Gene Gene information from NCBI Gene database.
Entrez ID 378884
Gene name NHL repeat containing E3 ubiquitin protein ligase 1
Gene symbol NHLRC1
Synonyms (NCBI Gene)
EPM2AEPM2BMALINMELF2bA204B7.2
Chromosome 6
Chromosome location 6p22.3
Summary 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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
84
miRTarBase ID miRNA Experiments Reference
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608072 21576 ENSG00000187566
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
PRTLALECPFCRR
ACRGCDTSDCLPVLHLIELLGSALRQSPAAHRAAPSAPGALTCHHTF
GGWGTLVNPTGLALCPKTGRVVVVHDGRRRVKIFDSGGGCAHQFGEKGDAAQDIRYPVDV
TITNDCHVVVTDAGDRSIKVFDFFGQIKLVIGGQFSLPWGVETTPQNGIVVTDAEAGSLH
LLDVDFAEGVLRRTERLQAHLCNPRGVAVSWLTGAIAVLEHPLALGTGVCSTRVKVFSSS
MQLVGQVDTFGLSLYFPSKITASAVTFDHQGNVIVADTSGPAILCLGKPEEFPVPKPMVT
HGLSHPVALTFTKENSLLVLDTASHSIKVYKVDWG
Sequence length 395
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Ubiquitin mediated proteolysis   Glycogen synthesis
Myoclonic epilepsy of Lafora
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
27
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)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Lafora disease Pathogenic; Likely pathogenic rs1783750860, rs1362520746, rs2150702964, rs2150703022, rs967125703, rs769144119, rs1217276014, rs1193841505, rs200559475, rs769301934, rs28940575, rs28940576, rs587776542, rs121917876, rs950907157
View all (16 more)
RCV001330611
RCV001381622
RCV001384327
RCV001730042
RCV001799565
View all (27 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Myoclonic epilepsy of Lafora 1 Pathogenic rs28940576 RCV005632153
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Myoclonic epilepsy of Lafora 2 Likely pathogenic; Pathogenic rs769301934, rs28940575, rs28940576, rs587776542, rs587776543, rs121917875, rs121917876, rs137852859, rs750465793, rs780082503 RCV003989327
RCV000002704
RCV000002705
RCV000002706
RCV000002707
View all (5 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NHLRC1-related disorder Pathogenic rs28940576 RCV003952338
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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.
Phenotype Name Clinical Significance Source Evidence Score
BILIARY TRACT CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CERVICAL CARCINOMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Action Myoclonus-Renal Failure Syndrome Action Myoclonus-Renal Failure Syndrome CTD_human_DG 25401298
★☆☆☆☆
Found in Text Mining only
Apraxias Apraxia HPO_DG
★☆☆☆☆
Found in Text Mining only
Atkin syndrome Atkin-Flaitz syndrome BEFREE 30049290
★☆☆☆☆
Found in Text Mining only
Atypical absence seizure Absence Seizure HPO_DG
★☆☆☆☆
Found in Text Mining only
Atypical Inclusion-Body Disease Inclusion-Body Disease CTD_human_DG 25401298
★☆☆☆☆
Found in Text Mining only
Brain atrophy Brain atrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
Carcinoma, Endometrioid Endometrioid cancer BEFREE 27348205, 28277316
★☆☆☆☆
Found in Text Mining only
Cerebral atrophy Cerebral Atrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
Cognition Disorders Cognitive disorder BEFREE 12019207
★☆☆☆☆
Found in Text Mining only
Complex partial seizure with impairment of consciousness Dyscognitive seizures HPO_DG
★☆☆☆☆
Found in Text Mining only