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Aliases for NDE1 Gene

Aliases for NDE1 Gene

  • NudE Neurodevelopment Protein 1 2 3 5
  • NUDE 3 4
  • NudE Nuclear Distribution Gene E Homolog 1 (A. Nidulans) 2
  • NudE Nuclear Distribution E Homolog 1 (A. Nidulans) 2
  • LIS1-Interacting Protein NUDE1, Rat Homolog 3
  • Nuclear Distribution Protein NudE Homolog 1 3
  • NudE Nuclear Distribution Gene E Homolog 1 3
  • NudE Nuclear Distribution E Homolog 1 3
  • HOM-TES-87 3
  • NUDE1 3
  • LIS4 3
  • MHAC 3
  • NDE 3

External Ids for NDE1 Gene

Previous GeneCards Identifiers for NDE1 Gene

  • GC16P015664
  • GC16P015710
  • GC16P015651
  • GC16P015739
  • GC16P015130
  • GC16P015740
  • GC16P015743
  • GC16P015745
  • GC16P015647
  • GC16P015648
  • GC16P015649
  • GC16P015650
  • GC16P015654
  • GC16P015656
  • GC16P015658

Summaries for NDE1 Gene

Entrez Gene Summary for NDE1 Gene

  • This gene encodes a member of the nuclear distribution E (NudE) family of proteins. The encoded protein is localized at the centrosome and interacts with other centrosome components as part of a multiprotein complex that regulates dynein function. This protein plays an essential role in microtubule organization, mitosis and neuronal migration. Mutations in this gene cause lissencephaly 4, a disorder characterized by lissencephaly, severe brain atrophy, microcephaly, and severe cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

GeneCards Summary for NDE1 Gene

NDE1 (NudE Neurodevelopment Protein 1) is a Protein Coding gene. Diseases associated with NDE1 include Microhydranencephaly and Lissencephaly 4. Among its related pathways are Organelle biogenesis and maintenance and Regulation of PLK1 Activity at G2/M Transition. Gene Ontology (GO) annotations related to this gene include identical protein binding and microtubule binding. An important paralog of this gene is NDEL1.

UniProtKB/Swiss-Prot for NDE1 Gene

  • Required for centrosome duplication and formation and function of the mitotic spindle. Essential for the development of the cerebral cortex. May regulate the production of neurons by controlling the orientation of the mitotic spindle during division of cortical neuronal progenitors of the proliferative ventricular zone of the brain. Orientation of the division plane perpendicular to the layers of the cortex gives rise to two proliferative neuronal progenitors whereas parallel orientation of the division plane yields one proliferative neuronal progenitor and a post-mitotic neuron. A premature shift towards a neuronal fate within the progenitor population may result in an overall reduction in the final number of neurons and an increase in the number of neurons in the deeper layers of the cortex.

Gene Wiki entry for NDE1 Gene

Additional gene information for NDE1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NDE1 Gene

Genomics for NDE1 Gene

GeneHancer (GH) Regulatory Elements for NDE1 Gene

Promoters and enhancers for NDE1 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
GH16I015638 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 550.8 -0.3 -280 9 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF143 SP3 SSRP1 GLIS1 GC16P015643 MARF1 NDE1 MIR484 ENSG00000263335 ENSG00000183458 PKD1P1 LOC100505915 PKD1P6 ENSG00000227827
GH16I015649 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.4 +7.4 7421 2.4 HDGF PKNOX1 ARNT ARID4B SIN3A YBX1 DMAP1 SLC30A9 CBX5 ZNF143 GC16P015660 NDE1 ABCC1 LOC100505915 ENSG00000262171 ENSG00000263335 MPV17L C16orf45 MIR484
GH16I015670 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 25.2 +29.7 29671 4.5 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ENSG00000263335 NDE1 MARF1 RRN3 ENSG00000277920 C16orf45 GC16M015668 GC16P015660
GH16I015588 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 13.4 -51.9 -51945 5.4 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 PARN ENSG00000263335 BFAR LOC100505915 RRN3 ABCC1 PKD1P6 ENSG00000262171 NDE1 PKD1P1
GH16I015635 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 18.3 -6.6 -6591 3.2 ZNF687 CBFB EBF1 ELF1 ATF2 FOXK2 IKZF1 NBN ATF7 ZBTB33 NDE1 ENSG00000263335 C16orf45 MARF1 ENSG00000183458 MIR6506
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NDE1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NDE1 gene promoter:

Genomic Locations for NDE1 Gene

Genomic Locations for NDE1 Gene
chr16:15,643,267-15,726,353
(GRCh38/hg38)
Size:
83,087 bases
Orientation:
Plus strand
chr16:15,737,124-15,820,210
(GRCh37/hg19)

Genomic View for NDE1 Gene

Genes around NDE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NDE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NDE1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NDE1 Gene

Proteins for NDE1 Gene

  • Protein details for NDE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NXR1-NDE1_HUMAN
    Recommended name:
    Nuclear distribution protein nudE homolog 1
    Protein Accession:
    Q9NXR1
    Secondary Accessions:
    • Q49AQ2

    Protein attributes for NDE1 Gene

    Size:
    346 amino acids
    Molecular mass:
    38808 Da
    Quaternary structure:
    • Self-associates. Interacts with CNTRL, LIS1, dynein, SLMAP and TCP1 (By similarity). Interacts with CENPF, dynactin, tubulin gamma, PAFAH1B1, PCM1 and PCNT. Interacts with ZNF365.

