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    EPM2A EPM2A glucan phosphatase, laforin [ Homo sapiens (human) ]

    Gene ID: 7957, updated on 17-Jun-2019

    Summary

    Official Symbol
    EPM2Aprovided by HGNC
    Official Full Name
    EPM2A glucan phosphatase, laforinprovided by HGNC
    Primary source
    HGNC:HGNC:3413
    See related
    Ensembl:ENSG00000112425 MIM:607566
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    EPM2; MELF
    Summary
    This gene encodes a dual-specificity phosphatase and may be involved in the regulation of glycogen metabolism. The protein acts on complex carbohydrates to prevent glycogen hyperphosphorylation, thus avoiding the formation of insoluble aggregates. Loss-of-function mutations in this gene have been associated with Lafora disease, a rare, adult-onset recessive neurodegenerative disease, which results in myoclonus epilepsy and usually results in death several years after the onset of symptoms. The disease is characterized by the accumulation of insoluble particles called Lafora bodies, which are derived from glycogen. [provided by RefSeq, Jan 2018]
    Expression
    Ubiquitous expression in heart (RPKM 6.9), kidney (RPKM 4.5) and 24 other tissues See more
    Orthologs

    Genomic context

    See EPM2A in Genome Data Viewer
    Location:
    6q24.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (145382540..145736023, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (145946440..146057128, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene utrophin Neighboring gene small nucleolar RNA, H/ACA box 98 Neighboring gene tRNA-Gln (anticodon TTG) 4-1 Neighboring gene RNA, U1 small nuclear 33, pseudogene Neighboring gene zinc finger protein 131 pseudogene Neighboring gene uncharacterized LOC100507557 Neighboring gene uncharacterized LOC105378039 Neighboring gene F-box protein 30 Neighboring gene SNF2 histone linker PHD RING helicase

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Disease, organism-specific biosystem (from REACTOME)
      Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
    • Diseases of carbohydrate metabolism, organism-specific biosystem (from REACTOME)
      Diseases of carbohydrate metabolism, organism-specific biosystemThe processes by which dietary carbohydrate is digested to monosaccharides and these are taken up from the gut lumen into cells where they are oxidized to yield energy or consumed in biosynthetic pro...
    • Diseases of metabolism, organism-specific biosystem (from REACTOME)
      Diseases of metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Glucose metabolism, organism-specific biosystem (from REACTOME)
      Glucose metabolism, organism-specific biosystemGlucose is the major form in which dietary sugars are made available to cells of the human body. Its breakdown is a major source of energy for all cells, and is essential for the brain and red blood ...
    • Glycogen storage diseases, organism-specific biosystem (from REACTOME)
      Glycogen storage diseases, organism-specific biosystemThe regulated turnover of glycogen plays a central, tissue-specific role in the maintenance of blood glucose levels and in the provision of glucose to tissues such as muscle and brain in response to ...
    • Glycogen synthesis, organism-specific biosystem (from REACTOME)
      Glycogen synthesis, organism-specific biosystemGlycogen, a highly branched glucose polymer, is formed and broken down in most human tissues, but is most abundant in liver and muscle, where it serves as a major stored fuel. Glycogen metabolism has...
    • Metabolism, organism-specific biosystem (from REACTOME)
      Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Metabolism of carbohydrates, organism-specific biosystem (from REACTOME)
      Metabolism of carbohydrates, organism-specific biosystemThese pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the b...
    • Myoclonic epilepsy of Lafora, organism-specific biosystem (from REACTOME)
      Myoclonic epilepsy of Lafora, organism-specific biosystemLafora disease is a progressive neurodegenerative disorder with onset typically late in childhood, characterized by seizures and progressive neurological deterioration and death within ten years of o...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    negative regulation of TOR signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of macroautophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    laforin
    Names
    EPM2A, laforin glucan phosphatase
    LAFPTPase
    epilepsy, progressive myoclonus type 2, Lafora disease (laforin)
    epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)
    glucan phosphatase
    glycogen phosphatase
    lafora PTPase
    NP_001018051.1
    NP_001346986.1
    NP_001346993.1
    NP_001347000.1
    NP_001355058.1
    NP_001355059.1
    NP_001355060.1
    NP_001355061.1
    NP_005661.1
    XP_011534415.1
    XP_011534418.1
    XP_016866790.1
    XP_016866791.1
    XP_024302318.1
    XP_024302319.1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012832.2 RefSeqGene

