Free for academic non-profit institutions. Other users need a Commercial license

Aliases for NIPA2 Gene

Aliases for NIPA2 Gene

  • NIPA Magnesium Transporter 2 2 3
  • Non Imprinted In Prader-Willi/Angelman Syndrome 2 2 3 5
  • Non-Imprinted In Prader-Willi/Angelman Syndrome Region Protein 2 3 4
  • Magnesium Transporter NIPA2 3
  • SLC57A2 3

External Ids for NIPA2 Gene

Previous GeneCards Identifiers for NIPA2 Gene

  • GC15M020423
  • GC15M020553
  • GC15M020556
  • GC15M023004
  • GC15M001317

Summaries for NIPA2 Gene

Entrez Gene Summary for NIPA2 Gene

  • This gene encodes a possible magnesium transporter. This gene is located adjacent to the imprinted domain in the Prader-Willi syndrome deletion region of chromosome 15. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 7 and 21.[provided by RefSeq, May 2010]

GeneCards Summary for NIPA2 Gene

NIPA2 (NIPA Magnesium Transporter 2) is a Protein Coding gene. Diseases associated with NIPA2 include Angelman Syndrome and Prader-Willi Syndrome. 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 NIPA2 Gene

  • Acts as a selective Mg(2+) transporter.

Gene Wiki entry for NIPA2 Gene

Additional gene information for NIPA2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NIPA2 Gene

Genomics for NIPA2 Gene

GeneHancer (GH) Regulatory Elements for NIPA2 Gene

Promoters and enhancers for NIPA2 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
GH15J022837 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 674.3 +0.8 757 3.8 HDGF ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B E2F8 NIPA2 LOC102723534 CYFIP1 ENSG00000259098 PIR62888
GH15J023564 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 21.5 +727.1 727140 2.3 PKNOX1 SMAD1 ARNT SIN3A YY1 POLR2B CBX5 E2F8 SP3 NFYC MKRN3 NIPA2 GC15M023573
GH15J023038 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 13.4 +200.6 200614 2.2 HDGF PKNOX1 CLOCK ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ZNF207 TUBGCP5 NIPA2 LOC102723534 ENSG00000259098 CYFIP1
GH15J022785 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.5 -52.0 -51975 2.4 HDGF ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 ZNF207 ZNF143 NIPA1 CYFIP1 NIPA2 LOC729900 PIR54317
GH15J022886 Enhancer 1 Ensembl ENCODE 14.8 +49.5 49514 2.9 HDAC1 PKNOX1 TAF9B CHAMP1 EGR1 ZNF366 SIRT6 FOS ATF7 SMARCA5 PIR44215 NIPA2 PIR45624 CYFIP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NIPA2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NIPA2 gene promoter:
  • Msx-1
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • Pax-2b
  • Pax-2a
  • Pax-2
  • Olf-1

Genomic Locations for NIPA2 Gene

Genomic Locations for NIPA2 Gene
29,744 bases
Plus strand
29,744 bases
Minus strand

Genomic View for NIPA2 Gene

Genes around NIPA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIPA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIPA2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIPA2 Gene

Proteins for NIPA2 Gene

  • Protein details for NIPA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Magnesium transporter NIPA2
    Protein Accession:
    Secondary Accessions:
    • F8W7Y8
    • Q96F03
    • Q9BVS2

    Protein attributes for NIPA2 Gene

    360 amino acids
    Molecular mass:
    39185 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for NIPA2 Gene


neXtProt entry for NIPA2 Gene

Post-translational modifications for NIPA2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NIPA2 Gene

Domains & Families for NIPA2 Gene

Gene Families for NIPA2 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for NIPA2 Gene


Suggested Antigen Peptide Sequences for NIPA2 Gene

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 NIPA2: view

Function for NIPA2 Gene

Molecular function for NIPA2 Gene

UniProtKB/Swiss-Prot Function:
Acts as a selective Mg(2+) transporter.

Gene Ontology (GO) - Molecular Function for NIPA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015095 magnesium ion transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with NIPA2: view
genes like me logo Genes that share phenotypes with NIPA2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for NIPA2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NIPA2 Gene

Localization for NIPA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIPA2 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 NIPA2 gene
Compartment Confidence
plasma membrane 5
endosome 3
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NIPA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005769 early endosome IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IBA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NIPA2: view

Pathways & Interactions for NIPA2 Gene

genes like me logo Genes that share pathways with NIPA2: view

Pathways by source for NIPA2 Gene

Interacting Proteins for NIPA2 Gene

STRING Interaction Network Preview (showing 4 interactants - click image to see details)
Selected Interacting proteins: Q8N8Q9-NIPA2_HUMAN ENSP00000337618 for NIPA2 Gene via IID STRING

Gene Ontology (GO) - Biological Process for NIPA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0015693 magnesium ion transport IBA --
GO:1903830 magnesium ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with NIPA2: view

No data available for SIGNOR curated interactions for NIPA2 Gene

Drugs & Compounds for NIPA2 Gene

No Compound Related Data Available

Transcripts for NIPA2 Gene

Unigene Clusters for NIPA2 Gene

Non imprinted in Prader-Willi/Angelman syndrome 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NIPA2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e ^ 11 ^ 12 ^ 13 ^ 14a ·
SP1: - - - - - -
SP2: - - - - - - -
SP3: - - - - - - - - - - -
SP4: - - -
SP5: - - - - - -
SP6: - - - - - -
SP8: -
SP10: - - - - - - - - - - - - -
SP11: - - - - - - - - - - -
SP12: - - - - - - -
SP13: - - - - - -
SP14: - - - -
SP16: - - - - - - - - - - - -
SP17: - - - - - - - - - -
SP18: - -

