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 lisse... See more...

Aliases for NDE1 Gene

Aliases for NDE1 Gene

  • NudE Neurodevelopment Protein 1 2 3 5
  • Nuclear Distribution Protein NudE Homolog 1 3 4
  • 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
  • Epididymis Secretory Sperm Binding Protein 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
  • NudE 4
  • NDE 3

External Ids for NDE1 Gene

Previous GeneCards Identifiers for NDE1 Gene

  • GC16P015664
  • GC16P015710
  • GC16P015651
  • GC16P015739
  • GC16P015130
  • GC16P015740
  • GC16P015743
  • GC16P015745
  • GC16P015647
  • GC16P015648
  • GC16P015668
  • GC16P015670
  • GC16P015666
  • GC16P015649
  • GC16P015650
  • GC16P015654
  • GC16P015656
  • GC16P015658
  • GC16P015661

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 Regulation of PLK1 Activity at G2/M Transition and Mitotic Metaphase and Anaphase. 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 Summary 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 , Rfam classification and piRNA Summary for NDE1 Gene

Genomics for NDE1 Gene

GeneHancer (GH) Regulatory Elements for NDE1 Gene

Promoters and enhancers for NDE1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NDE1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NDE1

Top Transcription factor binding sites by QIAGEN in the NDE1 gene promoter:
  • IRF-2
  • ISGF-3
  • Lmo2
  • NF-kappaB
  • NF-kappaB1

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)
Size:
83,087 bases
Orientation:
Plus strand

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:
    335 amino acids
    Molecular mass:
    37721 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).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NDE1 Gene

Domains & Families for NDE1 Gene

Gene Families for NDE1 Gene

HGNC:
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:
  • Nuclear distribution protein nudE homolog 1 (NDE1_HUMAN)

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 IPI 22843697
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

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
plasma membrane 5
cytoskeleton 5
nucleus 4
cytosol 4
extracellular 2
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 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 IBA,IDA 17600710
GO:0000777 condensed chromosome kinetochore IEA --
GO:0005623 cell IEA --
GO:0005694 chromosome 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,IBA 19468067
GO:0001764 neuron migration IEA --
GO:0007020 microtubule nucleation IBA 21873635
GO:0007049 cell cycle IEA --
genes like me logo Genes that share ontologies with NDE1: view

Drugs & Compounds for NDE1 Gene

(1) Drugs for NDE1 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine-5-Diphosphoribose Experimental Pharma Target 0
genes like me logo Genes that share compounds with NDE1: view

Transcripts for NDE1 Gene

mRNA/cDNA for NDE1 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR 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

Expression for NDE1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

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

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 31 30
  • 93.89 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NDE1 31 30
  • 89.95 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NDE1 31 30
  • 84.58 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nde1 17 31 30
  • 84.5 (n)
oppossum
(Monodelphis domestica)
Mammalia NDE1 31
  • 83 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nde1 30
  • 82.7 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NDE1 31
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves NDE1 31 30
  • 72.65 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NDE1 31
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nde1 30
  • 66.77 (n)
Str.8167 30
African clawed frog
(Xenopus laevis)
Amphibia LOC398067 30
zebrafish
(Danio rerio)
Actinopterygii nde1 31 30
  • 62.84 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta nudE 31
  • 29 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8970 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for NDE1: view image

Paralogs for NDE1 Gene

Paralogs for NDE1 Gene

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

  • NDE1_HUMAN
  • I3L2R3_HUMAN
  • I3L2R9_HUMAN
  • I3L2S8_HUMAN
  • I3L2T8_HUMAN
  • I3L3G9_HUMAN
  • I3L464_HUMAN
  • I3L522_HUMAN
  • I3L533_HUMAN
  • L8E8T4_HUMAN

Pseudogenes.org Pseudogenes for NDE1 Gene

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

Variants for NDE1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NDE1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
636781 Uncertain Significance: Aortic aneurysm, familial thoracic 4; not provided 15,720,269(+) C/T MISSENSE_VARIANT,INTRON_VARIANT
639217 Uncertain Significance: Aortic aneurysm, familial thoracic 4 15,720,993(+) G/A MISSENSE_VARIANT,INTRON_VARIANT
639271 Uncertain Significance: Aortic aneurysm, familial thoracic 4 15,724,399(+) G/A MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT
640443 Uncertain Significance: Aortic aneurysm, familial thoracic 4 15,717,279(+) G/C MISSENSE_VARIANT,INTRON_VARIANT
645057 Uncertain Significance: Aortic aneurysm, familial thoracic 4 15,721,520(+) C/T MISSENSE_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for NDE1 Gene

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

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

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NDE1 Gene

MalaCards: The human disease database

(18) MalaCards diseases for NDE1 Gene - From: 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 23 54
  2. Novel NDE1 homozygous mutation resulting in microhydranencephaly and not microlyssencephaly. (PMID: 22526350) Guven A … Tolun A (Neurogenetics 2012) 3 4 54
  3. Human mutations in NDE1 cause extreme microcephaly with lissencephaly [corrected]. (PMID: 21529751) Alkuraya FS … Walsh CA (American journal of human genetics 2011) 3 4 54
  4. 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 54
  5. Elucidating the relationship between DISC1, NDEL1 and NDE1 and the risk for schizophrenia: evidence of epistasis and competitive binding. (PMID: 18469341) Burdick KE … Malhotra AK (Human molecular genetics 2008) 3 41 54

Products for NDE1 Gene

Sources for NDE1 Gene