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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	378884
Gene name Gene Name - the full gene name approved by the HGNC.	NHL repeat containing E3 ubiquitin protein ligase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NHLRC1
Synonyms (NCBI Gene) Gene synonyms aliases	EPM2A, EPM2B, MALIN, MELF2, bA204B7.2
Chromosome Chromosome number	6
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	6p22.3
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a single subunit E3 ubiquitin ligase. Laforin is polyubiquitinated by the encoded protein. Defects in this intronless gene lead to an accumulation of laforin and onset of Lafora disease, also known as progressive myoclo

Show/Hide all(24)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28940575	A>T	Pathogenic	Missense variant, coding sequence variant
rs28940576	G>C	Pathogenic	Missense variant, coding sequence variant
rs121917875	G>A,C,T	Pathogenic	Missense variant, stop gained, coding sequence variant, synonymous variant
rs121917876	A>T	Pathogenic	Missense variant, coding sequence variant
rs137852859	T>G	Pathogenic	Missense variant, coding sequence variant
rs139029314	G>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant
rs140850172	A>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs143537405	A>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs146636139	T>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs200201752	T>C	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs200595273	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs587776542	CT>-	Pathogenic	Frameshift variant, coding sequence variant
rs587776543	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs750465793	G>T	Conflicting-interpretations-of-pathogenicity, pathogenic	Coding sequence variant, missense variant
rs757954108	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs769301934	C>T	Pathogenic	Coding sequence variant, missense variant
rs794726964	C>A	Pathogenic	Stop gained, coding sequence variant
rs796052758	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1157872508	A>-,AA	Pathogenic	Stop gained, coding sequence variant, frameshift variant
rs1369766718	A>C,G	Likely-pathogenic	Coding sequence variant, missense variant
rs1403101337	G>A,C	Likely-pathogenic	Stop gained, coding sequence variant, synonymous variant
rs1554136433	->T	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554136440	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1582030118	GCGCGCAT>-	Likely-pathogenic	Coding sequence variant, frameshift variant

Show/Hide all(84)

