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Gene

GAA

alpha glucosidase

Summary

Cytogenetic location
17q25.3
Coordinates
Chromosome 17: 80,101,581–80,119,881 (GRCh38)
Exons
20 exons across 18.3 kb
Protein
952 amino acids
Inheritance
Autosomal recessive
MANE Select transcript
ENST00000302262.8NM_000152.5
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

  • Pompe Disease

    • Pompe Disease (Glycogen Storage Disease II)Autosomal recessive

      Glycogen storage disease due to acid maltase deficiency (AMD) is an autosomal recessive trait leading to metabolic myopathy that affects cardiac and respiratory muscles in addition to skeletal muscle and other tissues. AMD represents a wide spectrum of clinical presentations caused by an accumulation of glycogen in lysosomes: Glycogen storage disease due to acid maltase deficiency, infantile onset, non-classic infantile onset and adult onset. Early onset forms are more severe and often fatal.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong
      • On the ACMG secondary findings list
      What knowing changes

      Enzyme replacement therapy (alglucosidase alfa; cipaglucosidase alfa + miglustat, superior in late-onset disease); respiratory support (BiPAP/CPAP/mechanical ventilation); physiotherapy; gene therapy in clinical trials

Broader groupings

  • Lysosomal Storage Disease

    • Lysosomal storage disease (other and unspecified types)

      One of 59 genes linked to it

      Covers lysosomal storage diseases without a dedicated report, such as Farber disease and other ASAH1-related disorders, prosaposin (PSAP) deficiencies, multiple sulfatase deficiency, mucopolysaccharidosis types IX and X, and Dorfman-Chanarin disease; inheritance varies by subtype, most often autosomal recessive.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong
      • On the ACMG secondary findings list

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 GAA is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Variants with a page
Chromosome 17, with a bracket where GAA sits. GAA and 16 genes near it on chromosome 17, from 79,610,731 to 80,610,730.Chromosome 1717q25.3p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.379.8 Mb80 Mb80.2 Mb80.4 Mb80.6 MbRBFOX3: 79,089,345–79,611,317, reverse strandRBFOX3ENPP7: 79,728,809–79,742,930, forward strandENPP7CBX2: 79,778,135–79,788,394, forward strandCBX2CBX8: 79,792,132–79,801,683, reverse strandCBX8CBX4: 79,833,156–79,839,486, reverse strandCBX4TBC1D16: 79,932,343–80,035,887, reverse strandTBC1D16CCDC40: 80,036,000–80,100,613, forward strandCCDC40GAA: 80,101,581–80,119,881, forward strandGAAEIF4A3: 80,132,700–80,147,151, reverse strandEIF4A3CARD14: 80,169,992–80,216,073, forward strandCARD14SGSH: 80,206,716–80,220,928, reverse strandSGSHSLC26A11: 80,219,699–80,253,509, forward strandSLC26A11RNF213: 80,260,807–80,398,794, forward strandRNF213ENDOV: 80,415,147–80,438,086, forward strandENDOVNPTX1: 80,466,834–80,477,843, reverse strandNPTX1RPTOR: 80,544,819–80,966,371, forward strandRPTOR: 80,545,075–80,545,134, forward strandDiagram of GAA: 20 exons on the forward strand of chromosome 17Exon 2: 75 known disease-causing sitesExon 3: 20 known disease-causing sitesExon 4: 41 known disease-causing sitesExon 5: 23 known disease-causing sitesExon 6: 29 known disease-causing sitesExon 7: 28 known disease-causing sitesExon 8: 32 known disease-causing sitesExon 9: 35 known disease-causing sitesExon 10: 30 known disease-causing sitesExon 11: 27 known disease-causing sitesExon 12: 40 known disease-causing sitesExon 13: 41 known disease-causing sitesExon 14: 41 known disease-causing sitesExon 15: 36 known disease-causing sitesExon 16: 34 known disease-causing sitesExon 17: 23 known disease-causing sitesExon 18: 25 known disease-causing sitesExon 19: 16 known disease-causing sitesExon 20: 2 known disease-causing sitesExon 1: 80,101,581–80,101,890, 310 basesExon 2: 80,104,555–80,105,132, 578 bases. 56 variants with a page in exon 2. List themExon 3: 80,105,749–80,105,894, 146 bases. 8 variants with a page in exon 3. List themExon 4: 80,107,557–80,107,722, 166 bases. 26 variants with a page in exon 4. List themExon 5: 80,107,800–80,107,896, 97 bases. 15 variants with a page in exon 5. List themExon 6: 80,108,290–80,108,409, 120 bases. 19 variants with a page in exon 6. List themExon 7: 80,108,489–80,108,607, 119 bases. 21 variants with a page in exon 7. List themExon 8: 80,108,697–80,108,828, 132 bases. 17 variants with a page in exon 8. List themExon 9: 80,109,945–80,110,055, 111 bases. 23 variants with a page in exon 9. List themExon 10: 80,110,727–80,110,840, 114 bases. 23 variants with a page in exon 10. List themExon 11: 80,110,941–80,111,025, 85 bases. 21 variants with a page in exon 11. List themExon 12: 80,111,983–80,112,100, 118 bases. 23 variants with a page in exon 12. List themExon 13: 80,112,578–80,112,711, 134 bases. 37 variants with a page in exon 13. List themExon 14: 80,112,876–80,113,027, 152 bases. 37 variants with a page in exon 14. List themExon 15: 80,113,218–80,113,366, 149 bases. 26 variants with a page in exon 15. List themExon 16: 80,116,968–80,117,109, 142 bases. 28 variants with a page in exon 16. List themExon 17: 80,117,600–80,117,749, 150 bases. 13 variants with a page in exon 17. List themExon 18: 80,118,193–80,118,357, 165 bases. 10 variants with a page in exon 18. List themExon 19: 80,118,653–80,118,805, 153 bases. 8 variants with a page in exon 19. List themExon 20: 80,119,272–80,119,881, 610 bases. 1 variant with a page in exon 20. List them124681012141618205′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 3.8 kb of the gene's 18.3 kb; 2,859 of those bases code for the protein.

How a genome test reads GAA

679

positions in GAA 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 18.3 kb of GAA, introns included, not only the 3.8 kb of exons.

Variants with a page (486)

The GAA variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A14Rfs*18c.40_47delExon 280,104,622Pathogenic3 stars out of 4 reviewed by expert panel
A150Gfs*27c.448dupExon 280,105,032Likely pathogenic3 stars out of 4 reviewed by expert panel
A382Lfs*10c.1143delExon 780,108,554Pathogenic3 stars out of 4 reviewed by expert panel
A486Pc.1456G>CExon 1080,110,745Likely pathogenic3 stars out of 4 reviewed by expert panel
A610Dfs*88c.1824_1828dupExon 1380,112,644Pathogenic3 stars out of 4 reviewed by expert panel
A691Sfs*7c.2066_2070dupExon 1580,113,240Pathogenic3 stars out of 4 reviewed by expert panel
A761Ifs*35c.2281delinsATExon 1680,117,059Pathogenic3 stars out of 4 reviewed by expert panel
c.-32-1G>CIntron 180,104,554Likely pathogenic3 stars out of 4 reviewed by expert panel
c.-32-2A>GIntron 180,104,553Likely pathogenic3 stars out of 4 reviewed by expert panel
c.-32-3C>AIntron 180,104,552Pathogenic3 stars out of 4 reviewed by expert panel

See all 486 GAA variants →

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.). GAA gene: alpha glucosidase. Retrieved 17 October 2026, from https://dantelabs.com/genes/gaa

Vancouver

Dante Labs. GAA gene: alpha glucosidase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/gaa

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