Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	7957
Gene name	EPM2A glucan phosphatase, laforin
Gene symbol	EPM2A
Synonyms (NCBI Gene)	EPM2MELFMELF2
Chromosome	6
Chromosome location	6q24.3
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

Show/Hide all (17)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104893950	G>A,C	Pathogenic	Intron variant, non coding transcript variant, coding sequence variant, genic downstream transcript variant, missense variant, stop gained
rs137852915	G>A	Pathogenic	Non coding transcript variant, 5 prime UTR variant, genic upstream transcript variant, missense variant, coding sequence variant
rs137852916	C>T	Pathogenic, uncertain-significance	Missense variant, intron variant, coding sequence variant
rs137852917	C>A,T	Likely-pathogenic, pathogenic	Non coding transcript variant, intron variant, genic downstream transcript variant, missense variant, coding sequence variant
rs146321088	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, coding sequence variant, synonymous variant, intron variant, missense variant, non coding transcript variant
rs147399860	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, missense variant
rs571938170	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, intron variant, coding sequence variant
rs587776553	->T	Pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant, stop gained
rs587776554	->A	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant, intron variant, genic downstream transcript variant, 3 prime UTR variant
rs777767978	T>C	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs781291421	C>A,T	Pathogenic, uncertain-significance, likely-pathogenic	Missense variant, intron variant, stop gained, coding sequence variant
rs796052427	T>A	Pathogenic	Non coding transcript variant, synonymous variant, missense variant, intron variant, genic downstream transcript variant, coding sequence variant
rs1131691331	A>TGCATG	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, intron variant, genic downstream transcript variant
rs1554263318	TGAATAATGCATGGCTTGGTGGCCTGCAATATTAAAATAGAAGTCTGTTGTGTGCTTCATTTCATTGGTGTGCCCAGTGGCCTCAATCCAGTGTCCTATTGGGAGACAATACACACCATCCACCAAGTTGTTTTCATTGTAAGTACAGCAACGGTCATGATGAGGTCCATTGCCT>-	Pathogenic	Splice acceptor variant, splice donor variant, coding sequence variant, non coding transcript variant, initiator codon variant, 5 prime UTR variant, genic upstream transcript variant
rs1554263320	->AATG	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant, 5 prime UTR variant, genic upstream transcript variant
rs1554263366	T>C	Pathogenic	Coding sequence variant, non coding transcript variant, 5 prime UTR variant, genic upstream transcript variant, missense variant
rs1582935082	G>A	Likely-pathogenic	Missense variant, coding sequence variant, intron variant