      Range
      5001..115552
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001018041.2NP_001018051.1  laforin isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment of the coding region compared to variant 1. The resulting isoform (b), also known as C-terISO, contains a shorter and distinct C-terminus compared to isoform a. Isoform b has been localized to the nucleus.
      Source sequence(s)
      AF284580, AF454491, AF454494, AJ130764, BC070047, BI463677
      Consensus CDS
      CCDS87454.1
      UniProtKB/Swiss-Prot
      O95278
      UniProtKB/TrEMBL
      H0Y6I8
      Related
      ENSP00000405913.2, ENST00000435470.2
      Conserved Domains (2) summary
      cd05806
      Location:1129
      CBM20_laforin; Laforin protein tyrosine phosphatase, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Laforin, encoded by the EPM2A gene, is a dual-specificity phosphatase that dephosphorylates complex carbohydrates. Mutations in the gene encoding ...
      cl21483
      Location:158304
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    2. NM_001360057.2NP_001346986.1  laforin isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the coding region, resulting in a frameshift and an early start codon, compared to variant 1. It encodes isoform c, which has a shorter and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AF454491, AF454493, BC005286, BI599200
      Consensus CDS
      CCDS87453.1
      Related
      ENSP00000492876.1, ENST00000638262.1
      Conserved Domains (1) summary
      cd05806
      Location:1129
      CBM20_laforin; Laforin protein tyrosine phosphatase, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Laforin, encoded by the EPM2A gene, is a dual-specificity phosphatase that dephosphorylates complex carbohydrates. Mutations in the gene encoding ...
    3. NM_001360064.2NP_001346993.1  laforin isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform d, which has a shorter N-terminus, compared to isoform a. Variants 4 and 5 encode the same isoform (d).
      Source sequence(s)
      AF454491, AL023806, AL365193
      Consensus CDS
      CCDS87452.1
      Related
      ENSP00000492701.1, ENST00000639423.1
      Conserved Domains (1) summary
      cl21483
      Location:20166
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    4. NM_001360071.2NP_001347000.1  laforin isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform d, which has a shorter N-terminus, compared to isoform a. Variants 4 and 5 encode the same isoform (d).
      Source sequence(s)
      AF454491, AF454493, BC005286, BI599200
      Consensus CDS
      CCDS87452.1
      Related
      ENSP00000498790.1, ENST00000650914.1
      Conserved Domains (1) summary
      cl21483
      Location:20166
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    5. NM_001368129.2NP_001355058.1  laforin isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variant 10, encodes isoform e.
      Source sequence(s)
      AL023806, AL365193
    6. NM_001368130.1NP_001355059.1  laforin isoform f

      Status: REVIEWED

      Source sequence(s)
      AL023806, AL365193
    7. NM_001368131.1NP_001355060.1  laforin isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9), as well as variants 4 and 5, encodes isoform d.
      Source sequence(s)
      AL023806, AL365193
    8. NM_001368132.1NP_001355061.1  laforin isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10), as well as variant 6, encodes isoform e.
      Source sequence(s)
      AL023806, AL365193
    9. NM_005670.4NP_005661.1  laforin isoform a

      See identical proteins and their annotated locations for NP_005661.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (a). Isoform a has been localized to the rough endoplasmic reticulum.
      Source sequence(s)
      AF284580, AF454494, BC005286
      Consensus CDS
      CCDS5206.1
      UniProtKB/Swiss-Prot
      O95278
      Related
      ENSP00000356489.3, ENST00000367519.9
      Conserved Domains (2) summary
      cd05806
      Location:1129
      CBM20_laforin; Laforin protein tyrosine phosphatase, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Laforin, encoded by the EPM2A gene, is a dual-specificity phosphatase that dephosphorylates complex carbohydrates. Mutations in the gene encoding ...
      cl21483
      Location:158304
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

    RNA

    1. NR_153398.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) includes an alternate 5' terminal exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AF454491, AL023806, BC005286, BE268120

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

      Range
      145382540..145736023 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446550.1XP_024302318.1  laforin isoform X1

      Conserved Domains (1) summary
      cd05806
      Location:1129
      CBM20_laforin; Laforin protein tyrosine phosphatase, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Laforin, encoded by the EPM2A gene, is a dual-specificity phosphatase that dephosphorylates complex carbohydrates. Mutations in the gene encoding ...
    2. XM_011536113.2XP_011534415.1  laforin isoform X2

      Conserved Domains (1) summary
      cd05806
      Location:1129
      CBM20_laforin; Laforin protein tyrosine phosphatase, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Laforin, encoded by the EPM2A gene, is a dual-specificity phosphatase that dephosphorylates complex carbohydrates. Mutations in the gene encoding ...
    3. XM_024446551.1XP_024302319.1  laforin isoform X3

      Conserved Domains (1) summary
      cl21483
      Location:20166
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    4. XM_011536116.1XP_011534418.1  laforin isoform X3

      See identical proteins and their annotated locations for XP_011534418.1

      UniProtKB/Swiss-Prot
      O95278
      UniProtKB/TrEMBL
      H0UI04
      Related
      ENSP00000491353.1, ENST00000638778.1
      Conserved Domains (1) summary
      cl21483
      Location:20166
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    5. XM_017011301.1XP_016866790.1  laforin isoform X4

      UniProtKB/Swiss-Prot
      O95278
    6. XM_017011302.1XP_016866791.1  laforin isoform X4

      UniProtKB/Swiss-Prot
      O95278
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