Skip to content
Use your HSA or FSA funds
Sequence your genome (opens in a new tab)

Gene

GPAA1

glycosylphosphatidylinositol anchor attachment 1

Summary

Cytogenetic location
8q24.3
Coordinates
Chromosome 8: 144,082,634–144,086,216 (GRCh38)
Exons
12 exons across 3.6 kb
Protein
621 amino acids
Also known as
GAA1, hGAA1
MANE Select transcript
ENST00000355091.9NM_003801.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • GPI Anchor Biosynthesis Defects

    • 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

How GPAA1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 8, with a bracket where GPAA1 sits. GPAA1 and 54 genes near it on chromosome 8, from 143,584,425 to 144,584,424.Chromosome 88q24.3p23.3p23.2p23.1p22p21.3p21.2p21.1p12p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12.1q12.2q12.3q13.1q13.2q13.3q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.3143.6 Mb143.8 Mb144 Mb144.2 Mb144.4 MbEEF1D: 143,579,697–143,599,541, reverse strandTIGD5: 143,597,831–143,603,224, forward strandTIGD5PYCR3: 143,603,210–143,609,773, reverse strandPYCR3GFUS: 143,612,617–143,618,048, reverse strandGFUSZNF623: 143,635,518–143,656,418, forward strandZNF623ZNF707: 143,684,452–143,713,898, forward strandCCDC166: 143,706,694–143,708,109, reverse strandCCDC166MAPK15: 143,716,279–143,722,458, forward strandMAPK15SACK1H: 143,723,933–143,740,732, reverse strandSACK1HIQANK1: 143,733,510–143,790,645, forward strandIQANK1SCRIB: 143,790,920–143,815,792, reverse strandSCRIBPUF60: 143,816,344–143,830,709, reverse strandPUF60NRBP2: 143,833,583–143,841,109, reverse strandNRBP2EPPK1: 143,857,324–143,878,468, reverse strandEPPK1PLEC: 143,915,152–143,977,039, reverse strandPLECPARP10: 143,977,151–144,019,930, reverse strandPARP10GRINA: 143,990,048–143,994,935, forward strandGRINASPATC1: 144,012,275–144,047,114, forward strandSPATC1OPLAH: 144,051,265–144,064,091, reverse strandEXOSC4: 144,078,560–144,081,408, forward strandEXOSC4: 144,078,642–144,084,330, forward strandGPAA1: 144,082,634–144,086,216, forward strandGPAA1CYC1: 144,095,039–144,097,525, forward strandCYC1SHARPIN: 144,097,513–144,108,124, reverse strandMAF1: 144,103,112–144,107,618, forward strandWDR97: 144,107,726–144,118,328, forward strandHGH1: 144,137,774–144,140,851, forward strandHGH1MROH1: 144,147,975–144,262,470, forward strandMROH1BOP1: 144,262,045–144,291,453, reverse strandBOP1SCX: 144,266,446–144,268,481, forward strandSCXHSF1: 144,291,521–144,314,729, forward strandHSF1DGAT1: 144,314,584–144,326,916, reverse strandDGAT1SCRT1: 144,330,565–144,336,503, reverse strandSCRT1SLC52A2: 144,333,957–144,361,447, forward strandSLC52A2CATSPERQ: 144,352,219–144,354,954, reverse strand: 144,353,228–144,355,609, reverse strandFBXL6: 144,355,427–144,359,376, reverse strandADCK5: 144,373,101–144,393,243, forward strandCPSF1: 144,393,229–144,409,864, reverse strandCPSF1SLC39A4: 144,409,742–144,416,894, reverse strandSLC39A4VPS28: 144,423,597–144,429,499, reverse strandVPS28TONSL: 144,428,763–144,444,488, reverse strandTONSLZFTRAF1: 144,447,345–144,462,908, reverse strandTMEM276-ZFTRAF1: 144,449,582–144,465,430, reverse strandTMEM276: 144,463,817–144,466,890, reverse strandKIFC2: 144,465,940–144,474,202, forward strandFOXH1: 144,473,412–144,475,873, reverse strandFOXH1PPP1R16A: 144,475,989–144,502,126, forward strandGPT: 144,502,608–144,507,494, forward strandGPTSLC33A2: 144,508,263–144,511,317, forward strandSLC33A2RECQL4: 144,511,284–144,517,890, reverse strandLRRC14: 144,517,957–144,526,244, forward strandLRRC24: 144,522,385–144,527,608, reverse strandC8orf82: 144,525,733–144,529,132, reverse strandARHGAP39: 144,529,179–144,685,879, reverse strandDiagram of GPAA1: 12 exons on the forward strand of chromosome 8Exon 1: 1 known disease-causing siteExon 2: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 6: 2 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 9: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 12: 1 known disease-causing siteExon 1: 144,082,634–144,082,804, 171 basesExon 2: 144,083,124–144,083,303, 180 basesExon 3: 144,083,389–144,083,500, 112 basesExon 4: 144,083,714–144,083,861, 148 basesExon 5: 144,083,939–144,084,040, 102 basesExon 6: 144,084,134–144,084,330, 197 basesExon 7: 144,084,413–144,084,609, 197 basesExon 8: 144,084,722–144,084,875, 154 basesExon 9: 144,085,043–144,085,138, 96 basesExon 10: 144,085,289–144,085,479, 191 basesExon 11: 144,085,573–144,085,743, 171 basesExon 12: 144,085,882–144,086,216, 335 bases1234567891011125′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 2.1 kb of the gene's 3.6 kb; 1,866 of those bases code for the protein.