Show/Hide all (58)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024904	hsa-miR-215-5p	Microarray	19074876
MIRT026512	hsa-miR-192-5p	Microarray	19074876
MIRT030853	hsa-miR-21-5p	Microarray	18591254
MIRT966833	hsa-miR-127-5p	CLIP-seq
MIRT966834	hsa-miR-1287	CLIP-seq
MIRT966835	hsa-miR-1290	CLIP-seq
MIRT966836	hsa-miR-186	CLIP-seq
MIRT966837	hsa-miR-27a	CLIP-seq
MIRT966838	hsa-miR-27b	CLIP-seq
MIRT966839	hsa-miR-3133	CLIP-seq
MIRT966840	hsa-miR-3140-3p	CLIP-seq
MIRT966841	hsa-miR-3167	CLIP-seq
MIRT966842	hsa-miR-320e	CLIP-seq
MIRT966843	hsa-miR-4776-3p	CLIP-seq
MIRT966844	hsa-miR-513a-5p	CLIP-seq
MIRT966845	hsa-miR-561	CLIP-seq
MIRT966846	hsa-miR-876-5p	CLIP-seq
MIRT966847	hsa-miR-1261	CLIP-seq
MIRT966848	hsa-miR-298	CLIP-seq
MIRT966849	hsa-miR-3140-5p	CLIP-seq
MIRT966850	hsa-miR-3174	CLIP-seq
MIRT966851	hsa-miR-3201	CLIP-seq
MIRT966852	hsa-miR-3607-3p	CLIP-seq
MIRT966853	hsa-miR-3611	CLIP-seq
MIRT966854	hsa-miR-3670	CLIP-seq
MIRT966855	hsa-miR-3929	CLIP-seq
MIRT966856	hsa-miR-4419b	CLIP-seq
MIRT966857	hsa-miR-4422	CLIP-seq
MIRT966858	hsa-miR-4433	CLIP-seq
MIRT966859	hsa-miR-4459	CLIP-seq
MIRT966860	hsa-miR-4478	CLIP-seq
MIRT966861	hsa-miR-4690-5p	CLIP-seq
MIRT966862	hsa-miR-4699-5p	CLIP-seq
MIRT966863	hsa-miR-4718	CLIP-seq
MIRT966864	hsa-miR-4766-5p	CLIP-seq
MIRT966865	hsa-miR-4768-3p	CLIP-seq
MIRT966866	hsa-miR-4779	CLIP-seq
MIRT966867	hsa-miR-4789-3p	CLIP-seq
MIRT966868	hsa-miR-4791	CLIP-seq
MIRT966869	hsa-miR-486-3p	CLIP-seq
MIRT966870	hsa-miR-512-3p	CLIP-seq
MIRT966871	hsa-miR-517a	CLIP-seq
MIRT966872	hsa-miR-517b	CLIP-seq
MIRT966873	hsa-miR-517c	CLIP-seq
MIRT966874	hsa-miR-548g	CLIP-seq
MIRT966875	hsa-miR-591	CLIP-seq
MIRT966876	hsa-miR-921	CLIP-seq
MIRT1986379	hsa-miR-1238	CLIP-seq
MIRT1986380	hsa-miR-3074-3p	CLIP-seq
MIRT1986381	hsa-miR-3200-3p	CLIP-seq
MIRT966852	hsa-miR-3607-3p	CLIP-seq
MIRT1986382	hsa-miR-376c	CLIP-seq
MIRT1986383	hsa-miR-4424	CLIP-seq
MIRT1986384	hsa-miR-4802-3p	CLIP-seq
MIRT1986385	hsa-miR-664	CLIP-seq
MIRT1986386	hsa-miR-943	CLIP-seq
MIRT2220944	hsa-miR-4786-5p	CLIP-seq
MIRT2220945	hsa-miR-769-5p	CLIP-seq