miRTarBase ID	miRNA	Experiments
MIRT1184312	hsa-miR-101	CLIP-seq
MIRT1184313	hsa-miR-1285	CLIP-seq
MIRT1184314	hsa-miR-151-5p	CLIP-seq
MIRT1184315	hsa-miR-151b	CLIP-seq
MIRT1184316	hsa-miR-224	CLIP-seq
MIRT1184317	hsa-miR-3131	CLIP-seq
MIRT1184318	hsa-miR-3187-5p	CLIP-seq
MIRT1184319	hsa-miR-3190	CLIP-seq
MIRT1184320	hsa-miR-3202	CLIP-seq
MIRT1184321	hsa-miR-3659	CLIP-seq
MIRT1184322	hsa-miR-3664-3p	CLIP-seq
MIRT1184323	hsa-miR-3672	CLIP-seq
MIRT1184324	hsa-miR-3689a-3p	CLIP-seq
MIRT1184325	hsa-miR-3689c	CLIP-seq
MIRT1184326	hsa-miR-3929	CLIP-seq
MIRT1184327	hsa-miR-421	CLIP-seq
MIRT1184328	hsa-miR-4281	CLIP-seq
MIRT1184329	hsa-miR-4419b	CLIP-seq
MIRT1184330	hsa-miR-4433	CLIP-seq
MIRT1184331	hsa-miR-4459	CLIP-seq
MIRT1184332	hsa-miR-4478	CLIP-seq
MIRT1184333	hsa-miR-4533	CLIP-seq
MIRT1184334	hsa-miR-4536	CLIP-seq
MIRT1184335	hsa-miR-4643	CLIP-seq
MIRT1184336	hsa-miR-4645-3p	CLIP-seq
MIRT1184337	hsa-miR-4658	CLIP-seq
MIRT1184338	hsa-miR-466	CLIP-seq
MIRT1184339	hsa-miR-4680-5p	CLIP-seq
MIRT1184340	hsa-miR-4709-5p	CLIP-seq
MIRT1184341	hsa-miR-4728-5p	CLIP-seq
MIRT1184342	hsa-miR-4768-3p	CLIP-seq
MIRT1184343	hsa-miR-4786-5p	CLIP-seq
MIRT1184344	hsa-miR-4789-3p	CLIP-seq
MIRT1184345	hsa-miR-485-5p	CLIP-seq
MIRT1184346	hsa-miR-510	CLIP-seq
MIRT1184347	hsa-miR-548u	CLIP-seq
MIRT1184348	hsa-miR-574-5p	CLIP-seq
MIRT1184349	hsa-miR-611	CLIP-seq
MIRT1184350	hsa-miR-612	CLIP-seq
MIRT1184351	hsa-miR-661	CLIP-seq
MIRT1184352	hsa-miR-769-5p	CLIP-seq
MIRT1184353	hsa-miR-890	CLIP-seq
MIRT2053448	hsa-miR-1183	CLIP-seq
MIRT1184324	hsa-miR-3689a-3p	CLIP-seq
MIRT1184325	hsa-miR-3689c	CLIP-seq
MIRT1184341	hsa-miR-4728-5p	CLIP-seq
MIRT2053449	hsa-miR-4738-3p	CLIP-seq
MIRT2053450	hsa-miR-548g	CLIP-seq
MIRT1184353	hsa-miR-890	CLIP-seq
MIRT1184322	hsa-miR-3664-3p	CLIP-seq
MIRT1184324	hsa-miR-3689a-3p	CLIP-seq
MIRT1184325	hsa-miR-3689c	CLIP-seq
MIRT2282663	hsa-miR-4452	CLIP-seq
MIRT2282664	hsa-miR-4727-5p	CLIP-seq
MIRT1184341	hsa-miR-4728-5p	CLIP-seq
MIRT2282665	hsa-miR-4769-3p	CLIP-seq
MIRT1184346	hsa-miR-510	CLIP-seq
MIRT1184351	hsa-miR-661	CLIP-seq
MIRT2391538	hsa-miR-1229	CLIP-seq
MIRT2391539	hsa-miR-1262	CLIP-seq
MIRT2391540	hsa-miR-193a-5p	CLIP-seq
MIRT2391541	hsa-miR-3130-3p	CLIP-seq
MIRT1184322	hsa-miR-3664-3p	CLIP-seq
MIRT1184323	hsa-miR-3672	CLIP-seq
MIRT1184324	hsa-miR-3689a-3p	CLIP-seq
MIRT1184325	hsa-miR-3689c	CLIP-seq
MIRT2391542	hsa-miR-4264	CLIP-seq
MIRT2391543	hsa-miR-4328	CLIP-seq
MIRT1184330	hsa-miR-4433	CLIP-seq
MIRT1184331	hsa-miR-4459	CLIP-seq
MIRT2391544	hsa-miR-4701-3p	CLIP-seq
MIRT1184341	hsa-miR-4728-5p	CLIP-seq
MIRT1184342	hsa-miR-4768-3p	CLIP-seq
MIRT2391545	hsa-miR-4793-3p	CLIP-seq
MIRT2391546	hsa-miR-4797-3p	CLIP-seq
MIRT2391547	hsa-miR-508-5p	CLIP-seq
MIRT2391548	hsa-miR-542-3p	CLIP-seq
MIRT2391549	hsa-miR-544	CLIP-seq
MIRT1184351	hsa-miR-661	CLIP-seq
MIRT2391550	hsa-miR-766	CLIP-seq
MIRT2282664	hsa-miR-4727-5p	CLIP-seq
MIRT2282665	hsa-miR-4769-3p	CLIP-seq
MIRT2282664	hsa-miR-4727-5p	CLIP-seq
MIRT2282665	hsa-miR-4769-3p	CLIP-seq