    Alternative splice isoforms for NDE1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NDE1 Gene

Post-translational modifications for NDE1 Gene

  • Phosphorylated in mitosis. Phosphorylated in vitro by CDC2. Phosphorylation at Thr-246 is essential for the G2/M transition (By similarity).

No data available for DME Specific Peptides for NDE1 Gene

Domains & Families for NDE1 Gene

Gene Families for NDE1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for NDE1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NDE1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NXR1

UniProtKB/Swiss-Prot:

NDE1_HUMAN :
  • Belongs to the nudE family.
Family:
  • Belongs to the nudE family.
genes like me logo Genes that share domains with NDE1: view

Function for NDE1 Gene

Molecular function for NDE1 Gene

UniProtKB/Swiss-Prot Function:
Required for centrosome duplication and formation and function of the mitotic spindle. Essential for the development of the cerebral cortex. May regulate the production of neurons by controlling the orientation of the mitotic spindle during division of cortical neuronal progenitors of the proliferative ventricular zone of the brain. Orientation of the division plane perpendicular to the layers of the cortex gives rise to two proliferative neuronal progenitors whereas parallel orientation of the division plane yields one proliferative neuronal progenitor and a post-mitotic neuron. A premature shift towards a neuronal fate within the progenitor population may result in an overall reduction in the final number of neurons and an increase in the number of neurons in the deeper layers of the cortex.

Phenotypes From GWAS Catalog for NDE1 Gene

Gene Ontology (GO) - Molecular Function for NDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16682949
GO:0008017 microtubule binding IBA,ISS --
GO:0019904 protein domain specific binding IEA --
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with NDE1: view
genes like me logo Genes that share phenotypes with NDE1: view

Human Phenotype Ontology for NDE1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NDE1 Gene

MGI Knock Outs for NDE1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for NDE1 Gene

Localization for NDE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NDE1 Gene

Cytoplasm, cytoskeleton. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Chromosome, centromere, kinetochore. Cytoplasm, cytoskeleton, spindle. Cleavage furrow. Note=Localizes to the interphase and S phase centrosome. During mitosis, partially associated with the mitotic spindle. Concentrates at the plus ends of microtubules coincident with kinetochores in metaphase and anaphase in a CENPF-dependent manner. Also localizes to the cleavage furrow during cytokinesis. manner. Also localizes to the cleavage furrow during cytokinesis.

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 NDE1 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 4
extracellular 1

Gene Ontology (GO) - Cellular Components for NDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IEA --
GO:0000776 kinetochore IDA,IEA 17600710
GO:0000777 condensed chromosome kinetochore IEA --
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NDE1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NDE1 Gene

Pathways & Interactions for NDE1 Gene

genes like me logo Genes that share pathways with NDE1: view

SIGNOR curated interactions for NDE1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for NDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000086 G2/M transition of mitotic cell cycle TAS --
GO:0000132 establishment of mitotic spindle orientation IMP 19468067
GO:0001764 neuron migration IEA --
GO:0007020 microtubule nucleation IBA --
GO:0007049 cell cycle IEA --
genes like me logo Genes that share ontologies with NDE1: view

Drugs & Compounds for NDE1 Gene

No Compound Related Data Available

Transcripts for NDE1 Gene

Unigene Clusters for NDE1 Gene

NudE nuclear distribution E homolog 1 (A. nidulans):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NDE1 Gene

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

Relevant External Links for NDE1 Gene

GeneLoc Exon Structure for
NDE1
ECgene alternative splicing isoforms for
NDE1

Expression for NDE1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NDE1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NDE1 Gene

This gene is overexpressed in Whole Blood (x4.3).

Protein differential expression in normal tissues from HIPED for NDE1 Gene

This gene is overexpressed in Breast (30.8) and Bone (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NDE1 Gene



Protein tissue co-expression partners for NDE1 Gene

NURSA nuclear receptor signaling pathways regulating expression of NDE1 Gene:

NDE1

SOURCE GeneReport for Unigene cluster for NDE1 Gene:

Hs.655378

mRNA Expression by UniProt/SwissProt for NDE1 Gene:

Q9NXR1-NDE1_HUMAN
Tissue specificity: Expressed in the neuroepithelium throughout the developing brain, including the cerebral cortex and cerebellum.