Show/Hide all (78)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000045	Process	Autophagosome assembly	IEA
GO:0001558	Process	Regulation of cell growth	IEA
GO:0004373	Function	Alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity	IEA
GO:0004721	Function	Phosphoprotein phosphatase activity	IEA
GO:0004722	Function	Protein serine/threonine phosphatase activity	IDA	12915448
GO:0004722	Function	Protein serine/threonine phosphatase activity	IEA
GO:0004725	Function	Protein tyrosine phosphatase activity	IDA	11001928, 12915448
GO:0004725	Function	Protein tyrosine phosphatase activity	IEA
GO:0004725	Function	Protein tyrosine phosphatase activity	IMP	11739371
GO:0005515	Function	Protein binding	IPI	12915448, 14532330, 15930137, 18070875, 18617530, 21505799, 22961547, 24837458, 25538239, 25544560, 32814053, 33961781
GO:0005634	Component	Nucleus	IDA	18617530
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IDA	11739371, 17908927, 18617530
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005829	Component	Cytosol	IDA	12915448
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IEA
GO:0005977	Process	Glycogen metabolic process	IEA
GO:0005977	Process	Glycogen metabolic process	IEA
GO:0005977	Process	Glycogen metabolic process	IMP	25538239
GO:0005977	Process	Glycogen metabolic process	NAS	9931343
GO:0005978	Process	Glycogen biosynthetic process	IEA
GO:0005978	Process	Glycogen biosynthetic process	TAS
GO:0006470	Process	Protein dephosphorylation	IDA	11001928, 12915448
GO:0006796	Process	Phosphate-containing compound metabolic process	IEA
GO:0006816	Process	Calcium ion transport	IEA
GO:0006914	Process	Autophagy	IEA
GO:0006914	Process	Autophagy	IEA
GO:0007005	Process	Mitochondrion organization	IEA
GO:0007399	Process	Nervous system development	IEA
GO:0009892	Process	Negative regulation of metabolic process	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0010629	Process	Negative regulation of gene expression	IEA
GO:0010923	Process	Negative regulation of phosphatase activity	IDA	18617530
GO:0014009	Process	Glial cell proliferation	IEA
GO:0015813	Process	L-glutamate transmembrane transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0016239	Process	Positive regulation of macroautophagy	IEA
GO:0016239	Process	Positive regulation of macroautophagy	IMP	20453062
GO:0016311	Process	Dephosphorylation	IDA	18617530
GO:0016787	Function	Hydrolase activity	IEA
GO:0016791	Function	Phosphatase activity	IDA	18617530
GO:0016791	Function	Phosphatase activity	IDA	18617530
GO:0016791	Function	Phosphatase activity	IEA
GO:0019203	Function	Carbohydrate phosphatase activity	EXP	16901901
GO:0019203	Function	Carbohydrate phosphatase activity	IDA	25538239
GO:0019203	Function	Carbohydrate phosphatase activity	IEA
GO:0019203	Function	Carbohydrate phosphatase activity	TAS
GO:0030246	Function	Carbohydrate binding	IDA	25538239
GO:0030246	Function	Carbohydrate binding	IEA
GO:0030247	Function	Polysaccharide binding	IEA
GO:0030425	Component	Dendrite	IEA
GO:0031396	Process	Regulation of protein ubiquitination	IEA
GO:0032007	Process	Negative regulation of TOR signaling	IMP	20453062
GO:0035305	Process	Negative regulation of dephosphorylation	IDA	18617530
GO:0035335	Process	Peptidyl-tyrosine dephosphorylation	IMP	11739371
GO:0042306	Process	Regulation of protein import into nucleus	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0042803	Function	Protein homodimerization activity	IPI	18617530, 25538239, 25544560
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IEA
GO:0043204	Component	Perikaryon	IEA
GO:0045786	Process	Negative regulation of cell cycle	IEA
GO:0046835	Process	Carbohydrate phosphorylation	IEA
GO:0046959	Process	Habituation	IEA
GO:0046983	Function	Protein dimerization activity	IPI	18617530
GO:0061136	Process	Regulation of proteasomal protein catabolic process	IEA
GO:0098554	Component	Cytoplasmic side of endoplasmic reticulum membrane	IEA
GO:0098556	Component	Cytoplasmic side of rough endoplasmic reticulum membrane	IDA	11001928
GO:1903076	Process	Regulation of protein localization to plasma membrane	IEA
GO:2001069	Function	Glycogen binding	IDA	18617530
GO:2001069	Function	Glycogen binding	IDA	11739371, 18617530, 25544560
GO:2001070	Function	Starch binding	IEA

MIM	HGNC	e!Ensembl
607566	3413	ENSG00000112425

O95278

Protein name

Laforin (EC 3.1.3.-) (EC 3.1.3.16) (EC 3.1.3.48) (Glucan phosphatase) (Glycogen phosphatase) (Lafora PTPase) (LAFPTPase)

Protein function

Plays an important role in preventing glycogen hyperphosphorylation and the formation of insoluble aggregates, via its activity as glycogen phosphatase, and by promoting the ubiquitination of proteins involved in glycogen metabolism via its inte

PDB

4R30 , 4RKK

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00686	CBM_20	9 → 117	Starch binding domain	Family
PF00782	DSPc	164 → 311	Dual specificity phosphatase, catalytic domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in heart, skeletal muscle, kidney, pancreas and brain. Isoform 4 is also expressed in the placenta. {ECO:0000269|PubMed:14532330, ECO:0000269|PubMed:9771710}.

