This gene is located in the Prader-Willi syndrome region on chromosome 15. This gene is biallelically expressed in adult testis and brain but is paternally imprinted in fetal brain. Defects in this gene may be associated with Prader-Willi syndrome. [provided by RefSeq, Aug 2012] See more...

Aliases for NPAP1 Gene

Aliases for NPAP1 Gene

  • Nuclear Pore Associated Protein 1 2 3 5
  • Nuclear Pore-Associated Protein 1 3 4
  • C15orf2 3 4
  • Chromosome 15 Open Reading Frame 2 2
  • Protein C15orf2 3
  • NPAP1 5

External Ids for NPAP1 Gene

Previous HGNC Symbols for NPAP1 Gene

  • C15orf2

Previous GeneCards Identifiers for NPAP1 Gene

  • GC15P024951
  • GC15P024969
  • GC15P024982
  • GC15P025000

Summaries for NPAP1 Gene

Entrez Gene Summary for NPAP1 Gene

  • This gene is located in the Prader-Willi syndrome region on chromosome 15. This gene is biallelically expressed in adult testis and brain but is paternally imprinted in fetal brain. Defects in this gene may be associated with Prader-Willi syndrome. [provided by RefSeq, Aug 2012]

GeneCards Summary for NPAP1 Gene

NPAP1 (Nuclear Pore Associated Protein 1) is a Protein Coding gene. Diseases associated with NPAP1 include Prader-Willi Syndrome and Angelman Syndrome. An important paralog of this gene is POM121C.

UniProtKB/Swiss-Prot Summary for NPAP1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NPAP1 Gene

Genomics for NPAP1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NPAP1 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
GH15J024101 Promoter 0.4 Ensembl 5.6 -574.0 -573974 1.2 EZH2 PWRN1 LOC105370733 LOC105370734 PWRN3 NPAP1
GH15J024877 Promoter/Enhancer 1.4 FANTOM5 ENCODE CraniofacialAtlas 1.3 +202.5 202451 1 GATAD2A TFE3 GABPA RBFOX2 IRF2 KMT2B TAF1 RNF2 TGIF2 KAT7 RPL5P1 SNRPN SNURF NPAP1 piR-49623 SNODB728 SNHG14 ENSG00000286110
GH15J024772 Promoter/Enhancer 1.3 FANTOM5 ENCODE CraniofacialAtlas 0.2 +97.2 97166 1.7 CTCF GABPA RBFOX2 EZH2 TOE1 NRF1 RAD51 NR2C2 YY1 CREB1 RPL5P1 SNRPN SNURF piR-33185 piR-38352-186 NPAP1 ENSG00000286110 PWRN1 PWRN3
GH15J024696 Enhancer 0.6 Ensembl ENCODE 0.4 +21.1 21126 1 ZNF740 NFE2 POLR2A piR-35312-012 piR-40110-195 NPAP1 SNRPN ENSG00000286110 PWRN1 PWRN3
GH15J024685 Enhancer 0.2 Ensembl 0.4 +10.5 10526 1.4 piR-35312-012 NPAP1 piR-40110-195 ENSG00000286110 SNRPN PWRN1 PWRN3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPAP1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NPAP1

Genomic Locations for NPAP1 Gene

Genomic Locations for NPAP1 Gene
chr15:24,675,775-24,683,393
(GRCh38/hg38)
Size:
7,619 bases
Orientation:
Plus strand
chr15:24,920,541-24,928,593
(GRCh37/hg19)
Size:
8,053 bases
Orientation:
Plus strand

Genomic View for NPAP1 Gene

Genes around NPAP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPAP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPAP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPAP1 Gene

Proteins for NPAP1 Gene

  • Protein details for NPAP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZP6-NPAP1_HUMAN
    Recommended name:
    Nuclear pore-associated protein 1
    Protein Accession:
    Q9NZP6

    Protein attributes for NPAP1 Gene

    Size:
    1156 amino acids
    Molecular mass:
    120954 Da
    Quaternary structure:
    • Associates with the nuclear pore complex (NPC).

neXtProt entry for NPAP1 Gene

Post-translational modifications for NPAP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NPAP1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NPAP1 Gene

Domains & Families for NPAP1 Gene

Gene Families for NPAP1 Gene

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

Protein Domains for NPAP1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NPAP1 Gene

GenScript: Design optimal peptide antigens:
  • Protein C15orf2 (CO002_HUMAN)
genes like me logo Genes that share domains with NPAP1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for NPAP1 Gene

Function for NPAP1 Gene

Molecular function for NPAP1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in spermatogenesis.

Phenotypes From GWAS Catalog for NPAP1 Gene

Gene Ontology (GO) - Molecular Function for NPAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0008139 nuclear localization sequence binding IBA 21873635
GO:0017056 structural constituent of nuclear pore IBA 21873635
genes like me logo Genes that share ontologies with NPAP1: view
genes like me logo Genes that share phenotypes with NPAP1: view

Human Phenotype Ontology for NPAP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NPAP1

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for NPAP1 Gene

Localization for NPAP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPAP1 Gene

Nucleus, nucleoplasm. Nucleus inner membrane. Note=Colocalizes with the NPC and nuclear lamins at the nuclear periphery.

