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NDE1 nudE neurodevelopment protein 1 [ Homo sapiens (human) ]

Gene ID: 54820, updated on 7-Apr-2024

Summary

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Official Symbol
NDE1provided by HGNC
Official Full Name
nudE neurodevelopment protein 1provided by HGNC
Primary source
HGNC:HGNC:17619
See related
Ensembl:ENSG00000072864 MIM:609449; AllianceGenome:HGNC:17619
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NDE; LIS4; MHAC; NUDE; NUDE1; HOM-TES-87
Summary
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]
Expression
Broad expression in esophagus (RPKM 68.2), prostate (RPKM 53.0) and 18 other tissues See more
Orthologs
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Genomic context

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See NDE1 in Genome Data Viewer
Location:
16p13.11
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (15643382..15726353)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (15648287..15731290)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15737239..15820210)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene meiosis regulator and mRNA stability factor 1 Neighboring gene uncharacterized LOC124903649 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15743803-15744304 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15744305-15744804 Neighboring gene Sharpr-MPRA regulatory region 7034 Neighboring gene microRNA 484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15766651-15767392 Neighboring gene Sharpr-MPRA regulatory region 12074 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15814393-15815196 Neighboring gene myosin heavy chain 11 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15830279-15831035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15851025-15851658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15851659-15852292 Neighboring gene uncharacterized LOC124903650 Neighboring gene uncharacterized LOC124903651

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. [Microlissencephaly due to pathogenic variants of NDE1: from pathology to normal brain development]. Cabet S, et al. Med Sci (Paris), 2020 Oct. PMID 33026328
  2. Nde1 promotes diverse dynein functions through differential interactions and exhibits an isoform-specific proteasome association. Monda JK, et al. Mol Biol Cell, 2018 Sep 15. PMID 30024347, Free PMC Article
  3. The NDE1 genomic locus can affect treatment of psychiatric illness through gene expression changes related to microRNA-484. Bradshaw NJ, et al. Open Biol, 2017 Nov. PMID 29142105, Free PMC Article
  4. Human NDE1 splicing and mammalian brain development. Mosca S, et al. Sci Rep, 2017 Mar 7. PMID 28266585, Free PMC Article
  5. Dynein Separately Partners with NDE1 and Dynactin To Orchestrate T Cell Focused Secretion. Nath S, et al. J Immunol, 2016 Sep 15. PMID 27534551, Free PMC Article

See all (88) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Comprehensive analysis indicated that NDE1 is a potential biomarker for pan-cancer and promotes bladder cancer progression.
    Title: Comprehensive analysis indicated that NDE1 is a potential biomarker for pan-cancer and promotes bladder cancer progression.
  2. Novel lissencephaly-associated NDEL1 variant reveals distinct roles of NDE1 and NDEL1 in nucleokinesis and human cortical malformations.
    Title: Novel lissencephaly-associated NDEL1 variant reveals distinct roles of NDE1 and NDEL1 in nucleokinesis and human cortical malformations.
  3. 16p13.11 microduplication in 45 new patients: refined clinical significance and genotype-phenotype correlations.
    Title: 16p13.11 microduplication in 45 new patients: refined clinical significance and genotype-phenotype correlations.
  4. CENP-F stabilizes kinetochore-microtubule attachments and limits dynein stripping of corona cargoes.
    Title: CENP-F stabilizes kinetochore-microtubule attachments and limits dynein stripping of corona cargoes.
  5. [Microlissencephaly due to pathogenic variants of NDE1: from pathology to normal brain development].", trans "Variations pathogenes de NDE1 et microlissencephalie - De la pathologie au developpement cerebral normal.
    Title: [Microlissencephaly due to pathogenic variants of NDE1: from pathology to normal brain development].
  6. These studies identify the LIS1/NDE1 complex as an important FGF signaling regulator and provide insights into the bidirectional regulation of cell signaling and transport machinery for endocytosis.
    Title: The LIS1/NDE1 Complex Is Essential for FGF Signaling by Regulating FGF Receptor Intracellular Trafficking.
  7. Nde1 makes unique contributions to human neurodevelopment through its regulation of both dynein and proteasome function.
    Title: Nde1 promotes diverse dynein functions through differential interactions and exhibits an isoform-specific proteasome association.
  8. Our results show how evolutionary changes in cis as well as trans acting signals have played a fundamental role in determining NDE1 species specific splicing isoforms supporting the notion that alternative splicing plays a central role in human genome evolution, and possibly human cognitive predominance.
    Title: Human NDE1 splicing and mammalian brain development.
  9. the severity of NDE1-associated microcephaly results not from defects in mitosis, but rather the inability of neural progenitors to ever reach this stage
    Title: Severe NDE1-mediated microcephaly results from neural progenitor cell cycle arrests at multiple specific stages.
  10. Variation at the NDE1 locus may alter risk of mental illness, in part through modification of miR-484. NDE1 SNP rs2242549 associates with significant changes in gene expression of DISC1 network.
    Title: The NDE1 genomic locus can affect treatment of psychiatric illness through gene expression changes related to microRNA-484.
Submit: New GeneRIF Correction See all GeneRIFs (37)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Lissencephaly 4
MedGen: C3151461 OMIM: 614019 GeneReviews: Not available
Compare labs
NDE1-related microhydranencephaly
MedGen: C1857977 OMIM: 605013 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20101

