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Gene

GPT2

glutamic--pyruvic transaminase 2

Summary

Cytogenetic location
16q11.2
Coordinates
Chromosome 16: 46,884,362–46,931,289 (GRCh38)
Exons
12 exons across 46.9 kb
Protein
523 amino acids
Also known as
ALT2
MANE Select transcript
ENST00000340124.9NM_133443.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

    • Hereditary Spastic Paraplegia

      • Hereditary Spastic Paraplegia (All Types)

        One of 66 genes linked to it

        Umbrella term covering all hereditary spastic paraplegias, including SPG4 (SPAST), the most common dominant form, and SPG5A, SPG6, SPG10, SPG18, SPG30 and SPG31.

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

    How GPT2 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 16, with a bracket where GPT2 sits. GPT2 and 8 genes near it on chromosome 16, from 46,407,826 to 47,407,825.Chromosome 1616q11.2p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.346.6 Mb46.8 Mb47 Mb47.2 Mb47.4 MbSHCBP1: 46,578,565–46,621,404, reverse strandSHCBP1VPS35: 46,656,132–46,689,518, reverse strandVPS35ORC6: 46,689,301–46,698,399, forward strandORC6MYLK3: 46,701,568–46,790,407, reverse strandMYLK3HDIP1: 46,796,603–46,831,476, reverse strandHDIP1GPT2: 46,884,362–46,931,289, forward strandGPT2DNAJA2: 46,955,362–46,973,709, reverse strandDNAJA2NETO2: 47,077,703–47,144,028, reverse strandNETO2ITFG1: 47,154,387–47,464,149, reverse strandITFG1Diagram of GPT2: 12 exons on the forward strand of chromosome 16Exon 2: 2 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 6: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 11: 1 known disease-causing siteExon 1: 46,884,362–46,884,467, 106 basesExon 2: 46,884,694–46,884,958, 265 basesExon 3: 46,897,648–46,897,737, 90 basesExon 4: 46,900,682–46,900,790, 109 basesExon 5: 46,906,842–46,906,975, 134 basesExon 6: 46,909,684–46,909,927, 244 basesExon 7: 46,916,628–46,916,707, 80 basesExon 8: 46,918,621–46,918,757, 137 basesExon 9: 46,922,242–46,922,416, 175 basesExon 10: 46,924,389–46,924,544, 156 basesExon 11: 46,926,925–46,927,037, 113 basesExon 12: 46,928,907–46,931,289, 2,383 bases1510125′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 4 kb of the gene's 46.9 kb; 1,572 of those bases code for the protein.

    Sequencing GPT2

    3Low

    How hard GPT2 is to sequence with short reads, out of 100

    • Mappability0%
    • Homology0%
    • Repeats1.3%
    • GC content33%
    • Reference coverage0%

    8

    positions in GPT2 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 46.9 kb of GPT2, introns included, not only the 4 kb of exons.

    Genes linked to the same conditions

    Traits linked to GPT2

    The Human Phenotype Ontology lists these as features of the rare conditions GPT2 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 Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
    • 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.). GPT2 gene: glutamic--pyruvic transaminase 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/gpt2

    Vancouver

    Dante Labs. GPT2 gene: glutamic--pyruvic transaminase 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/gpt2

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