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Gene

GNPAT

glyceronephosphate O-acyltransferase

Summary

Cytogenetic location
1q42.2
Coordinates
Chromosome 1: 231,241,212–231,277,973 (GRCh38)
Exons
16 exons across 36.8 kb
Protein
680 amino acids
Inheritance
Autosomal recessive
Also known as
DHAPAT, DAPAT, DAP-AT
MANE Select transcript
ENST00000366647.9NM_014236.4
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

  • Peroxisomal Enzyme Disorders & Refsum Disease

    • Glyceronephosphate O-Acyltransferase DeficiencyAutosomal recessive

      Caused by variants in GNPAT, which impairs plasmalogen production and causes rhizomelic chondrodysplasia punctata type 2, with shortened limbs, cataracts and developmental delay.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing can end a diagnostic search and guide supportive care and family planning.

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 GNPAT is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where GNPAT sits. GNPAT and 14 genes near it on chromosome 1, from 230,759,593 to 231,759,592.Chromosome 11q42.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44230.8 Mb231 Mb231.2 Mb231.4 Mb231.6 MbCAPN9: 230,747,266–230,804,397, forward strandCAPN9C1orf198: 230,837,119–230,869,589, reverse strandC1orf198TTC13: 230,902,936–230,978,893, reverse strandTTC13ARV1: 230,978,981–231,000,735, forward strandARV1FAM89A: 230,999,826–231,040,270, reverse strandFAM89ATRIM67: 231,162,058–231,221,565, forward strandTRIM67FSAF1: 231,223,763–231,241,187, reverse strandFSAF1GNPAT: 231,241,212–231,277,973, forward strandGNPATEXOC8: 231,332,753–231,337,852, reverse strandEXOC8SPRTN: 231,337,104–231,375,416, forward strandSPRTNEGLN1: 231,359,560–231,422,749, reverse strandEGLN1: 231,363,797–231,528,603, reverse strandTSNAX: 231,528,541–231,566,524, forward strandTSNAXTSNAX-DISC1: 231,528,653–231,819,244, forward strandTSNAX-DISC1DISC1: 231,626,663–232,041,272, forward strandDISC1Diagram of GNPAT: 16 exons on the forward strand of chromosome 1Exon 1: 1 known disease-causing siteExon 2: 2 known disease-causing sitesExon 3: 3 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 7: 6 known disease-causing sitesExon 8: 1 known disease-causing siteExon 9: 3 known disease-causing sitesExon 10: 5 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 12: 4 known disease-causing sitesExon 13: 1 known disease-causing siteExon 1: 231,241,212–231,241,456, 245 basesExon 2: 231,250,961–231,251,143, 183 basesExon 3: 231,260,507–231,260,683, 177 basesExon 4: 231,262,723–231,262,852, 130 basesExon 5: 231,265,293–231,265,420, 128 basesExon 6: 231,265,712–231,265,787, 76 basesExon 7: 231,266,014–231,266,165, 152 basesExon 8: 231,266,277–231,266,407, 131 basesExon 9: 231,267,680–231,267,903, 224 basesExon 10: 231,270,758–231,271,000, 243 basesExon 11: 231,272,312–231,272,391, 80 basesExon 12: 231,273,922–231,274,062, 141 basesExon 13: 231,275,221–231,275,320, 100 basesExon 14: 231,275,405–231,275,498, 94 basesExon 15: 231,276,135–231,276,196, 62 basesExon 16: 231,277,499–231,277,973, 475 bases12468101214165′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 2.6 kb of the gene's 36.8 kb; 2,043 of those bases code for the protein.

How a genome test reads GNPAT

39

positions in GNPAT 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 36.8 kb of GNPAT, introns included, not only the 2.6 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.). GNPAT gene: glyceronephosphate O-acyltransferase. Retrieved 17 October 2026, from https://dantelabs.com/genes/gnpat

Vancouver

Dante Labs. GNPAT gene: glyceronephosphate O-acyltransferase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/gnpat

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