Evidence on tissue expression from TISSUES for NDE1 Gene

  • Intestine(4.4)
  • Liver(4.2)
  • Nervous system(3.9)
  • Stomach(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NDE1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • mouth
  • nose
  • outer ear
  • skull
  • tongue
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with NDE1: view

Primer Products

Orthologs for NDE1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NDE1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NDE1 33 34
  • 93.89 (n)
dog
(Canis familiaris)
Mammalia NDE1 33 34
  • 89.95 (n)
cow
(Bos Taurus)
Mammalia NDE1 33 34
  • 84.58 (n)
mouse
(Mus musculus)
Mammalia Nde1 33 16 34
  • 84.5 (n)
oppossum
(Monodelphis domestica)
Mammalia NDE1 34
  • 83 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nde1 33
  • 82.7 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NDE1 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves NDE1 33 34
  • 72.65 (n)
lizard
(Anolis carolinensis)
Reptilia NDE1 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nde1 33
  • 66.77 (n)
Str.8167 33
African clawed frog
(Xenopus laevis)
Amphibia LOC398067 33
zebrafish
(Danio rerio)
Actinopterygii nde1 33 34
  • 62.84 (n)
fruit fly
(Drosophila melanogaster)
Insecta nudE 34
  • 29 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8970 34
  • 41 (a)
OneToMany
Species where no ortholog for NDE1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for NDE1 Gene

ENSEMBL:
Gene Tree for NDE1 (if available)
TreeFam:
Gene Tree for NDE1 (if available)

Paralogs for NDE1 Gene

Paralogs for NDE1 Gene

(1) SIMAP similar genes for NDE1 Gene using alignment to 10 proteins:

Pseudogenes.org Pseudogenes for NDE1 Gene

genes like me logo Genes that share paralogs with NDE1: view

Variants for NDE1 Gene

Sequence variations from dbSNP and Humsavar for NDE1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1028181943 uncertain-significance, Lissencephaly, Recessive 15,725,639(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1029371842 uncertain-significance, Aortic aneurysm, familial thoracic 4 15,718,395(+) C/T genic_downstream_transcript_variant, intron_variant
rs1033302963 uncertain-significance, Lissencephaly, Recessive, Thoracic aortic aneurysm and aortic dissection 15,703,187(+) G/A genic_downstream_transcript_variant, intron_variant
rs1046974765 uncertain-significance, Lissencephaly, Recessive 15,643,695(+) A/C 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1050162 conflicting-interpretations-of-pathogenicity, benign, not specified, Thoracic aortic aneurysm and aortic dissection, Lissencephaly, Recessive 15,717,205(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NDE1 Gene

Variant ID Type Subtype PubMed ID
nsv9361 CNV gain 18304495
nsv827569 CNV loss 20364138
nsv469626 CNV loss 16826518
nsv457428 CNV gain 19166990
nsv435664 CNV deletion 17901297
nsv1125134 CNV deletion 24896259
nsv1049647 CNV gain+loss 25217958
nsv1047898 CNV loss 25217958
esv3638041 CNV gain 21293372
esv3638039 CNV loss 21293372
esv3582042 CNV loss 25503493
esv2714015 CNV deletion 23290073
dgv4924n54 CNV gain 21841781

Variation tolerance for NDE1 Gene

Residual Variation Intolerance Score: 23% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.24; 76.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NDE1 Gene

Human Gene Mutation Database (HGMD)
NDE1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NDE1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NDE1 Gene

Disorders for NDE1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for NDE1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search NDE1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NDE1_HUMAN
  • Lissencephaly 4 (LIS4) [MIM:614019]: A neurodevelopmental disorder characterized by lissencephaly, severe brain atrophy, extreme microcephaly, and profound mental retardation. {ECO:0000269 PubMed:21529751, ECO:0000269 PubMed:21529752}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microhydranencephaly (MHAC) [MIM:605013]: A severe neurodevelopmental disorder characterized by microcephaly, severe motor and mental retardation, spasticity, and brain malformations that include gross dilation of the ventricles with complete absence of the cerebral hemispheres or severe delay in their development. {ECO:0000269 PubMed:22526350}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for NDE1

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 NDE1: view

No data available for Genatlas for NDE1 Gene

Publications for NDE1 Gene

  1. Human Nudel and NudE as regulators of cytoplasmic dynein in poleward protein transport along the mitotic spindle. (PMID: 12556484) Yan X … Zhu X (Molecular and cellular biology 2003) 3 4 22 58
  2. Novel NDE1 homozygous mutation resulting in microhydranencephaly and not microlyssencephaly. (PMID: 22526350) Guven A … Tolun A (Neurogenetics 2012) 3 4 58
  3. The essential role of centrosomal NDE1 in human cerebral cortex neurogenesis. (PMID: 21529752) Bakircioglu M … Woods CG (American journal of human genetics 2011) 3 4 58
  4. Human mutations in NDE1 cause extreme microcephaly with lissencephaly [corrected]. (PMID: 21529751) Alkuraya FS … Walsh CA (American journal of human genetics 2011) 3 4 58
  5. DISC1, PDE4B, and NDE1 at the centrosome and synapse. (PMID: 18983980) Bradshaw NJ … Millar JK (Biochemical and biophysical research communications 2008) 3 22 58

Products for NDE1 Gene

Sources for NDE1 Gene

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