Gene Gene information from NCBI Gene database.
Entrez ID 123606
Gene name NIPA magnesium transporter 1
Gene symbol NIPA1
Synonyms (NCBI Gene)
FSP3SLC57A1SPG6
Chromosome 15
Chromosome location 15q11.2
Summary This gene encodes a magnesium transporter that associates with early endosomes and the cell surface in a variety of neuronal and epithelial cells. This protein may play a role in nervous system development and maintenance. Multiple transcript variants enc
SNPs SNP information provided by dbSNP.
3
SNP ID Visualize variation Clinical significance Consequence
rs104894490 G>A,C Pathogenic Missense variant, coding sequence variant
rs104894496 C>G Pathogenic Missense variant, intron variant, coding sequence variant
rs139372534 G>A,C Likely-benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
miRNA miRNA information provided by mirtarbase database.
798
miRTarBase ID miRNA Experiments Reference
MIRT021392 hsa-miR-9-5p Sequencing 20371350
MIRT024858 hsa-miR-215-5p Microarray 19074876
MIRT026118 hsa-miR-192-5p Microarray 19074876
MIRT027921 hsa-miR-96-5p Sequencing 20371350
MIRT647065 hsa-miR-6887-3p HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
14
GO ID Ontology Definition Evidence Reference
GO:0005515 Function Protein binding IPI 32296183
GO:0005768 Component Endosome IEA
GO:0005769 Component Early endosome IEA
GO:0005886 Component Plasma membrane IEA
GO:0005886 Component Plasma membrane TAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608145 17043 ENSG00000170113
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q7RTP0
Protein name Magnesium transporter NIPA1 (Non-imprinted in Prader-Willi/Angelman syndrome region protein 1) (Spastic paraplegia 6 protein)
Protein function Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Fe(2+), Sr(2+), Ba(2+), Zn(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity).
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF05653 Mg_trans_NIPA 27 314 Magnesium transporter NIPA Family
Tissue specificity TISSUE SPECIFICITY: Widely expressed with highest levels in neuronal tissues. {ECO:0000269|PubMed:14508710}.
Sequence
Sequence length 329
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Miscellaneous transport and binding events
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
14
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
Hereditary spastic paraplegia Pathogenic rs104894490 RCV000516051
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary spastic paraplegia 6 Pathogenic rs104894496, rs104894490, rs1895598333 RCV000002628
RCV000002629
RCV000002631
RCV001219670
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spastic paraplegia Pathogenic rs104894490 RCV001003981
★★★★☆
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
15Q11.2 MICRODELETION SYNDROME Disgenet, Orphanet
Disgenet, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Amyotrophic lateral sclerosis risk factor ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
AUTOSOMAL DOMINANT SPASTIC PARAPLEGIA TYPE 6 Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Familial cancer of breast Benign ClinVar
★★☆☆☆
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
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 20685689, 22378146, 30342764, 31286297
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Amyotrophic Lateral Sclerosis Amyotrophic lateral sclerosis Pubtator 30342764, 33414559, 35869263 Associate
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Angelman Syndrome Angelman Syndrome BEFREE 22302102, 28387067
★☆☆☆☆
Found in Text Mining only
Anorexia Nervosa Anorexia BEFREE 30878790
★☆☆☆☆
Found in Text Mining only
Anorexia Nervosa Anorexia nervosa Pubtator 30878790 Associate
★☆☆☆☆
Found in Text Mining only
Atrophy Atrophy Pubtator 16143870 Stimulate
★☆☆☆☆
Found in Text Mining only
Autism Spectrum Disorder Autism Pubtator 33562221 Associate
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism Pubtator 16183798, 30878790 Associate
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism BEFREE 20029941, 30878790
★☆☆☆☆
Found in Text Mining only
Autosomal dominant spastic paraplegia type 6 Spastic Paraplegia Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations