Aliases for NPNT Gene

Aliases for NPNT Gene

  • Nephronectin 2 3 4 5
  • Preosteoblast EGF-Like Repeat Protein With MAM Domain 3 4
  • EGFL6L 3 4
  • POEM 3 4
  • Protein EGFL6-Like 4

External Ids for NPNT Gene

Previous GeneCards Identifiers for NPNT Gene

  • GC04P107175
  • GC04P107036
  • GC04P106816
  • GC04P102551

Summaries for NPNT Gene

GeneCards Summary for NPNT Gene

NPNT (Nephronectin) is a Protein Coding gene. Diseases associated with NPNT include Fraser Syndrome 1 and Fibrosarcomatous Osteosarcoma. Among its related pathways are ECM-receptor interaction. Gene Ontology (GO) annotations related to this gene include calcium ion binding and integrin binding. An important paralog of this gene is EGFL6.

UniProtKB/Swiss-Prot Summary for NPNT Gene

  • Functional ligand of integrin alpha-8/beta-1 in kidney development. Regulates the expression of GDNF with integrin alpha-8/beta-1 which is essential for kidney development. May also play a role in the development and function of various tissues, regulating cell adhesion, spreading and survival through the binding of several integrins (By similarity).

Additional gene information for NPNT Gene

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

Genomics for NPNT Gene

GeneHancer (GH) Regulatory Elements for NPNT Gene

Promoters and enhancers for NPNT 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
GH04J105894 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +2.0 2025 4.3 FOXK2 EP300 NCOR1 ZIC2 FOXA1 ZBTB26 TGIF2 SKI HDAC2 ZNF341 INTS12 NPNT ENSG00000250740
GH04J106314 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 4.3 +421.8 421775 4.6 FOXK2 ZBTB40 ZNF217 EP300 SIN3A TCF12 POLR2G USF1 GTF2E2 PHF8 TBCK AIMP1 lnc-GIMD1-6 NPNT piR-43099-451
GH04J106364 Enhancer 1 FANTOM5 Ensembl ENCODE 5.3 +470.9 470875 2.4 JUND FOS SKI FOXA2 CEBPB FOSL2 POLR2A FOSL1 CREM STAT3 lnc-TBCK-2 NPNT GIMD1 TBCK
GH04J106369 Enhancer 0.6 Ensembl 5.5 +475.4 475375 1.4 CTCF ZNF10 REST RAD21 SMC3 SPI1 EHMT2 GATA3 RCOR1 ZNF654 GIMD1 TBCK NPNT LINC02173
GH04J106311 Enhancer 0.8 ENCODE dbSUPER 4.3 +418.3 418316 2 TOE1 ZBTB17 USF1 JUND NR2F1 SCRT1 BHLHE40 MITF RAD51 ZNF362 TBCK NPNT AIMP1 lnc-GIMD1-6 HSALNG0036220
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPNT on UCSC Golden Path with GeneCards custom track

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

Top Transcription factor binding sites by QIAGEN in the NPNT gene promoter:
  • AP-1
  • ATF-2
  • Bach2
  • c-Jun
  • COMP1
  • E47
  • Evi-1
  • HEN1
  • STAT1
  • STAT1alpha

Genomic Locations for NPNT Gene

Genomic Locations for NPNT Gene
chr4:105,894,526-106,004,027
(GRCh38/hg38)
Size:
109,502 bases
Orientation:
Plus strand
chr4:106,815,932-106,925,184
(GRCh37/hg19)
Size:
109,253 bases
Orientation:
Plus strand

Genomic View for NPNT Gene

Genes around NPNT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NPNT Gene

Proteins for NPNT Gene

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

    Protein Symbol:
    Q6UXI9-NPNT_HUMAN
    Recommended name:
    Nephronectin
    Protein Accession:
    Q6UXI9
    Secondary Accessions:
    • A6NFT9
    • A8K1W4
    • B4DIT4
    • B4DYK3
    • B4E2H7
    • B4E3H2
    • D6RCA1
    • E9PCK8
    • E9PCQ1
    • E9PE64
    • E9PF04

    Protein attributes for NPNT Gene

    Size:
    565 amino acids
    Molecular mass:
    61907 Da
    Quaternary structure:
    • Homodimer and homotrimer.

    Alternative splice isoforms for NPNT Gene

neXtProt entry for NPNT Gene

Post-translational modifications for NPNT Gene

  • Glycosylation at Ser264, Asn273, and Thr376
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

No data available for DME Specific Peptides for NPNT Gene

Domains & Families for NPNT Gene

Gene Families for NPNT Gene

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

Protein Domains for NPNT Gene

Suggested Antigen Peptide Sequences for NPNT Gene

GenScript: Design optimal peptide antigens:
  • Protein EGFL6-like (NPNT_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6UXI9

UniProtKB/Swiss-Prot:

NPNT_HUMAN :
  • The MAM domain is required for localization at the cell surface.
  • Belongs to the nephronectin family.
Domain:
  • The MAM domain is required for localization at the cell surface.
Family:
  • Belongs to the nephronectin family.
genes like me logo Genes that share domains with NPNT: view

Function for NPNT Gene

Molecular function for NPNT Gene

UniProtKB/Swiss-Prot Function:
Functional ligand of integrin alpha-8/beta-1 in kidney development. Regulates the expression of GDNF with integrin alpha-8/beta-1 which is essential for kidney development. May also play a role in the development and function of various tissues, regulating cell adhesion, spreading and survival through the binding of several integrins (By similarity).

Phenotypes From GWAS Catalog for NPNT Gene

Gene Ontology (GO) - Molecular Function for NPNT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding NAS 11470831
GO:0005201 extracellular matrix structural constituent RCA 25037231
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with NPNT: view

Phenotypes for NPNT Gene

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

Animal Models for NPNT Gene

MGI Knock Outs for NPNT:
  • Npnt Npnt<tm1.1Lfr>

Animal Model Products

  • Taconic Biosciences Mouse Models for NPNT

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

Localization for NPNT Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPNT Gene

Secreted, extracellular space, extracellular matrix. Note=Trapped on the cell surface or in the extracellular matrix. {ECO:0000250}.

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 NPNT gene
Compartment Confidence
extracellular 4
plasma membrane 3
cytosol 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NPNT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region ISS 15754038
GO:0005604 basement membrane IEA --
GO:0016020 membrane IEA --
GO:0030485 smooth muscle contractile fiber IEA --
GO:0031012 extracellular matrix IEA --
genes like me logo Genes that share ontologies with NPNT: view

Pathways & Interactions for NPNT Gene

PathCards logo

SuperPathways for NPNT Gene

SuperPathway Contained pathways
1 ECM-receptor interaction
genes like me logo Genes that share pathways with NPNT: view

Pathways by source for NPNT Gene

1 KEGG pathway for NPNT Gene

SIGNOR curated interactions for NPNT Gene

Is activated by:

Gene Ontology (GO) - Biological Process for NPNT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001657 ureteric bud development ISS 15754038
GO:0001658 branching involved in ureteric bud morphogenesis ISS 15754038
GO:0007155 cell adhesion IEA --
GO:0007160 cell-matrix adhesion ISS 15754038
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with NPNT: view

Drugs & Compounds for NPNT Gene

No Compound Related Data Available

Transcripts for NPNT Gene

mRNA/cDNA for NPNT Gene

6 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
16 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 NPNT

Clone Products

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16
SP1: - - - -
SP2: - - - - -
SP3: - - - -
SP4: - - -
SP5:
SP6: -
SP7: - - -
SP8: - -
SP9:

Relevant External Links for NPNT Gene

GeneLoc Exon Structure for
NPNT

Expression for NPNT Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Thyroid (x8.8), Artery - Aorta (x6.4), Lung (x4.8), Artery - Tibial (x4.5), and Artery - Coronary (x4.2).

Protein differential expression in normal tissues from HIPED for NPNT Gene

This gene is overexpressed in Gallbladder (28.4) and Milk (9.0).

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



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

SOURCE GeneReport for Unigene cluster for NPNT Gene:

Hs.518921

mRNA Expression by UniProt/SwissProt for NPNT Gene:

Q6UXI9-NPNT_HUMAN
Tissue specificity: Expressed in kidney and lung and to a lower extent in brain, pregnant uterus, placenta, thyroid gland and blood vessels.

Evidence on tissue expression from TISSUES for NPNT Gene

  • Nervous system(4.2)
  • Kidney(2.6)
  • Lung(2)
  • Thyroid gland(2)
genes like me logo Genes that share expression patterns with NPNT: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NPNT Gene

Orthologs for NPNT Gene

This gene was present in the common ancestor of animals.

Orthologs for NPNT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPNT 31 30
  • 98.27 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NPNT 31 30
  • 91.04 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NPNT 31 30
  • 89.66 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Npnt 17 31 30
  • 88.14 (n)
oppossum
(Monodelphis domestica)
Mammalia NPNT 31
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NPNT 31
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPNT 31 30
  • 73.66 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPNT 31
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia npnt 30
  • 66.97 (n)
zebrafish
(Danio rerio)
Actinopterygii npnt 31 30
  • 60.56 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea mua-3 31
  • 4 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 4 (a)
OneToMany
Species where no ortholog for NPNT 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rat (Rattus norvegicus)
  • 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 NPNT Gene

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

Paralogs for NPNT Gene

Paralogs for NPNT Gene

(11) SIMAP similar genes for NPNT Gene using alignment to 6 proteins:

  • NPNT_HUMAN
  • D6RE63_HUMAN
  • D6RH31_HUMAN
  • H0Y8M1_HUMAN
  • H0YA60_HUMAN
  • H0YAK9_HUMAN
genes like me logo Genes that share paralogs with NPNT: view

Variants for NPNT Gene

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

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs35132891 - p.Gln159His
rs35488797 - p.Met476Thr
rs35613262 - p.Gly473Ser
rs4340795 - p.Ile234Val

Additional dbSNP identifiers (rs#s) for NPNT Gene

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

Variant ID Type Subtype PubMed ID
esv2418320 CNV deletion 18987734
nsv1000196 CNV loss 25217958
nsv1014993 CNV gain 25217958

Variation tolerance for NPNT Gene

Residual Variation Intolerance Score: 90.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.61; 91.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPNT Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NPNT Gene

MalaCards: The human disease database

(4) MalaCards diseases for NPNT Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search NPNT in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NPNT

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

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

Publications for NPNT Gene

  1. Identification and characterization of a novel human nephronectin gene in silico. (PMID: 15754038) Huang JT … Lee V (International journal of molecular medicine 2005) 2 3 4 23 54
  2. Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. (PMID: 20010835) Hancock DB … London SJ (Nature genetics 2010) 3 41 54
  3. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PMID: 20332099) Kalsi G … Riley BP (Human molecular genetics 2010) 3 41 54
  4. MicroRNA miR-378 regulates nephronectin expression modulating osteoblast differentiation by targeting GalNT-7. (PMID: 19844573) Kahai S … Yang BB (PloS one 2009) 3 23 54
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 54

Products for NPNT Gene

Sources for NPNT Gene