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Gene

HCN1

hyperpolarization activated cyclic nucleotide gated potassium channel 1

Summary

Cytogenetic location
5p12
Coordinates
Chromosome 5: 45,254,948–45,696,380 (GRCh38)
Exons
8 exons across 441.4 kb
Protein
890 amino acids
Also known as
BCNG-1, HAC-2
Previous symbols
BCNG1
MANE Select transcript
ENST00000303230.6NM_021072.4
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

    • 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.

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

    How HCN1 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 5, with a bracket where HCN1 sits. HCN1 and 1 gene near it on chromosome 5, from 44,813,515 to 46,137,813.Chromosome 55p12p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.345 Mb45.2 Mb45.4 Mb45.6 Mb45.8 Mb46 MbMRPS30: 44,808,941–44,820,428, forward strandMRPS30HCN1: 45,254,948–45,696,380, reverse strandHCN1Diagram of HCN1: 8 exons on the reverse strand of chromosome 5Exon 6: 1 known disease-causing siteExon 4: 4 known disease-causing sitesExon 2: 7 known disease-causing sitesExon 1: 2 known disease-causing sitesExon 8: 45,254,948–45,262,810, 7,863 basesExon 7: 45,267,089–45,267,253, 165 basesExon 6: 45,303,599–45,303,839, 241 basesExon 5: 45,353,100–45,353,246, 147 basesExon 4: 45,396,492–45,396,710, 219 basesExon 3: 45,461,846–45,462,007, 162 basesExon 2: 45,645,185–45,645,608, 424 basesExon 1: 45,695,669–45,696,380, 712 bases876543215′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 9.9 kb of the gene's 441.4 kb; 2,673 of those bases code for the protein.

    How a genome test reads HCN1

    14

    positions in HCN1 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 441.4 kb of HCN1, introns included, not only the 9.9 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.). HCN1 gene: hyperpolarization activated cyclic nucleotide gated potassium channel 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/hcn1

    Vancouver

    Dante Labs. HCN1 gene: hyperpolarization activated cyclic nucleotide gated potassium channel 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/hcn1

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