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

Gene ID: 7957, updated on 26-Jan-2024

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; AllianceGenome:HGNC:3413
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; MELF2
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
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Genomic context

See EPM2A in Genome Data Viewer
Location:
6q24.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (145383353..145736023, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (146574195..146956629, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (145946441..146057159, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90719 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144754756-144755258 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144780729-144780932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25221 Neighboring gene utrophin Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:144790768-144791444 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:144794141-144795340 Neighboring gene small nucleolar RNA, H/ACA box 98 Neighboring gene Sharpr-MPRA regulatory region 2668 Neighboring gene Sharpr-MPRA regulatory region 10150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25222 Neighboring gene NANOG hESC enhancer GRCh37_chr6:145107948-145108449 Neighboring gene Sharpr-MPRA regulatory region 9645 Neighboring gene MPRA-validated peak6190 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:145134839-145135340 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145190998-145191517 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:145218575-145219774 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:145272790-145273457 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:145275769-145276268 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:145298093-145298720 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145327891-145328441 Neighboring gene NANOG hESC enhancer GRCh37_chr6:145424274-145424879 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:145456814-145458013 Neighboring gene tRNA-Gln (anticodon TTG) 4-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25223 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145851539-145852203 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145852204-145852867 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145852881-145853456 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145853457-145854032 Neighboring gene RNA, U1 small nuclear 33, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:145874002-145874503 Neighboring gene zinc finger protein 131 pseudogene Neighboring gene Sharpr-MPRA regulatory region 3301 Neighboring gene Sharpr-MPRA regulatory region 9117 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:145994233-145994904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:145994905-145995576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25226 Neighboring gene uncharacterized LOC105378039 Neighboring gene uncharacterized LOC124901419 Neighboring gene EPM2A divergent transcript

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 Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in 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_016866791.1
XP_024302318.1
XP_024302319.1
XP_047275319.1
XP_047275320.1
XP_054212398.1
XP_054212399.1
XP_054212400.1
XP_054212401.1
XP_054212402.1
XP_054212403.1
XP_054212404.1
XP_054212405.1

NCBI Reference Sequences (RefSeq)

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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_012832.3 RefSeqGene

    Range
    5503..115718
    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
    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
    Conserved Domains (1) summary
    cd14526
    Location:1158
    DSP_laforin-like; dual specificity phosphatase domain of laforin and similar domains
  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
    Consensus CDS
    CCDS87452.1
  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
    Conserved Domains (1) summary
    cd14526
    Location:1158
    DSP_laforin-like; dual specificity phosphatase domain of laforin and similar domains
  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
    B3KMU5, B4DRZ2, O95278, O95483, Q5T3F5, Q6IS15, Q8IU96, Q8IX24, Q8IX25, Q9BS66, Q9UEN2
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    145383353..145736023 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446550.2XP_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_011536113.3XP_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_024446551.2XP_024302319.1  laforin isoform X4

    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_011536116.2XP_011534418.1  laforin isoform X4

    See identical proteins and their annotated locations for XP_011534418.1

    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_047419364.1XP_047275320.1  laforin isoform X5

  6. XM_017011302.2XP_016866791.1  laforin isoform X5

    UniProtKB/Swiss-Prot
    O95278
    Conserved Domains (1) summary
    cd14526
    Location:1158
    DSP_laforin-like; dual specificity phosphatase domain of laforin and similar domains
  7. XM_047419363.1XP_047275319.1  laforin isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    146574195..146956629 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356424.1XP_054212399.1  laforin isoform X1

  2. XM_054356425.1XP_054212400.1  laforin isoform X2

  3. XM_054356423.1XP_054212398.1  laforin isoform X6

    UniProtKB/Swiss-Prot
    B3KMU5, B4DRZ2, O95278, O95483, Q5T3F5, Q6IS15, Q8IU96, Q8IX24, Q8IX25, Q9BS66, Q9UEN2
  4. XM_054356428.1XP_054212403.1  laforin isoform X4

  5. XM_054356427.1XP_054212402.1  laforin isoform X4

  6. XM_054356430.1XP_054212405.1  laforin isoform X5

  7. XM_054356429.1XP_054212404.1  laforin isoform X5

  8. XM_054356426.1XP_054212401.1  laforin isoform X3