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables microtubule binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables microtubule binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in centrosome duplication ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in centrosome localization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cerebral cortex development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromosome segregation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in establishment of chromosome localization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in establishment of chromosome localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in establishment of mitotic spindle orientation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in establishment of mitotic spindle orientation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in microtubule nucleation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic centrosome separation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuroblast proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle transport along microtubule IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in centrosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cleavage furrow IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of kinesin complex IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in kinetochore IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in kinetochore IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 
located_in microtubule IEA
Inferred from Electronic Annotation
more info
  
located_in spindle pole centrosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
nuclear distribution protein nudE homolog 1
Names
LIS1-interacting protein NUDE1, rat homolog
epididymis secretory sperm binding protein
nudE nuclear distribution E homolog 1
nudE nuclear distribution gene E homolog 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_021210.1 RefSeqGene

    Range
    11979..88087
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001143979.2 → NP_001137451.1  nuclear distribution protein nudE homolog 1

    See identical proteins and their annotated locations for NP_001137451.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC026401, AF001548, AK000108, BC001421, BC033900
    Consensus CDS
    CCDS10564.1
    UniProtKB/Swiss-Prot
    Q49AQ2, Q9NXR1
    UniProtKB/TrEMBL
    A0A6Q8PGV6, X5DR54
    Related
    ENSP00000379643.1, ENST00000396355.5
    Conserved Domains (2) summary
    pfam04880
    Location:134 → 309
    NUDE_C; NUDE protein, C-terminal conserved region
    cl25732
    Location:27 → 186
    SMC_N; RecF/RecN/SMC N terminal domain

  2. NM_017668.3 → NP_060138.1  nuclear distribution protein nudE homolog 1

    See identical proteins and their annotated locations for NP_060138.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AF001548, BC001421
    Consensus CDS
    CCDS10564.1
    UniProtKB/Swiss-Prot
    Q49AQ2, Q9NXR1
    UniProtKB/TrEMBL
    A0A6Q8PGV6, X5DR54
    Related
    ENSP00000379642.1, ENST00000396354.6
    Conserved Domains (2) summary
    pfam04880
    Location:134 → 309
    NUDE_C; NUDE protein, C-terminal conserved region
    cl25732
    Location:27 → 186
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    15643382..15726353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434261.1 → XP_047290217.1  nuclear distribution protein nudE homolog 1 isoform X8

