Human Gene GAA (uc002jxp.3)
  Description: Homo sapiens glucosidase, alpha; acid (GAA), transcript variant 1, mRNA.
RefSeq Summary (NM_000152): This gene encodes lysosomal alpha-glucosidase, which is essential for the degradation of glycogen to glucose in lysosomes. The encoded preproprotein is proteolytically processed to generate multiple intermediate forms and the mature form of the enzyme. Defects in this gene are the cause of glycogen storage disease II, also known as Pompe's disease, which is an autosomal recessive disorder with a broad clinical spectrum. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016].
Transcript (Including UTRs)
   Position: hg19 chr17:78,075,355-78,093,679 Size: 18,325 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr17:78,078,386-78,093,130 Size: 14,745 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:78,075,355-78,093,679)mRNA (may differ from genome)Protein (952 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LYAG_HUMAN
DESCRIPTION: RecName: Full=Lysosomal alpha-glucosidase; EC=3.2.1.20; AltName: Full=Acid maltase; AltName: Full=Aglucosidase alfa; Contains: RecName: Full=76 kDa lysosomal alpha-glucosidase; Contains: RecName: Full=70 kDa lysosomal alpha-glucosidase; Flags: Precursor;
FUNCTION: Essential for the degradation of glygogen to glucose in lysosomes.
CATALYTIC ACTIVITY: Hydrolysis of terminal, non-reducing (1->4)- linked alpha-D-glucose residues with release of alpha-D-glucose.
SUBCELLULAR LOCATION: Lysosome. Lysosome membrane.
PTM: The different forms of acid glucosidase are obtained by proteolytic processing.
PTM: Phosphorylation of mannose residues ensures efficient transport of the enzyme to the lysosomes via the mannose 6- phosphate receptor.
POLYMORPHISM: There are three common alleles of GAA: GAA*1, GAA*2 and GAA*4. The sequence shown is that of allele GAA*1, which is the most common. Alleles GAA*2 and GAA*4 are much rarer.
DISEASE: Defects in GAA are the cause of glycogen storage disease type 2 (GSD2) [MIM:232300]; also called acid alpha-glucosidase (GAA) deficiency or acid maltase deficiency (AMD). GSD2 is a metabolic disorder with a broad clinical spectrum. The severe infantile form, or Pompe disease, presents at birth with massive accumulation of glycogen in muscle, heart and liver. Cardiomyopathy and muscular hypotonia are the cardinal features of this form whose life expectancy is less than two years. The juvenile and adult forms present as limb-girdle muscular dystrophy beginning in the lower limbs. Final outcome depends on respiratory muscle failure. Patients with the adult form can be free of clinical symptoms for most of their life but finally develop a slowly progressive myopathy.
SIMILARITY: Belongs to the glycosyl hydrolase 31 family.
SIMILARITY: Contains 1 P-type (trefoil) domain.
WEB RESOURCE: Name=GAA; Note=Mutations in alpha-glucosidase; URL="http://cluster15.erasmusmc.nl/klgn/pompe/mutations.html";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/GAA";
WEB RESOURCE: Name=Wikipedia; Note=Alpha-glucosidase entry; URL="http://en.wikipedia.org/wiki/Alpha-glucosidase";
WEB RESOURCE: Name=Glucosidase, alpha, acid (Pompe disease) (GAA); Note=Leiden Open Variation Database (LOVD); URL="http://www.lovd.nl/GAA";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GAA
CDC HuGE Published Literature: GAA
Positive Disease Associations: delayed onset of glycogenosis type II.
Related Studies:
  1. delayed onset of glycogenosis type II.
    Boerkoel CF et al. 1995, Leaky splicing mutation in the acid maltase gene is associated with delayed onset of glycogenosis type II., American journal of human genetics. 1995 Apr;56(4):887-97. [PubMed 7717400]

