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Aliases for NIPA1 Gene

Aliases for NIPA1 Gene

  • Non Imprinted In Prader-Willi/Angelman Syndrome 1 2 3 5
  • Non-Imprinted In Prader-Willi/Angelman Syndrome Region Protein 1 3 4
  • Spastic Paraplegia 6 Protein 3 4
  • SPG6 3 4
  • Non-Imprinted In Prader-Willi/Angelman Syndrome 1 3
  • Spastic Paraplegia 6 (Autosomal Dominant) 2
  • FSP3 3

External Ids for NIPA1 Gene

Previous HGNC Symbols for NIPA1 Gene

  • SPG6

Previous GeneCards Identifiers for NIPA1 Gene

  • GC15M020462
  • GC00U914364
  • GC15M020594
  • GC15M023043
  • GC15M001354

Summaries for NIPA1 Gene

Entrez Gene Summary for NIPA1 Gene

  • 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 encoding different isoforms have been found for this gene. Mutations in this gene have been associated with autosomal dominant spastic paraplegia 6. [provided by RefSeq, Nov 2008]

GeneCards Summary for NIPA1 Gene

NIPA1 (Non Imprinted In Prader-Willi/Angelman Syndrome 1) is a Protein Coding gene. Diseases associated with NIPA1 include Spastic Paraplegia 6, Autosomal Dominant and Spastic Paraplegia 6. Among its related pathways are Miscellaneous transport and binding events and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. GO annotations related to this gene include magnesium ion transmembrane transporter activity. An important paralog of this gene is NIPAL3.

UniProtKB/Swiss-Prot for NIPA1 Gene

  • Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Fe(2+), Sr(2+), Ba(2+), Mn(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity).

Gene Wiki entry for NIPA1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NIPA1 Gene

Genomics for NIPA1 Gene

Regulatory Elements for NIPA1 Gene

Enhancers for NIPA1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around NIPA1 on UCSC Golden Path with GeneCards custom track

Genomic Location for NIPA1 Gene

22,773,063 bp from pter
22,829,791 bp from pter
56,729 bases
Plus strand

Genomic View for NIPA1 Gene

Genes around NIPA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIPA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIPA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIPA1 Gene

Proteins for NIPA1 Gene

  • Protein details for NIPA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Magnesium transporter NIPA1
    Protein Accession:
    Secondary Accessions:
    • B2RA76
    • Q5HYA9
    • Q7KZB0
    • Q86XW4

    Protein attributes for NIPA1 Gene

    329 amino acids
    Molecular mass:
    34562 Da
    Quaternary structure:
    • Homodimer.
    • Sequence=BAC67707.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC67707.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305};

    Alternative splice isoforms for NIPA1 Gene


neXtProt entry for NIPA1 Gene

Proteomics data for NIPA1 Gene at MOPED

Post-translational modifications for NIPA1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NIPA1 Gene

No data available for DME Specific Peptides for NIPA1 Gene

Domains & Families for NIPA1 Gene

Protein Domains for NIPA1 Gene


Suggested Antigen Peptide Sequences for NIPA1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the NIPA family.
  • Belongs to the NIPA family.
genes like me logo Genes that share domains with NIPA1: view

No data available for Gene Families for NIPA1 Gene

Function for NIPA1 Gene

Molecular function for NIPA1 Gene

UniProtKB/Swiss-Prot Function:
Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Fe(2+), Sr(2+), Ba(2+), Mn(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity).

Phenotypes for NIPA1 Gene

genes like me logo Genes that share phenotypes with NIPA1: view

Human Phenotype Ontology for NIPA1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for NIPA1 Gene

miRTarBase miRNAs that target NIPA1

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for NIPA1 Gene

Localization for NIPA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIPA1 Gene

Cell membrane; Multi-pass membrane protein. Early endosome. Note=Recruited to the cell membrane in response to low extracellular magnesium. {ECO:0000250}.

