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Gene

HINT1

histidine triad nucleotide binding protein 1

Summary

Cytogenetic location
5q23.3
Coordinates
Chromosome 5: 131,159,027–131,165,256 (GRCh38)
Exons
3 exons across 6.2 kb
Protein
126 amino acids
Also known as
PKCI-1
Previous symbols
PRKCNH1, HINT
MANE Select transcript
ENST00000304043.10NM_005340.7
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

    • Charcot-Marie-Tooth Disease

      • One of 62 genes linked to it

        A group of inherited peripheral neuropathies causing progressive weakness and wasting of the distal muscles and loss of sensation, mainly in the feet and hands.

        • ClinGen rates the link definitive
        • 1 GenCC submitter rates it definitive or strong
        What knowing changes

        Genetic counseling, subtype-specific monitoring, physical therapy, orthotics, neurotoxic drug avoidance, gene-specific clinical trials, surveillance for associated features

    How HINT1 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    Chromosome 5, with a bracket where HINT1 sits. HINT1 and 5 genes near it on chromosome 5, from 130,662,142 to 131,662,141.Chromosome 55q23.3p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3130.8 Mb131 Mb131.2 Mb131.4 Mb131.6 MbHINT1: 131,159,027–131,165,256, reverse strandHINT1LYRM7: 131,170,845–131,205,428, forward strandLYRM7CDC42SE2: 131,245,493–131,398,447, forward strandCDC42SE2RAPGEF6: 131,423,858–131,635,272, reverse strandRAPGEF6: 131,425,891–131,796,983, reverse strandFNIP1: 131,641,714–131,797,041, reverse strandFNIP1Diagram of HINT1: 3 exons on the reverse strand of chromosome 5Exon 3: 8 known disease-causing sitesExon 2: 4 known disease-causing sitesExon 1: 3 known disease-causing sitesExon 3: 131,159,027–131,159,611, 585 basesExon 2: 131,162,572–131,162,676, 105 basesExon 1: 131,165,095–131,165,256, 162 bases3215′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 0.9 kb of the gene's 6.2 kb; 381 of those bases code for the protein.

    How a genome test reads HINT1

    17

    positions in HINT1 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 6.2 kb of HINT1, introns included, not only the 0.9 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.). HINT1 gene: histidine triad nucleotide binding protein 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/hint1

    Vancouver

    Dante Labs. HINT1 gene: histidine triad nucleotide binding protein 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hint1

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