Aliases for NIPAL1 Gene

Aliases for NIPAL1 Gene

  • NIPA Like Domain Containing 1 2 3 5
  • Non-Imprinted In Prader-Willi/Angelman Syndrome Region Protein 3 3 4
  • Magnesium Transporter NIPA3 3 4
  • NIPA-Like Protein 1 3 4
  • NPAL1 3 4
  • NIPA3 4

External Ids for NIPAL1 Gene

Previous HGNC Symbols for NIPAL1 Gene

  • NPAL1

Previous GeneCards Identifiers for NIPAL1 Gene

  • GC04P047714
  • GC04P048018
  • GC04P047339

Summaries for NIPAL1 Gene

GeneCards Summary for NIPAL1 Gene

NIPAL1 (NIPA Like Domain Containing 1) is a Protein Coding gene. Diseases associated with NIPAL1 include Angelman 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 NIPA2.

UniProtKB/Swiss-Prot Summary for NIPAL1 Gene

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

Additional gene information for NIPAL1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NIPAL1 Gene

Genomics for NIPAL1 Gene

GeneHancer (GH) Regulatory Elements for NIPAL1 Gene

Promoters and enhancers for NIPAL1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J048014 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 511.3 +105.0 105014 8.7 ZNF217 CTCF NRF1 POLR2G ZFX ZIC2 POLR2A ZBTB10 ZNF423 ZBTB26 CNGA1 NIPAL1 RNU6-838P NFXL1 HSALNG0034264 piR-37026-454
GH04J047911 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 -0.3 -341 4 ZBTB40 ZNF217 EP300 SIN3A NRF1 MYC USF1 POLR2G PHF8 JUND NFXL1 LOC101927157 NIPAL1 CNGA1 lnc-CORIN-4
GH04J048079 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 16.2 +166.6 166558 3.4 TCF12 EP300 NFIC GATA3 FOSL2 CEBPB ZNF592 GTF2A2 JUN KLF13 TXK NIPAL1 RNU6-838P CNGA1 ENSG00000259959 SLAIN2 CWH43 piR-55985-142 RF00026-781
GH04J047823 Enhancer 1.1 VISTA Ensembl ENCODE CraniofacialAtlas 10.9 -89.2 -89224 2.2 MEF2B IKZF1 PAX5 MEF2A MTA2 IKZF2 NFXL1 NIPAL1 CNGA1 ENSG00000282917 CORIN piR-46847-172
GH04J048093 Enhancer 1 Ensembl ENCODE dbSUPER 11 +179.9 179859 2 JUND EP300 NFIC ZBTB17 FOS JUN RCOR1 TAL1 MAX PKNOX1 CNGA1 TXK NIPAL1 RF00026-781 RNU6-838P piR-55985-142
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NIPAL1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NIPAL1

Top Transcription factor binding sites by QIAGEN in the NIPAL1 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • NF-Y
  • NF-YA
  • NF-YB
  • NF-YC

Genomic Locations for NIPAL1 Gene

Genomic Locations for NIPAL1 Gene
chr4:47,914,142-48,040,173
(GRCh38/hg38)
Size:
126,032 bases
Orientation:
Plus strand
chr4:47,916,159-48,042,188
(GRCh37/hg19)
Size:
126,030 bases
Orientation:
Plus strand

Genomic View for NIPAL1 Gene

Genes around NIPAL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIPAL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIPAL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIPAL1 Gene

Proteins for NIPAL1 Gene

  • Protein details for NIPAL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6NVV3-NIPA3_HUMAN
    Recommended name:
    Magnesium transporter NIPA3
    Protein Accession:
    Q6NVV3
    Secondary Accessions:
    • B3KTB0
    • Q68DA9

    Protein attributes for NIPAL1 Gene

    Size:
    410 amino acids
    Molecular mass:
    44638 Da
    Quaternary structure:
    No Data Available

neXtProt entry for NIPAL1 Gene

Post-translational modifications for NIPAL1 Gene

  • Glycosylation at Asn25, Asn35, Asn50, and Asn55
  • Modification sites at PhosphoSitePlus

Other Protein References for NIPAL1 Gene

No data available for DME Specific Peptides for NIPAL1 Gene

Domains & Families for NIPAL1 Gene

Gene Families for NIPAL1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for NIPAL1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NIPAL1 Gene

GenScript: Design optimal peptide antigens:
  • Non-imprinted in Prader-Willi/Angelman syndrome region protein 3 (NIPA3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6NVV3

UniProtKB/Swiss-Prot:

NIPA3_HUMAN :
  • Belongs to the NIPA family.
Family:
  • Belongs to the NIPA family.
genes like me logo Genes that share domains with NIPAL1: view

Function for NIPAL1 Gene

Molecular function for NIPAL1 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+), Cu(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity).

