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Gene

CNGA3

cyclic nucleotide gated channel subunit alpha 3

Summary

Cytogenetic location
2q11.2
Coordinates
Chromosome 2: 98,346,456–98,398,601 (GRCh38)
Exons
8 exons across 52.1 kb
Protein
694 amino acids
Inheritance
Autosomal recessive
Also known as
CCNC1, CCNCa, CNG3
Previous symbols
CNCG3, ACHM2
MANE Select transcript
ENST00000272602.7NM_001298.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Achromatopsia

    • CNGA3-Related RetinopathyAutosomal recessive

      A cone disorder caused by changes in both copies of CNGA3, a common cause of achromatopsia.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

    • Achromatopsia (ACHM) is a rare autosomal recessive retinal disorder characterized by color blindness, nystagmus, photophobia, and severely reduced visual acuity due to the absence or impairment of cone function.

      • 3 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How CNGA3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where CNGA3 sits. CNGA3 and 7 genes near it on chromosome 2, from 97,872,529 to 98,872,528.Chromosome 22q11.2p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.398 Mb98.2 Mb98.4 Mb98.6 Mb98.8 MbTMEM131: 97,756,333–97,996,226, reverse strandTMEM131VWA3B: 98,087,116–98,313,299, forward strandVWA3BCNGA3: 98,346,456–98,398,601, forward strandCNGA3INPP4A: 98,444,246–98,594,392, forward strandINPP4ACOA5: 98,598,242–98,608,542, reverse strandCOA5UNC50: 98,608,174–98,618,604, forward strandUNC50MGAT4A: 98,619,106–98,732,639, reverse strandMGAT4ACRACDL: 98,793,845–98,936,628, reverse strandCRACDLDiagram of CNGA3: 8 exons on the forward strand of chromosome 2Exon 2: 3 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 6: 8 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 8: 76 known disease-causing sitesExon 1: 98,346,456–98,346,534, 79 basesExon 2: 98,369,939–98,370,076, 138 basesExon 3: 98,377,687–98,377,800, 114 basesExon 4: 98,380,175–98,380,354, 180 basesExon 5: 98,383,388–98,383,441, 54 basesExon 6: 98,389,658–98,389,774, 117 basesExon 7: 98,391,864–98,391,970, 107 basesExon 8: 98,395,844–98,398,601, 2,758 bases123456785′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.5 kb of the gene's 52.1 kb; 2,085 of those bases code for the protein.

How a genome test reads CNGA3

104

positions in CNGA3 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 52.1 kb of CNGA3, introns included, not only the 3.5 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). CNGA3 gene: cyclic nucleotide gated channel subunit alpha 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/cnga3

Vancouver

Dante Labs. CNGA3 gene: cyclic nucleotide gated channel subunit alpha 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cnga3

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