Sequence

MRFRFGVVVPPAVAGARPELLVVGSRPELGRWEPRGAVRLRPAGTAAGDGALALQEPGLW
LGEVELAAEEAAQDGAEPGRVDTFWYKFLKREPGGELSWEGNGPHHDRCCTYNENNLVDG
VYCLPIGHWIEATGHTNEMKHTTDFYFNIAGHQAMHYSRILPNIWLGSCPRQVEHVTIKL
KHELGITAVMNFQTEWDIVQNSSGCNRYPEPMTPDTMIKLYREEGLAYIWMPTPDMSTEG
RVQMLPQAVCLLHALLEKGHIVYVHCNAGVGRSTAAVCGWLQYVMGWNLRKVQYFLMAKR
PAVYIDEEALARAQEDFFQKFGKVRSSVCSL

Sequence length

331

B3EWF7

Protein name

Laforin, isoform 9

Family and domains

Sequence

MHPKEGAEQHVFSPVPGAPTPPPNRCGRLVLGPRLPAAGTPGPGIRAAAARHALPLWGGG
ATRRGRRPAGAAGGGVAARAGALGAARCRPPEAGRHRGGRRGPGPAGAGPVARGGGAGGR
GGGAGRGGAGPRGHVLVQVPEAGAGRRALLGRYCQQTPAPGAERELRPAPPTGASASGRP
RRPRRRASRAFCPRPCALPGRPGLTLLCRPRCRRQPRLRLPTDSLDPYSAPGRLPAHSVA
CPSDLVSAHPVLSFFPTAPASRASALRLPPGAPFALRVPLDLRVPPFAGPLAARPRAADG
FNSPTPPWLGFVSSFSCSNSLKKTQNDPTNETSVFANPRQQCAT

Sequence length

344

Interactions

View interactions

	Reactome
			Glycogen synthesis Myoclonic epilepsy of Lafora

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Likely pathogenic	rs1179064700	RCV001814452	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
EPM2A-related disorder	Likely pathogenic; Pathogenic	rs104893950	RCV004757945	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Lafora disease	Likely pathogenic; Pathogenic	rs201053542, rs780648601, rs1204045237, rs369463720, rs750988816, rs1361221383, rs104893950, rs137852917, rs137852915, rs587776553, rs137852916, rs587776554, rs104893955, rs796052427, rs796052424 View all (7 more)	RCV005253811 RCV005253828 RCV003447596 RCV002246579 RCV005253959 View all (18 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Myoclonic epilepsy of Lafora 1	Pathogenic; Likely pathogenic	rs1204045237, rs2128614455, rs104893950, rs137852917, rs137852915, rs587776553, rs137852916, rs587776554, rs104893955, rs796052424, rs1384780611, rs2534173440, rs2534173846, rs187930476	RCV005630940 RCV005630277 RCV004576870 RCV004576871 RCV004576872 View all (9 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Progressive myoclonic epilepsy	Likely pathogenic; Pathogenic	rs201053542, rs1362231306, rs780648601, rs1204045237, rs2128555980, rs2128649765, rs1775923311, rs369463720, rs750988816, rs1361221383, rs104893950, rs137852917, rs137852915, rs137852916, rs104893955 View all (11 more)	RCV001352138 RCV001379905 RCV001380053 RCV001389133 RCV001960562 View all (22 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Self-limited epilepsy with centrotemporal spikes	Pathogenic	rs1554263366	RCV000655996	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (14)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cataract	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CONGENITAL NEUROLOGIC ANOMALIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, ROLANDIC	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALIGNANT EPITHELIAL TUMOR OF OVARY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Myoclonic epilepsy, progressive, X-linked	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seizure	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Severe global developmental delay	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

EPM2A (EPM2A glucan phosphatase, laforin)