  2. XM_047434259.1 → XP_047290215.1  nuclear distribution protein nudE homolog 1 isoform X5

  3. XM_047434264.1 → XP_047290220.1  nuclear distribution protein nudE homolog 1 isoform X12

  4. XM_047434260.1 → XP_047290216.1  nuclear distribution protein nudE homolog 1 isoform X7

  5. XM_047434258.1 → XP_047290214.1  nuclear distribution protein nudE homolog 1 isoform X4

  6. XM_006720897.5 → XP_006720960.1  nuclear distribution protein nudE homolog 1 isoform X3

    See identical proteins and their annotated locations for XP_006720960.1

    Conserved Domains (3) summary
    PRK14160
    Location:33 → 220
    PRK14160; heat shock protein GrpE; Provisional
    pfam04880
    Location:166 → 344
    NUDE_C; NUDE protein, C-terminal conserved region
    cl03075
    Location:66 → 159
    GrpE; nucleotide exchange factor GrpE

  7. XM_047434267.1 → XP_047290223.1  nuclear distribution protein nudE homolog 1 isoform X17

  8. XM_047434262.1 → XP_047290218.1  nuclear distribution protein nudE homolog 1 isoform X1

  9. XM_017023353.3 → XP_016878842.1  nuclear distribution protein nudE homolog 1 isoform X6

    UniProtKB/TrEMBL
    I3L3G9, X5DRB5
    Conserved Domains (3) summary
    PRK14160
    Location:1 → 188
    PRK14160; heat shock protein GrpE; Provisional
    pfam04880
    Location:134 → 312
    NUDE_C; NUDE protein, C-terminal conserved region
    cl03075
    Location:34 → 127
    GrpE; nucleotide exchange factor GrpE

  10. XM_017023349.3 → XP_016878838.1  nuclear distribution protein nudE homolog 1 isoform X2

    UniProtKB/Swiss-Prot
    Q9NXR1
    Conserved Domains (3) summary
    PRK14160
    Location:1 → 188
    PRK14160; heat shock protein GrpE; Provisional
    pfam04880
    Location:134 → 312
    NUDE_C; NUDE protein, C-terminal conserved region
    cl03075
    Location:34 → 127
    GrpE; nucleotide exchange factor GrpE

  11. XM_017023354.3 → XP_016878843.1  nuclear distribution protein nudE homolog 1 isoform X13

    UniProtKB/TrEMBL
    I3L3G9, X5DRB5

  12. XM_047434263.1 → XP_047290219.1  nuclear distribution protein nudE homolog 1 isoform X10

  13. XM_047434265.1 → XP_047290221.1  nuclear distribution protein nudE homolog 1 isoform X14

  14. XM_017023355.3 → XP_016878844.1  nuclear distribution protein nudE homolog 1 isoform X16

    UniProtKB/TrEMBL
    I3L3G9, X5DRB5
    Related
    ENSP00000460436.2, ENST00000572756.6

  15. XM_047434266.1 → XP_047290222.1  nuclear distribution protein nudE homolog 1 isoform X15

  16. XM_017023352.3 → XP_016878841.1  nuclear distribution protein nudE homolog 1 isoform X11

    UniProtKB/TrEMBL
    A0A6Q8PG46, X5DP35
    Conserved Domains (3) summary
    PRK14160
    Location:1 → 188
    PRK14160; heat shock protein GrpE; Provisional
    pfam04880
    Location:134 → 265
    NUDE_C; NUDE protein, C-terminal conserved region
    cl03075
    Location:34 → 127
    GrpE; nucleotide exchange factor GrpE

  17. XM_017023350.2 → XP_016878839.1  nuclear distribution protein nudE homolog 1 isoform X9

  18. XM_005255396.6 → XP_005255453.1  nuclear distribution protein nudE homolog 1 isoform X1

    See identical proteins and their annotated locations for XP_005255453.1

    Conserved Domains (3) summary
    PRK14160
    Location:1 → 188
    PRK14160; heat shock protein GrpE; Provisional
    pfam04880
    Location:134 → 312
    NUDE_C; NUDE protein, C-terminal conserved region
    cl03075
    Location:34 → 127
    GrpE; nucleotide exchange factor GrpE