Subcellular locations from

Jensen Localization Image for NIPA1 Gene COMPARTMENTS Subcellular localization image for NIPA1 gene
Compartment Confidence
plasma membrane 5
endosome 4

Gene Ontology (GO) - Cellular Components for NIPA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005769 early endosome IEA --
genes like me logo Genes that share ontologies with NIPA1: view

Pathways & Interactions for NIPA1 Gene

genes like me logo Genes that share pathways with NIPA1: view

Pathways by source for NIPA1 Gene

Interacting Proteins for NIPA1 Gene

Gene Ontology (GO) - Biological Process for NIPA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015693 magnesium ion transport IEA --
GO:0055085 transmembrane transport TAS --
genes like me logo Genes that share ontologies with NIPA1: view

No data available for SIGNOR curated interactions for NIPA1 Gene

Drugs & Compounds for NIPA1 Gene

No Compound Related Data Available

Transcripts for NIPA1 Gene

Unigene Clusters for NIPA1 Gene

Non imprinted in Prader-Willi/Angelman syndrome 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NIPA1 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c · 8d
SP1: - -
SP2: -
SP3: - - - - - -
SP4: - - -

Relevant External Links for NIPA1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NIPA1 Gene

mRNA expression in normal human tissues for NIPA1 Gene

mRNA differential expression in normal tissues according to GTEx for NIPA1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x6.1) and Brain - Substantia nigra (x4.3).

Protein differential expression in normal tissues from HIPED for NIPA1 Gene

This gene is overexpressed in Spinal cord (20.8), Frontal cortex (17.0), and Fetal Liver (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for NIPA1 Gene

SOURCE GeneReport for Unigene cluster for NIPA1 Gene Hs.511797

mRNA Expression by UniProt/SwissProt for NIPA1 Gene

Tissue specificity: Widely expressed with highest levels in neuronal tissues.
genes like me logo Genes that share expression patterns with NIPA1: view

Protein tissue co-expression partners for NIPA1 Gene

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for NIPA1 Gene

Orthologs for NIPA1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NIPA1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia NIPA1 35
  • 92.59 (n)
  • 99.38 (a)
NIPA1 36
  • 98 (a)
(Canis familiaris)
Mammalia NIPA1 35
  • 92.01 (n)
  • 99.68 (a)
NIPA1 36
  • 99 (a)
(Mus musculus)
Mammalia Nipa1 35
  • 91.56 (n)
  • 99.69 (a)
Nipa1 16
Nipa1 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Nipa1 35
  • 91.77 (n)
  • 99.37 (a)
(Monodelphis domestica)
Mammalia NIPA1 36
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia NIPA1 36
  • 96 (a)
(Pan troglodytes)
Mammalia NIPA1 36
  • 100 (a)
(Gallus gallus)
Aves NIPA1 35
  • 78.15 (n)
  • 95.56 (a)
NIPA1 36
  • 65 (a)
(Anolis carolinensis)
Reptilia NIPA1 36
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nipa1 35
  • 69.56 (n)
  • 72 (a)
(Danio rerio)
Actinopterygii Dr.24227 35
nipa1 35
  • 61.81 (n)
  • 61.26 (a)
nipa1 36
  • 60 (a)
fruit fly
(Drosophila melanogaster)
Insecta spict 36
  • 33 (a)
(Caenorhabditis elegans)
Secernentea nipa-1 36
  • 32 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 19 (a)
Species with no ortholog for NIPA1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NIPA1 Gene

Gene Tree for NIPA1 (if available)
Gene Tree for NIPA1 (if available)

Paralogs for NIPA1 Gene

Paralogs for NIPA1 Gene

(3) SIMAP similar genes for NIPA1 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with NIPA1: view

Variants for NIPA1 Gene

Sequence variations from dbSNP and Humsavar for NIPA1 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
VAR_023440 Spastic paraplegia 6, autosomal dominant (SPG6)
VAR_023441 Spastic paraplegia 6, autosomal dominant (SPG6)
rs11858281 -- 22,797,846(-) aaaaT(C/T)GGTTT intron-variant
rs12101767 -- 22,800,413(-) caaaa(C/T)ttgca intron-variant
rs12102090 -- 22,802,698(-) cacca(A/G)ggaac intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NIPA1 Gene