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 NPAP1 gene
Compartment Confidence
nucleus 4
plasma membrane 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for NPAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005637 nuclear inner membrane IEA --
GO:0005643 nuclear pore IBA 21873635
GO:0005654 nucleoplasm IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with NPAP1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NPAP1 Gene

Pathways & Interactions for NPAP1 Gene

PathCards logo

SuperPathways for NPAP1 Gene

No Data Available

Interacting Proteins for NPAP1 Gene

Gene Ontology (GO) - Biological Process for NPAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006405 RNA export from nucleus IBA 21873635
GO:0006606 protein import into nucleus IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007283 spermatogenesis NAS 10783265
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with NPAP1: view

No data available for Pathways by source and SIGNOR curated interactions for NPAP1 Gene

Drugs & Compounds for NPAP1 Gene

No Compound Related Data Available

Transcripts for NPAP1 Gene

mRNA/cDNA for NPAP1 Gene

1 REFSEQ mRNAs :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NPAP1

Alternative Splicing Database (ASD) splice patterns (SP) for NPAP1 Gene

No ASD Table

Relevant External Links for NPAP1 Gene

GeneLoc Exon Structure for
NPAP1

Expression for NPAP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NPAP1 Gene

mRNA differential expression in normal tissues according to GTEx for NPAP1 Gene

This gene is overexpressed in Testis (x17.8).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NPAP1

SOURCE GeneReport for Unigene cluster for NPAP1 Gene:

Hs.649663

mRNA Expression by UniProt/SwissProt for NPAP1 Gene:

Q9NZP6-NPAP1_HUMAN
Tissue specificity: Testis-specific in adults. In fetal brain expressed only from the paternal allele.
genes like me logo Genes that share expression patterns with NPAP1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for NPAP1 Gene

Orthologs for NPAP1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for NPAP1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NPAP1 30 31
  • 99.25 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LOC102151589 30
  • 59.23 (n)
-- 31
  • 35 (a)
OneToMany
-- 31
  • 35 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia NPAP1 31
  • 32 (a)
OneToOne
Species where no ortholog for NPAP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for NPAP1 Gene

ENSEMBL:
Gene Tree for NPAP1 (if available)
TreeFam:
Gene Tree for NPAP1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NPAP1: view image

Paralogs for NPAP1 Gene

Variants for NPAP1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NPAP1 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
713578 Benign: not provided 24,676,365(+) G/A SYNONYMOUS_VARIANT
727389 Benign: not provided 24,675,936(+) C/T SYNONYMOUS_VARIANT
734399 Benign: not provided 24,678,648(+) C/T SYNONYMOUS_VARIANT
738331 Likely Benign: not provided 24,679,122(+) C/T SYNONYMOUS_VARIANT
738363 Likely Benign: not provided 24,678,207(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for NPAP1 Gene

Structural Variations from Database of Genomic Variants (DGV) for NPAP1 Gene

Variant ID Type Subtype PubMed ID
esv2674507 CNV deletion 23128226
esv3635898 CNV gain 21293372
nsv1046100 CNV gain 25217958
nsv568530 CNV loss 21841781
nsv819553 CNV gain 19587683

Variation tolerance for NPAP1 Gene

Residual Variation Intolerance Score: 95.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.62; 56.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPAP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPAP1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPAP1 Gene

Disorders for NPAP1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for NPAP1 Gene - From: LncRNADisease, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
prader-willi syndrome
  • pws
angelman syndrome
  • as
chromosome 15q13.3 deletion syndrome
  • chromosome 15q13.3 microdeletion syndrome
schaaf-yang syndrome
  • shfyng
mannosidosis, beta a, lysosomal
  • mansb
- elite association - COSMIC cancer census association via MalaCards
Search NPAP1 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with NPAP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NPAP1 Gene

Publications for NPAP1 Gene

  1. The imprinted NPAP1/C15orf2 gene in the Prader-Willi syndrome region encodes a nuclear pore complex associated protein. (PMID: 22694955) Neumann LC … Horsthemke B (Human molecular genetics 2012) 2 3 4
  2. Identification of a testis-specific gene (C15orf2) in the Prader-Willi syndrome region on chromosome 15. (PMID: 10783265) Färber C … Horsthemke B (Genomics 2000) 2 3 4
  3. The C15orf2 gene in the Prader-Willi syndrome region is subject to genomic imprinting and positive selection. (PMID: 20020165) Wawrzik M … Horsthemke B (Neurogenetics 2010) 3 4
  4. C15orf2 and a novel noncoding transcript from the Prader-Willi/Angelman syndrome region show monoallelic expression in fetal brain. (PMID: 17337158) Buiting K … Horsthemke B (Genomics 2007) 3 4
  5. The imprinted NPAP1 gene in the Prader-Willi syndrome region belongs to a POM121-related family of retrogenes. (PMID: 24482533) Neumann LC … Horsthemke B (Genome biology and evolution 2014) 3

Products for NPAP1 Gene

Sources for NPAP1 Gene