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Gene

PGAP2

post-GPI attachment to proteins 2

Summary

Cytogenetic location
11p15.4
Coordinates
Chromosome 11: 3,808,560–3,826,371 (GRCh38)
Exons
7 exons across 17.8 kb
Protein
315 amino acids
Inheritance
Autosomal recessive
Also known as
FRAG1, CWH43-N
Previous symbols
MRT21, MRT17
MANE Select transcript
ENST00000278243.9NM_014489.4
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 reports relevant to this gene

  • GPI Anchor Biosynthesis Defects

    • Hyperphosphatasia With Impaired Intellectual Development (Mabry Syndrome)Autosomal recessive

      A group of GPI anchor defects (PIGV, PIGO, PGAP2, PGAP3, PIGW, PIGY) in which a persistently high alkaline phosphatase accompanies developmental delay, seizures and short end bones of the fingers.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Some affected children have had seizure control improved with pyridoxine (vitamin B6), so a diagnosis can guide a specialist trial of treatment.

    • Disorders of GPI Anchor Biosynthesis

      A group of inherited conditions caused by variants in the PIG, PGAP and related genes needed to make and attach the GPI anchor, typically causing developmental delay, low muscle tone and epilepsy.

      • 3 GenCC submitters rate it definitive or strong

Broader groupings

  • Congenital Disorders of Glycosylation

    • Congenital Disorders of Glycosylation (CDG)

      One of 98 genes linked to it

      A large group of inherited conditions in which sugar chains (glycans) are not correctly built or attached to proteins and lipids, often affecting the brain, liver, blood clotting, growth and many other body systems. Most are autosomal recessive, but some are X-linked or autosomal dominant.

      • 3 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How PGAP2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 11, with a bracket where PGAP2 sits. PGAP2 and 11 genes near it on chromosome 11, from 3,317,466 to 4,317,465.Chromosome 1111p15.4p15.5p15.4p15.3p15.2p15.1p14.3p14.2p14.1p13p12p11.2p11.12p11.11q11q12.1q12.2q12.3q13.1q13.2q13.3q13.4q13.5q14.1q14.2q14.3q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q253.4 Mb3.6 Mb3.8 Mb4 Mb4.2 MbZNF195: 3,339,261–3,379,222, reverse strandZNF195ART5: 3,638,503–3,643,187, reverse strandART5ART1: 3,645,106–3,668,548, forward strandART1CHRNA10: 3,665,587–3,671,384, reverse strandCHRNA10NUP98: 3,671,083–3,797,792, reverse strandNUP98PGAP2: 3,808,560–3,826,371, forward strandPGAP2RHOG: 3,826,978–3,841,346, reverse strandRHOGSTIM1: 3,854,527–4,093,210, forward strandSTIM1RRM1: 4,094,707–4,140,686, forward strandRRM1SSU72L5: 4,233,217–4,234,287, forward strandSSU72L5SSU72L2: 4,241,641–4,242,706, reverse strandSSU72L2SSU72L4: 4,287,084–4,288,185, reverse strandSSU72L4Diagram of PGAP2: 7 exons on the forward strand of chromosome 11Exon 2: 3 known disease-causing sitesExon 3: 1 known disease-causing siteExon 4: 5 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 7: 1 known disease-causing siteExon 1: 3,808,560–3,808,651, 92 basesExon 2: 3,811,250–3,811,424, 175 basesExon 3: 3,817,353–3,817,535, 183 basesExon 4: 3,823,883–3,824,135, 253 basesExon 5: 3,824,270–3,824,376, 107 basesExon 6: 3,825,020–3,825,128, 109 basesExon 7: 3,825,328–3,826,371, 1,044 bases12345675′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 2 kb of the gene's 17.8 kb; 948 of those bases code for the protein.

How a genome test reads PGAP2

16

positions in PGAP2 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 17.8 kb of PGAP2, introns included, not only the 2 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.). PGAP2 gene: post-GPI attachment to proteins 2. Retrieved 16 October 2026, from https://dantelabs.com/genes/pgap2

Vancouver

Dante Labs. PGAP2 gene: post-GPI attachment to proteins 2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pgap2

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