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Aliases for NIPA1 Gene

Aliases for NIPA1 Gene

  • NIPA Magnesium Transporter 1 2 3
  • 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
  • Spastic Paraplegia 6 (Autosomal Dominant) 2
  • Magnesium Transporter NIPA1 3
  • SLC57A1 3
  • 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 (NIPA Magnesium Transporter 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 Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Miscellaneous transport and binding events. Gene Ontology (GO) annotations related to this gene include magnesium ion transmembrane transporter activity. An important paralog of this gene is NIPAL1.

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

Additional gene information for NIPA1 Gene

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

Genomics for NIPA1 Gene

GeneHancer (GH) Regulatory Elements for NIPA1 Gene

Promoters and enhancers for NIPA1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J022785 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 657.6 +13.6 13603 2.4 HDGF ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 ZNF207 ZNF143 NIPA1 CYFIP1 NIPA2 LOC729900 PIR54317
GH15J022757 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 655.7 -14.9 -14902 1.7 MXI1 ZNF384 ZNF316 ATF7 MAFK ZNF687 PHF21A L3MBTL2 RNF2 NFYC NIPA1 LOC100132817 LOC283683
GH15J022795 Enhancer 0.8 ENCODE 5.1 +23.2 23219 2.3 HDGF CTCF BACH1 STAT5A EBF1 BATF KLF5 IRF4 GATA3 POLR2A NIPA2 CYFIP1 NIPA1 LOC729900 PIR54317
GH15J022776 Enhancer 0.8 ENCODE 0.7 +3.2 3150 0.2 HDGF HDAC1 PKNOX1 ATF1 TAF9B ZBTB40 POLR2B EGR1 ATF7 CREM LOC729900 PIR31482 NIPA1 LOC283683
GH15J022778 Enhancer 0.7 ENCODE 0.4 +6.1 6100 0.9 HDAC1 MEIS2 CEBPG CTBP1 ZNF316 FOXK2 NFE2 SMARCE1 SOX6 MTA2 NIPA2 CYFIP1 LOC729900 NIPA1 LOC283683 PIR54317
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NIPA1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NIPA1 gene promoter:
  • C/EBPalpha
  • MZF-1
  • RREB-1
  • Roaz
  • AREB6

Genomic Locations for NIPA1 Gene

Genomic Locations for NIPA1 Gene
56,729 bases
Plus strand
56,729 bases
Minus 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

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

Gene Families for NIPA1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

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

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).

Gene Ontology (GO) - Molecular Function for NIPA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015095 magnesium ion transmembrane transporter activity IEA,TAS --
genes like me logo Genes that share ontologies with NIPA1: view
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 Models for NIPA1 Gene

MGI Knock Outs for NIPA1:
  • Nipa1 Nipa1<tm1a(KOMP)Wtsi>

Animal Model Products

miRNA for NIPA1 Gene

miRTarBase miRNAs that target NIPA1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
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 --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA,IBA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NIPA1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NIPA1 Gene

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

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: ENSP00000337452 Q7RTP0-NIPA1_HUMAN for NIPA1 Gene via STRING IID

Gene Ontology (GO) - Biological Process for NIPA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0015693 magnesium ion transport IEA,IBA --
GO:0055085 transmembrane transport TAS --
GO:1903830 magnesium ion transmembrane transport IEA --
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

mRNA/cDNA for NIPA1 Gene

Unigene Clusters for NIPA1 Gene

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

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for NIPA1 Gene

Protein tissue co-expression partners for NIPA1 Gene

NURSA nuclear receptor signaling pathways regulating expression of NIPA1 Gene:


SOURCE GeneReport for Unigene cluster for NIPA1 Gene:


mRNA Expression by UniProt/SwissProt for NIPA1 Gene:

Tissue specificity: Widely expressed with highest levels in neuronal tissues.

Evidence on tissue expression from TISSUES for NIPA1 Gene

  • Nervous system(4.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NIPA1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • head
  • prostate
  • urethra
  • urinary bladder
  • foot
  • lower limb
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with NIPA1: view

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
(Pan troglodytes)
Mammalia NIPA1 34
  • 100 (a)
(Ornithorhynchus anatinus)
Mammalia NIPA1 34
  • 96 (a)
(Monodelphis domestica)
Mammalia NIPA1 34
  • 94 (a)
(Bos Taurus)
Mammalia NIPA1 34 33
  • 92.59 (n)
(Canis familiaris)
Mammalia NIPA1 34 33
  • 92.01 (n)
(Rattus norvegicus)
Mammalia Nipa1 33
  • 91.77 (n)
(Mus musculus)
Mammalia Nipa1 16 34 33
  • 91.56 (n)
(Gallus gallus)
Aves NIPA1 34 33
  • 78.15 (n)
(Anolis carolinensis)
Reptilia NIPA1 34
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nipa1 33
  • 69.56 (n)
(Danio rerio)
Actinopterygii nipa1 34 33
  • 61.81 (n)
Dr.24227 33
fruit fly
(Drosophila melanogaster)
Insecta spict 34
  • 33 (a)
(Caenorhabditis elegans)
Secernentea nipa-1 34
  • 32 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 19 (a)
Species where no ortholog for NIPA1 was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for NIPA1: view image

