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Gene

PIGN

phosphatidylinositol glycan anchor biosynthesis class N

Summary

Cytogenetic location
18q21.33
Coordinates
Chromosome 18: 62,041,164–62,187,056 (GRCh38)
Exons
31 exons across 145.9 kb
Protein
931 amino acids
Inheritance
Autosomal recessive
Also known as
MCD4, PIG-N
MANE Select transcript
ENST00000640252.2NM_176787.5
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

    • PIGN-Related Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome (MCAHS1)Autosomal recessive

      A GPI anchor defect caused by variants in PIGN, with low muscle tone, early seizures, developmental delay and congenital anomalies.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
    • Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome

      A group of GPI anchor defects (PIGN, PIGA, PIGT, PIGQ and related genes) with low muscle tone, seizures, developmental delay and congenital anomalies.

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

      • ClinGen rates the link definitive
      • 4 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.

      • ClinGen rates the link definitive
      • 4 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 PIGN is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 18, with a bracket where PIGN sits. PIGN and 4 genes near it on chromosome 18, from 61,614,110 to 62,614,109.Chromosome 1818q21.33p11.32p11.31p11.23p11.22p11.21p11.1q11.1q11.2q12.1q12.2q12.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q2361.8 Mb62 Mb62.2 Mb62.4 Mb62.6 MbRNF152: 61,808,067–61,895,097, reverse strandRNF152PIGN: 62,041,164–62,187,056, reverse strandPIGNRELCH: 62,187,255–62,310,249, forward strandRELCHTNFRSF11A: 62,325,086–62,391,288, forward strandTNFRSF11AZCCHC2: 62,522,994–62,587,709, forward strandZCCHC2Diagram of PIGN: 31 exons on the reverse strand of chromosome 18Exon 30: 2 known disease-causing sitesExon 28: 1 known disease-causing siteExon 27: 5 known disease-causing sitesExon 26: 4 known disease-causing sitesExon 25: 3 known disease-causing sitesExon 24: 3 known disease-causing sitesExon 23: 5 known disease-causing sitesExon 22: 6 known disease-causing sitesExon 21: 4 known disease-causing sitesExon 20: 2 known disease-causing sitesExon 19: 5 known disease-causing sitesExon 18: 6 known disease-causing sitesExon 17: 8 known disease-causing sitesExon 16: 2 known disease-causing sitesExon 15: 3 known disease-causing sitesExon 14: 2 known disease-causing sitesExon 13: 2 known disease-causing sitesExon 12: 3 known disease-causing sitesExon 11: 3 known disease-causing sitesExon 10: 6 known disease-causing sitesExon 9: 3 known disease-causing sitesExon 8: 10 known disease-causing sitesExon 7: 5 known disease-causing sitesExon 6: 4 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 4: 7 known disease-causing sitesExon 31: 62,041,164–62,045,979, 4,816 basesExon 30: 62,072,673–62,072,725, 53 basesExon 29: 62,074,779–62,074,821, 43 basesExon 28: 62,082,673–62,082,746, 74 basesExon 27: 62,084,531–62,084,606, 76 basesExon 26: 62,085,209–62,085,264, 56 basesExon 25: 62,088,756–62,088,842, 87 basesExon 24: 62,090,476–62,090,578, 103 basesExon 23: 62,095,848–62,095,950, 103 basesExon 22: 62,101,075–62,101,183, 109 basesExon 21: 62,102,794–62,102,902, 109 basesExon 20: 62,105,543–62,105,634, 92 basesExon 19: 62,106,789–62,106,881, 93 basesExon 18: 62,106,986–62,107,085, 100 basesExon 17: 62,109,834–62,109,973, 140 basesExon 16: 62,113,134–62,113,316, 183 basesExon 15: 62,114,561–62,114,639, 79 basesExon 14: 62,138,243–62,138,298, 56 basesExon 13: 62,138,983–62,139,075, 93 basesExon 12: 62,140,420–62,140,479, 60 basesExon 11: 62,143,306–62,143,346, 41 basesExon 10: 62,145,909–62,146,025, 117 basesExon 9: 62,146,971–62,147,101, 131 basesExon 8: 62,148,214–62,148,338, 125 basesExon 7: 62,154,545–62,154,651, 107 basesExon 6: 62,157,129–62,157,227, 99 basesExon 5: 62,157,687–62,157,808, 122 basesExon 4: 62,161,133–62,161,385, 253 basesExon 3: 62,162,253–62,162,329, 77 basesExon 2: 62,163,531–62,163,656, 126 basesExon 1: 62,186,844–62,187,056, 213 bases313025201510515′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 7.9 kb of the gene's 145.9 kb; 2,796 of those bases code for the protein.

How a genome test reads PIGN

161

positions in PIGN where ClinVar classes a change as pathogenic or likely pathogenic

6 of them (3.7%) fall in regions short reads find hard.

  • Segmental duplications (6 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 145.9 kb of PIGN, introns included, not only the 7.9 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.). PIGN gene: phosphatidylinositol glycan anchor biosynthesis class N. Retrieved 16 October 2026, from https://dantelabs.com/genes/pign

Vancouver

Dante Labs. PIGN gene: phosphatidylinositol glycan anchor biosynthesis class N [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pign

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