Sequencing GPAA1

4Easy

How hard GPAA1 is to sequence with short reads, out of 100

Almost all of GPAA1's exons sit where short reads map cleanly.

What adds to it: the share of GPAA1's exons in each kind of hard region

  • Mappability0%
  • Homology0%
  • Repeats0%
  • GC content41%
  • Reference coverage0%

A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scored

18

positions in GPAA1 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 3.6 kb of GPAA1, introns included, not only the 2.1 kb of exons.

ClinVar pathogenic variants (18)

The GPAA1 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.

  • Pathogenic 4
  • Pathogenic/likely pathogenic 1
  • Likely pathogenic 13
VariantConditionsClinVar classificationReview status
NM_003801.4(GPAA1):c.1477_1478del (p.Arg493fs) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Pathogenic/likely pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
NM_003801.4(GPAA1):c.643C>T (p.Arg215Ter) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
NM_003801.4(GPAA1):c.319_320del (p.Ser107fs) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.619del (p.Met207fs) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.1465C>T (p.Gln489Ter) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.1826C>T (p.Pro609Leu) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.43del (p.Arg15fs) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.152C>T (p.Ser51Leu) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.367-1G>A (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.527G>C (p.Trp176Ser) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.616+1G>T (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.814-1G>T (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.831G>A (p.Trp277Ter) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.869T>C (p.Leu290Pro) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.872T>C (p.Leu291Pro) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.1011-2_1011-1del (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.1165-1C>T (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter
NM_003801.4(GPAA1):c.1165G>C (p.Ala389Pro) (opens in a new tab)glycosylphosphatidylinositol biosynthesis defect 15Likely pathogenic1 star out of 4 criteria provided, single submitter

Genes linked to the same conditions

Traits linked to GPAA1

The Human Phenotype Ontology lists these as features of the rare conditions GPAA1 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 2026-10-18: 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 2026.10.18-8b139e39.

Cite this page

APA

Dante Labs. (n.d.). GPAA1 gene: glycosylphosphatidylinositol anchor attachment 1. Retrieved 18 October 2026, from https://dantelabs.com/genes/gpaa1

Vancouver

Dante Labs. GPAA1 gene: glycosylphosphatidylinositol anchor attachment 1 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/gpaa1

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test