Paralogs for NIPA1 Gene

Paralogs for NIPA1 Gene

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

  • L0R6L6_HUMAN
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 Variation AA Info Type
rs1030833580 uncertain-significance, Spastic Paraplegia, Dominant 22,828,062(+) G/A 3_prime_UTR_variant
rs104894490 pathogenic, Spastic paraplegia 6, Hereditary spastic paraplegia, Spastic paraplegia 6, autosomal dominant (SPG6) [MIM:600363] 22,812,252(+) G/A/C coding_sequence_variant, missense_variant
rs104894496 pathogenic, Spastic paraplegia 6, Spastic paraplegia 6, autosomal dominant (SPG6) [MIM:600363] 22,786,790(+) C/G coding_sequence_variant, intron_variant, missense_variant
rs1059774 benign, Spastic Paraplegia, Dominant 22,825,366(+) C/G 3_prime_UTR_variant
rs10611411 benign, Spastic Paraplegia, Dominant 22,824,673(+) TGT/T/TGTGT 3_prime_UTR_variant

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

Variant ID Type Subtype PubMed ID
dgv2403n100 CNV gain 25217958
dgv2404n100 CNV gain 25217958
dgv2405n100 CNV gain+loss 25217958
dgv2406n100 CNV gain 25217958
dgv2407n100 CNV gain+loss 25217958
dgv2408n100 CNV loss 25217958
dgv2409n100 CNV loss 25217958
dgv287n27 CNV gain 19166990
dgv4317n54 CNV loss 21841781
dgv4318n54 CNV gain 21841781
dgv4319n54 CNV gain+loss 21841781
dgv4320n54 CNV gain 21841781
dgv4322n54 CNV loss 21841781
dgv708e212 CNV loss 25503493
dgv709e212 CNV gain 25503493
dgv9n31 CNV loss 19718026
esv1007853 CNV deletion 20482838
esv1025847 CNV deletion 17803354
esv2413322 CNV deletion 18987734
esv2474417 CNV loss 19546169
esv2669861 CNV deletion 23128226
esv3188205 CNV deletion 24192839
esv34463 CNV gain 17911159
esv3552185 CNV deletion 23714750
esv3552186 CNV deletion 23714750
esv3569265 CNV gain 25503493
esv3635806 CNV loss 21293372
esv3635807 CNV gain 21293372
esv3635821 CNV loss 21293372
esv3635822 CNV gain 21293372
esv3892604 CNV gain+loss 25118596
esv3892626 CNV gain+loss 25118596
esv4116 CNV loss 18987735
nsv1040546 CNV gain 25217958
nsv1070679 CNV deletion 25765185
nsv1112666 CNV deletion 24896259
nsv1122945 CNV deletion 24896259
nsv1460 CNV deletion 18451855
nsv433290 CNV loss 18776910
nsv433429 CNV gain 18776910
nsv442359 CNV gain+loss 18776908
nsv456612 CNV loss 19166990
nsv456636 CNV loss 19166990
nsv469667 CNV loss 16826518
nsv471225 CNV gain 18288195
nsv471226 CNV loss 18288195
nsv471378 CNV loss 19718026
nsv511042 OTHER inversion 20534489
nsv568235 CNV loss 21841781
nsv832926 CNV gain+loss 17160897
nsv94557 CNV deletion 16902084

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)

Additional Variant Information for NIPA1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for NIPA1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
spastic paraplegia 6, autosomal dominant
  • spg6
spastic paraplegia 6
  • spastic paraplegia 6, autosomal dominant
hereditary spastic paraplegia
  • spastic paraplegia 3, autosomal dominant
  • paraplegia, lower
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.

Additional Disease Information for NIPA1

Genetic Association Database
Human Genome Epidemiology 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 JK (American journal of human genetics 2003) 2 3 4 22 58
  2. Distinct novel mutations affecting the same base in the NIPA1 gene cause autosomal dominant hereditary spastic paraplegia in two Chinese families. (PMID: 15643603) Chen S … Wang Y (Human mutation 2005) 3 4 22 58
  3. Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients. (PMID: 20398908) Saus E … Estivill X (Journal of psychiatric research 2010) 3 44 58
  4. A large genome scan for rare CNVs in amyotrophic lateral sclerosis. (PMID: 20685689) Blauw HM … van den Berg LH (Human molecular genetics 2010) 3 44 58
  5. Clinical and genetic study of SPG6 mutation in a Chinese family with hereditary spastic paraplegia. (PMID: 17928003) Liu SG … Ma X (Journal of the neurological sciences 2008) 3 22 58

Products for NIPA1 Gene

Sources for NIPA1 Gene

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