ECO:0000269 PubMed:7479749}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CNGA1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CNGA1: view

No data available for Genatlas for CNGA1 Gene

Publications for CNGA1 Gene

  1. Human rod photoreceptor cGMP-gated channel: amino acid sequence, gene structure, and functional expression. (PMID: 1379636) Dhallan RS … Nathans J (The Journal of neuroscience : the official journal of the Society for Neuroscience 1992) 3 4 22 58
  2. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij JC … Florijn RJ (Ophthalmology 2011) 3 44 58
  3. International Union of Pharmacology. LI. Nomenclature and structure-function relationships of cyclic nucleotide-regulated channels. (PMID: 16382102) Hofmann F … Kaupp UB (Pharmacological reviews 2005) 2 3 58
  4. Autosomal recessive retinitis pigmentosa in a Pakistani family mapped to CNGA1 with identification of a novel mutation. (PMID: 15570217) Zhang Q … Hejtmancik JF (Molecular vision 2004) 3 4 58
  5. Novel homozygous mutation in the alpha subunit of the rod cGMP gated channel (CNGA1) in two Spanish sibs affected with autosomal recessive retinitis pigmentosa. (PMID: 12362048) Paloma E … Balcells S (Journal of medical genetics 2002) 3 22 58

Products for CNGA1 Gene

Sources for CNGA1 Gene

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