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Gene

PGAP1

post-GPI attachment to proteins inositol deacylase 1

Summary

Cytogenetic location
2q33.1
Coordinates
Chromosome 2: 196,833,004–196,926,707 (GRCh38)
Exons
27 exons across 93.7 kb
Protein
922 amino acids
Also known as
FLJ12377, Bst1, SPG67
MANE Select transcript
ENST00000354764.9NM_024989.4
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

    How PGAP1 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 PGAP1 sits. PGAP1 and 5 genes near it on chromosome 2, from 196,379,856 to 197,379,855.Chromosome 22q33.1p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3196.4 Mb196.6 Mb196.8 Mb197 Mb197.2 MbHECW2: 196,189,099–196,593,684, reverse strandHECW2CCDC150: 196,639,554–196,763,490, forward strandCCDC150GTF3C3: 196,761,062–196,799,743, reverse strandGTF3C3C2orf66: 196,804,417–196,809,355, reverse strandC2orf66PGAP1: 196,833,004–196,926,707, reverse strandPGAP1ANKRD44: 196,967,017–197,311,173, reverse strandANKRD44Diagram of PGAP1: 27 exons on the reverse strand of chromosome 2Exon 25: 2 known disease-causing sitesExon 23: 2 known disease-causing sitesExon 22: 1 known disease-causing siteExon 21: 3 known disease-causing sitesExon 18: 1 known disease-causing siteExon 17: 1 known disease-causing siteExon 16: 1 known disease-causing siteExon 14: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 2: 2 known disease-causing sitesExon 1: 1 known disease-causing siteExon 27: 196,833,004–196,841,372, 8,369 basesExon 26: 196,842,721–196,842,825, 105 basesExon 25: 196,843,888–196,844,075, 188 basesExon 24: 196,844,524–196,844,574, 51 basesExon 23: 196,845,882–196,846,017, 136 basesExon 22: 196,847,003–196,847,200, 198 basesExon 21: 196,847,947–196,848,037, 91 basesExon 20: 196,864,987–196,865,080, 94 basesExon 19: 196,870,941–196,870,979, 39 basesExon 18: 196,872,441–196,872,549, 109 basesExon 17: 196,872,960–196,873,026, 67 basesExon 16: 196,873,528–196,873,579, 52 basesExon 15: 196,873,685–196,873,758, 74 basesExon 14: 196,875,746–196,875,821, 76 basesExon 13: 196,880,076–196,880,153, 78 basesExon 12: 196,885,424–196,885,475, 52 basesExon 11: 196,885,834–196,885,880, 47 basesExon 10: 196,890,828–196,890,911, 84 basesExon 9: 196,892,346–196,892,401, 56 basesExon 8: 196,893,140–196,893,245, 106 basesExon 7: 196,897,131–196,897,197, 67 basesExon 6: 196,898,317–196,898,369, 53 basesExon 5: 196,902,585–196,902,742, 158 basesExon 4: 196,912,882–196,913,053, 172 basesExon 3: 196,916,418–196,916,593, 176 basesExon 2: 196,919,997–196,920,150, 154 basesExon 1: 196,926,470–196,926,707, 238 bases2725201510515′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 11.1 kb of the gene's 93.7 kb; 2,769 of those bases code for the protein.

    How a genome test reads PGAP1

    30

    positions in PGAP1 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 93.7 kb of PGAP1, introns included, not only the 11.1 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.). PGAP1 gene: post-GPI attachment to proteins inositol deacylase 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/pgap1

    Vancouver

    Dante Labs. PGAP1 gene: post-GPI attachment to proteins inositol deacylase 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pgap1

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