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Gene

CNPY3

canopy FGF signaling regulator 3

Summary

Cytogenetic location
6p21.1
Coordinates
Chromosome 6: 42,929,480–42,939,294 (GRCh38)
Exons
6 exons across 9.8 kb
Protein
278 amino acids
Also known as
CAG4A
Previous symbols
TNRC5
MANE Select transcript
ENST00000372836.5NM_006586.5
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

    • Epilepsy (Full Panel)

      • Epilepsy

        One of 171 genes linked to it

        A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

        • 1 GenCC submitter rates it definitive or strong

    How CNPY3 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    Chromosome 6, with a bracket where CNPY3 sits. CNPY3 and 27 genes near it on chromosome 6, from 42,434,387 to 43,434,386.Chromosome 66p21.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2742.6 Mb42.8 Mb43 Mb43.2 Mb43.4 MbTRERF1: 42,224,931–42,452,225, reverse strandTRERF1UBR2: 42,563,969–42,693,505, forward strandUBR2PRPH2: 42,696,598–42,722,621, reverse strandPRPH2TBCC: 42,744,498–42,746,103, reverse strandTBCCBICRAL: 42,781,931–42,868,560, forward strandBICRALRPL7L1: 42,879,602–42,889,925, forward strandRPL7L1PEX39: 42,890,265–42,890,821, reverse strandPEX39PTCRA: 42,915,989–42,925,845, forward strandPTCRACNPY3: 42,929,480–42,939,294, forward strandCNPY3PEX6: 42,959,717–42,979,249, reverse strandPEX6GNMT: 42,960,268–42,970,699, forward strandGNMTPPP2R5D: 42,984,533–43,012,346, forward strandPPP2R5DMEA1: 43,011,143–43,016,868, reverse strandMEA1KLHDC3: 43,014,103–43,021,314, forward strandKLHDC3RRP36: 43,021,588–43,034,156, forward strandRRP36CUL7: 43,037,617–43,053,943, reverse strandKLC4: 43,040,777–43,075,099, forward strand: 43,051,066–43,058,185, reverse strandMRPL2: 43,054,029–43,059,464, reverse strandPTK7: 43,076,256–43,161,719, forward strandPTK7SRF: 43,170,910–43,181,506, forward strandSRFCUL9: 43,182,166–43,224,587, forward strandCUL9DNPH1: 43,225,629–43,229,490, reverse strandDNPH1TTBK1: 43,243,481–43,288,258, forward strandTTBK1SLC22A7: 43,295,694–43,305,543, forward strandSLC22A7CRIP3: 43,299,710–43,308,878, reverse strandCRIP3ZNF318: 43,307,134–43,369,687, reverse strandZNF318ABCC10: 43,427,366–43,451,783, forward strandABCC10Diagram of CNPY3: 6 exons on the forward strand of chromosome 6Exon 3: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 6: 2 known disease-causing sitesExon 1: 42,929,480–42,929,721, 242 basesExon 2: 42,934,475–42,934,598, 124 basesExon 3: 42,935,574–42,935,670, 97 basesExon 4: 42,937,717–42,937,839, 123 basesExon 5: 42,938,090–42,938,207, 118 basesExon 6: 42,938,568–42,939,294, 727 bases1234565′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 1.4 kb of the gene's 9.8 kb; 837 of those bases code for the protein.

    Sequencing CNPY3

    4

    positions in CNPY3 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 9.8 kb of CNPY3, introns included, not only the 1.4 kb of exons.

    Genes linked to the same conditions

    Traits linked to CNPY3

    The Human Phenotype Ontology lists these as features of the rare conditions CNPY3 can cause. Each trait's page lists the other genes linked to it.

    External links

    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 2026-10-17: 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 2026.10.17-8666dff2.

    Cite this page

    APA

    Dante Labs. (n.d.). CNPY3 gene: canopy FGF signaling regulator 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/cnpy3

    Vancouver

    Dante Labs. CNPY3 gene: canopy FGF signaling regulator 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cnpy3

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