Show/Hide all(37)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000209	Process	Protein polyubiquitination	IBA
GO:0000209	Process	Protein polyubiquitination	IDA	15930137
GO:0004842	Function	Ubiquitin-protein transferase activity	EXP	15930137
GO:0004842	Function	Ubiquitin-protein transferase activity	IDA	15930137, 18070875
GO:0004842	Function	Ubiquitin-protein transferase activity	IEA
GO:0004842	Function	Ubiquitin-protein transferase activity	TAS
GO:0005515	Function	Protein binding	IPI	15930137, 17908927, 21505799, 22578008, 22961547, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	17908927
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0005977	Process	Glycogen metabolic process	IEA
GO:0005978	Process	Glycogen biosynthetic process	IEA
GO:0005978	Process	Glycogen biosynthetic process	TAS
GO:0006914	Process	Autophagy	IEA
GO:0006914	Process	Autophagy	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0016567	Process	Protein ubiquitination	IEA
GO:0016567	Process	Protein ubiquitination	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0031396	Process	Regulation of protein ubiquitination	IEA
GO:0031398	Process	Positive regulation of protein ubiquitination	IEA
GO:0034976	Process	Response to endoplasmic reticulum stress	IEA
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IBA
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IDA	15930137
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IEA
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0061630	Function	Ubiquitin protein ligase activity	IBA
GO:0061630	Function	Ubiquitin protein ligase activity	IEA
GO:1903076	Process	Regulation of protein localization to plasma membrane	IEA

MIM	HGNC	e!Ensembl
608072	21576	ENSG00000187566

Protein

UniProt ID

Q6VVB1

Protein name

E3 ubiquitin-protein ligase NHLRC1 (EC 2.3.2.27) (Malin) (NHL repeat-containing protein 1) (RING-type E3 ubiquitin transferase NHLRC1)

Protein function

E3 ubiquitin-protein ligase. Together with the phosphatase EPM2A/laforin, appears to be involved in the clearance of toxic polyglucosan and protein aggregates via multiple pathways. In complex with EPM2A/laforin and HSP70, suppresses the cellula

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF14634	zf-RING_5	25 → 73	zinc-RING finger domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in brain, cerebellum, spinal cord, medulla, heart, liver, skeletal muscle and pancreas. {ECO:0000269|PubMed:12958597}.

Sequence

MAAEASESGPALHELMREAEISLLECKVCFEKFGHRQQRRPRNLSCGHVVCLACVAALAH
PRTLALECPFCRRACRGCDTSDCLPVLHLIELLGSALRQSPAAHRAAPSAPGALTCHHTF
GGWGTLVNPTGLALCPKTGRVVVVHDGRRRVKIFDSGGGCAHQFGEKGDAAQDIRYPVDV
TITNDCHVVVTDAGDRSIKVFDFFGQIKLVIGGQFSLPWGVETTPQNGIVVTDAEAGSLH
LLDVDFAEGVLRRTERLQAHLCNPRGVAVSWLTGAIAVLEHPLALGTGVCSTRVKVFSSS
MQLVGQVDTFGLSLYFPSKITASAVTFDHQGNVIVADTSGPAILCLGKPEEFPVPKPMVT
HGLSHPVALTFTKENSLLVLDTASHSIKVYKVDWG

Sequence length

395

Interactions

View interactions

	KEGG		Reactome
	Ubiquitin mediated proteolysis		Glycogen synthesis Myoclonic epilepsy of Lafora

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Lafora Disease	lafora disease	rs750465793, rs757954108, rs1194084403, rs1157872508, rs1403101337, rs78324544, rs28940575, rs28940576, rs587776542, rs121917876, rs769301934	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Psoriasis	Psoriasis	N/A	N/A	GWAS

Show/Hide Text Mining Associations (6)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Death	Associate	16529633
Epilepsies Myoclonic	Associate	35569391
Headache Disorders	Associate	16529633
Lafora Disease	Associate	12960212, 15781812, 15930137, 16190947, 16529633, 16950819, 17452581, 19322595, 19744044, 20738377, 21728993, 21887368, 22223637, 22961547, 25270369 View all (9 more)
Lung Neoplasms	Associate	36142605
Neurodegenerative Diseases	Associate	15930137

NHLRC1 (NHL repeat containing E3 ubiquitin protein ligase 1)