Phenotypes From GWAS Catalog for NIPAL1 Gene

Gene Ontology (GO) - Molecular Function for NIPAL1 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 NIPAL1: view
genes like me logo Genes that share phenotypes with NIPAL1: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NIPAL1 Gene

Localization for NIPAL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIPAL1 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
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 NIPAL1 gene
Compartment Confidence
plasma membrane 3
extracellular 1
mitochondrion 1
endosome 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for NIPAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NIPAL1: view

Pathways & Interactions for NIPAL1 Gene

genes like me logo Genes that share pathways with NIPAL1: view

Pathways by source for NIPAL1 Gene

Interacting Proteins for NIPAL1 Gene

;

Gene Ontology (GO) - Biological Process for NIPAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015693 magnesium ion transport IBA,IEA 21873635
GO:1903830 magnesium ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with NIPAL1: view

No data available for SIGNOR curated interactions for NIPAL1 Gene

Drugs & Compounds for NIPAL1 Gene

No Compound Related Data Available

Transcripts for NIPAL1 Gene

mRNA/cDNA for NIPAL1 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NIPAL1 Gene

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

Relevant External Links for NIPAL1 Gene

GeneLoc Exon Structure for
NIPAL1

Expression for NIPAL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NIPAL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NIPAL1 Gene

This gene is overexpressed in Esophagus - Mucosa (x10.6), Skin - Sun Exposed (Lower leg) (x8.5), Skin - Not Sun Exposed (Suprapubic) (x8.0), and Colon - Transverse (x5.2).

Protein differential expression in normal tissues from HIPED for NIPAL1 Gene

This gene is overexpressed in Ovary (49.0) and Spleen (16.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NIPAL1 Gene



Protein tissue co-expression partners for NIPAL1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NIPAL1

SOURCE GeneReport for Unigene cluster for NIPAL1 Gene:

Hs.134190
genes like me logo Genes that share expression patterns with NIPAL1: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for NIPAL1 Gene

Orthologs for NIPAL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NIPAL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NIPAL1 31 30
  • 99.84 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NIPAL1 31 30
  • 90.49 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NIPAL1 31 30
  • 88.56 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nipal1 30
  • 85.76 (n)
mouse
(Mus musculus)
Mammalia Nipal1 17 31 30
  • 84.96 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NIPAL1 31
  • 74 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NIPAL1 31
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves NIPAL1 31 30
  • 70.99 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NIPAL1 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nipal1 30
  • 66.26 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:101583 31
  • 62 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta spict 31
  • 45 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea nipa-1 31
  • 44 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.6171 30
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 57 (a)
OneToMany
Species where no ortholog for NIPAL1 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 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 NIPAL1 Gene

ENSEMBL:
Gene Tree for NIPAL1 (if available)
TreeFam:
Gene Tree for NIPAL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NIPAL1: view image

Paralogs for NIPAL1 Gene

Paralogs for NIPAL1 Gene

(4) SIMAP similar genes for NIPAL1 Gene using alignment to 3 proteins:

  • NIPA3_HUMAN
  • D6RIY2_HUMAN
  • H0Y8W0_HUMAN

Pseudogenes.org Pseudogenes for NIPAL1 Gene

genes like me logo Genes that share paralogs with NIPAL1: view

Variants for NIPAL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NIPAL1 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs13116684 - p.Ile324Val

Additional dbSNP identifiers (rs#s) for NIPAL1 Gene

Variation tolerance for NIPAL1 Gene

Residual Variation Intolerance Score: 70.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.40; 81.79% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NIPAL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NIPAL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for NIPAL1 Gene

Disorders for NIPAL1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NIPAL1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
angelman syndrome
  • as
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for NIPAL1

genes like me logo Genes that share disorders with NIPAL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NIPAL1 Gene

Publications for NIPAL1 Gene

  1. 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 54
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  3. NIPA-like domain containing 1 is a novel tumor-promoting factor in oral squamous cell carcinoma. (PMID: 29464350) Sasahira T … Kirita T (Journal of cancer research and clinical oncology 2018) 3 54
  4. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes. (PMID: 27899376) Nakayama A … Eurogout Consortium (Annals of the rheumatic diseases 2017) 3 54
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54

Products for NIPAL1 Gene

Sources for NIPAL1 Gene