Variant ID Type Subtype PubMed ID
dgv44n16 CNV Insertion 17901297
esv2751489 CNV Gain 17911159
esv34233 CNV Loss 17911159
essv13315 CNV CNV 17122850
nsv437797 CNV Loss 16327808
nsv511042 OTHER Inversion 20534489
nsv433429 CNV Gain 18776910
nsv903495 CNV Gain 21882294
esv2474417 CNV Loss 19546169
nsv442359 CNV CNV 18776908
dgv696e1 CNV Complex 17122850
dgv2234n71 CNV Loss 21882294
dgv2235n71 CNV Gain 21882294
dgv2236n71 CNV Gain+Loss 21882294
nsv433290 CNV Loss 18776910
dgv2239n71 CNV Gain 21882294
nsv456612 CNV Loss 19166990
dgv287n27 CNV Gain 19166990
nsv471225 CNV Gain 18288195
nsv471226 CNV Loss 18288195
esv34463 CNV Gain 17911159
dgv2242n71 CNV Gain 21882294
nsv456636 CNV Loss 19166990
dgv2243n71 CNV Gain 21882294
nsv832926 CNV Gain+Loss 17160897
nsv903559 CNV Gain+Loss 21882294
nsv903560 CNV Loss 21882294
dgv2246n71 CNV Gain 21882294
dgv2247n71 CNV Gain 21882294
nsv469667 CNV Loss 16826518
dgv9n31 CNV Deletion 19718026
nsv428297 CNV Gain+Loss 18775914
dgv2248n71 CNV Gain 21882294
nsv471378 CNV Deletion 19718026
nsv94557 CNV Loss 16902084
nsv1460 CNV Loss 18451855
esv2749407 CNV Deletion 23290073
esv2413322 CNV Deletion 18987734
esv4116 CNV Deletion 18987735
esv2669861 CNV Deletion 23128226
esv1007853 CNV Deletion 20482838
esv1025847 CNV Deletion 17803354
esv2749409 CNV Deletion 23290073

Variation tolerance for NIPA1 Gene

Residual Variation Intolerance Score: 13.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.74; 66.45% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NIPA1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NIPA1 Gene

Disorders for NIPA1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for NIPA1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
spastic paraplegia 6, autosomal dominant
  • familial spastic paraplegia autosomal dominant 3
spastic paraplegia 6
  • spastic paraplegia 6, autosomal dominant
  • paraplegia, lower
hereditary spastic paraplegia
  • familial spastic paraplegia
angelman syndrome
  • as
- elite association - COSMIC cancer census association via MalaCards
Search NIPA1 in MalaCards View complete list of genes associated with diseases


  • Spastic paraplegia 6, autosomal dominant (SPG6) [MIM:600363]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269 PubMed:14508710, ECO:0000269 PubMed:15643603}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NIPA1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with NIPA1: view

No data available for Genatlas for NIPA1 Gene

Publications for NIPA1 Gene

  1. NIPA1 gene mutations cause autosomal dominant hereditary spastic paraplegia (SPG6). (PMID: 14508710) Rainier S. … Fink J.K. (Am. J. Hum. Genet. 2003) 2 3 4 23 67
  2. Clinical and genetic study of SPG6 mutation in a Chinese family with hereditary spastic paraplegia. (PMID: 17928003) Liu S.G. … Ma X. (J. Neurol. Sci. 2008) 3 23
  3. Hereditary spastic paraplegia-associated mutations in the NIPA1 gene and its Caenorhabditis elegans homolog trigger neural degeneration in vitro and in vivo through a gain-of-function mechanism. (PMID: 19091982) Zhao J. … Hedera P. (J. Neurosci. 2008) 3 23
  4. NIPA1(SPG6), the basis for autosomal dominant form of hereditary spastic paraplegia, encodes a functional Mg2+ transporter. (PMID: 17166836) Goytain A. … Quamme G.A. (J. Biol. Chem. 2007) 3 23
  5. Clinical and genetic study of a Brazilian family with spastic paraplegia (SPG6 locus). (PMID: 16267846) Munhoz R.P. … Rogaeva E. (Mov. Disord. 2006) 3 23

Products for NIPA1 Gene

Sources for NIPA1 Gene