-  MalaCards Disease Associations
  MalaCards Gene Search: GAA
Diseases sorted by gene-association score: glycogen storage disease ii* (1351), glycogen storage disease due to acid maltase deficiency, infantile onset* (350), glycogen storage disease due to acid maltase deficiency, late-onset* (350), glycogen storage disease (87), danon disease (25), glycogen storage disease iiia (17), respiratory failure (14), glycogen storage disease iv (14), carbohydrate metabolic disorder (14), mcardle disease (13), mucopolysaccharidosis is (12), muscular dystrophy, rigid spine, 1 (11), lysosomal acid phosphatase deficiency (10), myopathy, x-linked, with excessive autophagy (9), mannosidosis, alpha-, types i and ii (8), mucopolysaccharidosis ii (7), fucosidosis (7), carotid artery dissection (7), mucopolysaccharidosis type vi (7), facioscapulohumeral muscular dystrophy 1 (7), neuromuscular disease (6), aspartylglucosaminuria (6), lysosomal storage disease (5), myopathy (5), inherited metabolic disorder (5), mannosidosis, beta (4), cardiomyopathy (3), mitochondrial disorders (1), cardiomyopathy, familial hypertrophic (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.21 RPKM in Testis
Total median expression: 954.02 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -196.00367-0.534 Picture PostScript Text
3' UTR -246.20549-0.448 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011013 - Glyco_hydro-type_carb-bd
IPR000322 - Glyco_hydro_31
IPR025887 - Glyco_hydro_31_N_dom
IPR017853 - Glycoside_hydrolase_SF
IPR000519 - P_trefoil
IPR017957 - P_trefoil_CS

Pfam Domains:
PF00088 - Trefoil (P-type) domain
PF01055 - Glycosyl hydrolases family 31
PF13802 - Galactose mutarotase-like
PF16863 - N-terminal barrel of NtMGAM and CtMGAM, maltase-glucoamylase

SCOP Domains:
51445 - (Trans)glycosidases
57492 - Trefoil

ModBase Predicted Comparative 3D Structure on P10253
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004558 alpha-1,4-glucosidase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0032450 maltose alpha-glucosidase activity
GO:0090599 alpha-glucosidase activity

Biological Process:
GO:0000023 maltose metabolic process
GO:0002026 regulation of the force of heart contraction
GO:0002086 diaphragm contraction
GO:0003007 heart morphogenesis
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
GO:0005985 sucrose metabolic process
GO:0006006 glucose metabolic process
GO:0006941 striated muscle contraction
GO:0007040 lysosome organization
GO:0007626 locomotory behavior
GO:0008152 metabolic process
GO:0009888 tissue development
GO:0043181 vacuolar sequestering
GO:0043312 neutrophil degranulation
GO:0046716 muscle cell cellular homeostasis
GO:0050884 neuromuscular process controlling posture
GO:0050885 neuromuscular process controlling balance
GO:0060048 cardiac muscle contraction

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0035577 azurophil granule membrane
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane


-  Descriptions from all associated GenBank mRNAs
  KJ896843 - Synthetic construct Homo sapiens clone ccsbBroadEn_06237 GAA gene, encodes complete protein.
KR711021 - Synthetic construct Homo sapiens clone CCSBHm_00019059 GAA (GAA) mRNA, encodes complete protein.
KR711022 - Synthetic construct Homo sapiens clone CCSBHm_00019210 GAA (GAA) mRNA, encodes complete protein.
AK299462 - Homo sapiens cDNA FLJ57046 complete cds, highly similar to Lysosomal alpha-glucosidase precursor (EC 3.2.1.20).
BC040431 - Homo sapiens glucosidase, alpha; acid, mRNA (cDNA clone MGC:48746 IMAGE:5739991), complete cds.
BC065262 - Homo sapiens cDNA clone IMAGE:6157057, partial cds.
Y00839 - H.sapiens GAA mRNA for lysosomal alpha-glucosidase (acid maltase).
JD406199 - Sequence 387223 from Patent EP1572962.
JD408839 - Sequence 389863 from Patent EP1572962.
JD458724 - Sequence 439748 from Patent EP1572962.
JD482259 - Sequence 463283 from Patent EP1572962.
JD533038 - Sequence 514062 from Patent EP1572962.
JD271248 - Sequence 252272 from Patent EP1572962.
JD202783 - Sequence 183807 from Patent EP1572962.
M34424 - Human acid alpha-glucosidase (GAA) mRNA, complete cds.
AB384912 - Synthetic construct DNA, clone: pF1KB4173, Homo sapiens GAA gene for lysosomal alpha-glucosidase precursor, complete cds, without stop codon, in Flexi system.
DQ907243 - Homo sapiens alpha-glucosidase (GAA) mRNA, GAA-P457L allele, complete cds.
LQ405261 - Sequence 1 from Patent WO2016149508.
S76893 - GAA=lysosomal alpha-D-glucosidase {exon 14} [human, Pompe's disease patient, fibroblasts, mRNA Partial Mutant, 152 nt].
LF209441 - JP 2014500723-A/16944: Polycomb-Associated Non-Coding RNAs.
LF328544 - JP 2014500723-A/136047: Polycomb-Associated Non-Coding RNAs.
LF328545 - JP 2014500723-A/136048: Polycomb-Associated Non-Coding RNAs.
JD489504 - Sequence 470528 from Patent EP1572962.
JD462945 - Sequence 443969 from Patent EP1572962.
JD283906 - Sequence 264930 from Patent EP1572962.
JD458258 - Sequence 439282 from Patent EP1572962.
JD128540 - Sequence 109564 from Patent EP1572962.
JD454730 - Sequence 435754 from Patent EP1572962.
JD141133 - Sequence 122157 from Patent EP1572962.
JD297404 - Sequence 278428 from Patent EP1572962.
JD124349 - Sequence 105373 from Patent EP1572962.
LF328546 - JP 2014500723-A/136049: Polycomb-Associated Non-Coding RNAs.
JD271026 - Sequence 252050 from Patent EP1572962.
BC015908 - Homo sapiens glucosidase, alpha; acid, mRNA (cDNA clone IMAGE:3922955).
JD115852 - Sequence 96876 from Patent EP1572962.
JD222622 - Sequence 203646 from Patent EP1572962.
JD446837 - Sequence 427861 from Patent EP1572962.
JD134193 - Sequence 115217 from Patent EP1572962.
JD255372 - Sequence 236396 from Patent EP1572962.
JD487563 - Sequence 468587 from Patent EP1572962.
JD528325 - Sequence 509349 from Patent EP1572962.
MA564121 - JP 2018138019-A/136047: Polycomb-Associated Non-Coding RNAs.
MA564122 - JP 2018138019-A/136048: Polycomb-Associated Non-Coding RNAs.
MA564123 - JP 2018138019-A/136049: Polycomb-Associated Non-Coding RNAs.
MA445018 - JP 2018138019-A/16944: Polycomb-Associated Non-Coding RNAs.
MB451204 - JP 2018511588-A/1: MRNA THERAPY FOR POMPE DISEASE.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00052 - Galactose metabolism
hsa00500 - Starch and sucrose metabolism
hsa01100 - Metabolic pathways
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein P10253 (Reactome details) participates in the following event(s):

R-HSA-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-9036727 GAA hydrolyzes lysosomal glycogen
R-HSA-6798695 Neutrophil degranulation
R-HSA-70221 Glycogen breakdown (glycogenolysis)
R-HSA-168249 Innate Immune System
R-HSA-8982491 Glycogen metabolism
R-HSA-168256 Immune System
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: LYAG_HUMAN, NM_000152, NP_001073272, P10253, Q09GN4, Q14351, Q16302, Q8IWE7
UCSC ID: uc002jxp.3
RefSeq Accession: NM_000152
Protein: P10253 (aka LYAG_HUMAN)
CCDS: CCDS32760.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene GAA:
gsd2 (Pompe Disease)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000152.3
exon count: 20CDS single in 3' UTR: no RNA size: 3782
ORF size: 2859CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5894.00frame shift in genome: no % Coverage: 99.81
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 255# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.