ExUns: 14b ^ 15 ^ 16a · 16b

Relevant External Links for NIPA2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NIPA2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NIPA2 Gene

Protein differential expression in normal tissues from HIPED for NIPA2 Gene

This gene is overexpressed in Blymphocyte (53.3) and Placenta (15.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NIPA2 Gene

Protein tissue co-expression partners for NIPA2 Gene

NURSA nuclear receptor signaling pathways regulating expression of NIPA2 Gene:


SOURCE GeneReport for Unigene cluster for NIPA2 Gene:


mRNA Expression by UniProt/SwissProt for NIPA2 Gene:

Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for NIPA2 Gene

  • Pancreas(4.5)
  • Intestine(4.3)
  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with NIPA2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NIPA2 Gene

Orthologs for NIPA2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NIPA2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NIPA2 34 33
  • 99.39 (n)
(Canis familiaris)
Mammalia NIPA2 34 33
  • 93.43 (n)
(Bos Taurus)
Mammalia NIPA2 34 33
  • 92.04 (n)
(Monodelphis domestica)
Mammalia NIPA2 34
  • 92 (a)
(Mus musculus)
Mammalia Nipa2 16 34 33
  • 90.71 (n)
(Rattus norvegicus)
Mammalia Nipa2 33
  • 90.62 (n)
(Ornithorhynchus anatinus)
Mammalia NIPA2 34
  • 85 (a)
(Gallus gallus)
Aves NIPA2 34 33
  • 79.63 (n)
(Anolis carolinensis)
Reptilia NIPA2 34
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nipa2 33
  • 74.91 (n)
Str.7576 33
African clawed frog
(Xenopus laevis)
Amphibia LOC398554 33
(Danio rerio)
Actinopterygii nipa2 34 33
  • 71.29 (n)
wufb72g02 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009838 33
  • 55.38 (n)
fruit fly
(Drosophila melanogaster)
Insecta spict 34 33
  • 54.64 (n)
(Caenorhabditis elegans)
Secernentea nipa-1 34 33
  • 57.72 (n)
(Glycine max)
eudicotyledons Gma.1991 33
(Oryza sativa)
Liliopsida Os05g0513400 33
  • 55.82 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 60 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU04457 33
  • 47.71 (n)
Species where no ortholog for NIPA2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • 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 NIPA2 Gene

Gene Tree for NIPA2 (if available)
Gene Tree for NIPA2 (if available)
Evolutionary constrained regions (ECRs) for NIPA2: view image

Paralogs for NIPA2 Gene

Paralogs for NIPA2 Gene

(5) SIMAP similar genes for NIPA2 Gene using alignment to 3 proteins:

  • L8E8V4_HUMAN
genes like me logo Genes that share paralogs with NIPA2: view

Variants for NIPA2 Gene

Sequence variations from dbSNP and Humsavar for NIPA2 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs371775791 likely-pathogenic, not provided 22,866,495(+) A/G coding_sequence_variant, missense_variant
rs1000003835 -- 22,864,668(+) T/A intron_variant
rs1000114619 -- 22,844,329(+) G/A intron_variant
rs1000117723 -- 22,852,273(+) C/A intron_variant
rs1000158020 -- 22,859,122(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NIPA2 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
esv2474417 CNV loss 19546169
esv2665115 CNV deletion 23128226
esv34463 CNV gain 17911159
esv3569265 CNV gain 25503493
esv3635806 CNV loss 21293372
esv3635807 CNV gain 21293372
esv3635821 CNV loss 21293372
esv3635822 CNV gain 21293372
esv3635823 CNV loss 21293372
esv3635825 CNV loss 21293372
esv3892604 CNV gain+loss 25118596
esv3892626 CNV gain+loss 25118596
nsv1040546 CNV gain 25217958
nsv433290 CNV loss 18776910
nsv433429 CNV gain 18776910
nsv437797 CNV loss 16327808
nsv442359 CNV gain+loss 18776908
nsv456612 CNV loss 19166990
nsv456636 CNV loss 19166990
nsv469615 CNV loss 16826518
nsv469667 CNV loss 16826518
nsv471225 CNV gain 18288195
nsv471226 CNV loss 18288195
nsv471377 CNV loss 19718026
nsv511042 OTHER inversion 20534489
nsv568226 CNV gain 21841781
nsv568235 CNV loss 21841781
nsv832926 CNV gain+loss 17160897

Variation tolerance for NIPA2 Gene

Residual Variation Intolerance Score: 28.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.01; 37.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NIPA2 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 NIPA2 Gene

Disorders for NIPA2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NIPA2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
angelman syndrome
  • as
prader-willi syndrome
  • pws
childhood absence epilepsy
  • absence seizure
- elite association - COSMIC cancer census association via MalaCards
Search NIPA2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NIPA2

genes like me logo Genes that share disorders with NIPA2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NIPA2 Gene

Publications for NIPA2 Gene

  1. Identification of four highly conserved genes between breakpoint hotspots BP1 and BP2 of the Prader-Willi/Angelman syndromes deletion region that have undergone evolutionary transposition mediated by flanking duplicons. (PMID: 14508708) Chai JH … Nicholls RD (American journal of human genetics 2003) 2 3 4 58
  2. Nine patients with a microdeletion 15q11.2 between breakpoints 1 and 2 of the Prader-Willi critical region, possibly associated with behavioural disturbances. (PMID: 19328872) Doornbos M … van Ravenswaaij-Arts CM (European journal of medical genetics 2009) 3 22 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for NIPA2 Gene

Sources for NIPA2 Gene

Loading form....