  19. XM_047434268.1 → XP_047290224.1  nuclear distribution protein nudE homolog 1 isoform X18

  20. XM_006720900.5 → XP_006720963.1  nuclear distribution protein nudE homolog 1 isoform X1

    See identical proteins and their annotated locations for XP_006720963.1

    Conserved Domains (3) summary
    PRK14160
    Location:1 → 188
    PRK14160; heat shock protein GrpE; Provisional
    pfam04880
    Location:134 → 312
    NUDE_C; NUDE protein, C-terminal conserved region
    cl03075
    Location:34 → 127
    GrpE; nucleotide exchange factor GrpE

  21. XM_017023357.3 → XP_016878846.1  nuclear distribution protein nudE homolog 1 isoform X19

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1301393..1384364
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329110.1 → XP_054185085.1  nuclear distribution protein nudE homolog 1 isoform X8

  2. XM_054329107.1 → XP_054185082.1  nuclear distribution protein nudE homolog 1 isoform X5

  3. XM_054329116.1 → XP_054185091.1  nuclear distribution protein nudE homolog 1 isoform X12

  4. XM_054329109.1 → XP_054185084.1  nuclear distribution protein nudE homolog 1 isoform X7

  5. XM_054329106.1 → XP_054185081.1  nuclear distribution protein nudE homolog 1 isoform X4

  6. XM_054329105.1 → XP_054185080.1  nuclear distribution protein nudE homolog 1 isoform X3

  7. XM_054329120.1 → XP_054185095.1  nuclear distribution protein nudE homolog 1 isoform X17

  8. XM_054329112.1 → XP_054185087.1  nuclear distribution protein nudE homolog 1 isoform X1

  9. XM_054329108.1 → XP_054185083.1  nuclear distribution protein nudE homolog 1 isoform X6

  10. XM_054329104.1 → XP_054185079.1  nuclear distribution protein nudE homolog 1 isoform X2

  11. XM_054329117.1 → XP_054185092.1  nuclear distribution protein nudE homolog 1 isoform X13

  12. XM_054329118.1 → XP_054185093.1  nuclear distribution protein nudE homolog 1 isoform X15

  13. XM_054329114.1 → XP_054185089.1  nuclear distribution protein nudE homolog 1 isoform X10

  14. XM_054329119.1 → XP_054185094.1  nuclear distribution protein nudE homolog 1 isoform X14

  15. XM_054329115.1 → XP_054185090.1  nuclear distribution protein nudE homolog 1 isoform X11

    UniProtKB/TrEMBL
    X5DP35

  16. XM_054329113.1 → XP_054185088.1  nuclear distribution protein nudE homolog 1 isoform X9

  17. XM_054329103.1 → XP_054185078.1  nuclear distribution protein nudE homolog 1 isoform X1

  18. XM_054329121.1 → XP_054185096.1  nuclear distribution protein nudE homolog 1 isoform X18

  19. XM_054329111.1 → XP_054185086.1  nuclear distribution protein nudE homolog 1 isoform X1

  20. XM_054329122.1 → XP_054185097.1  nuclear distribution protein nudE homolog 1 isoform X19

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    15648287..15731290
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054380543.1 → XP_054236518.1  nuclear distribution protein nudE homolog 1 isoform X8

  2. XM_054380540.1 → XP_054236515.1  nuclear distribution protein nudE homolog 1 isoform X5

  3. XM_054380549.1 → XP_054236524.1  nuclear distribution protein nudE homolog 1 isoform X12

  4. XM_054380542.1 → XP_054236517.1  nuclear distribution protein nudE homolog 1 isoform X7

  5. XM_054380539.1 → XP_054236514.1  nuclear distribution protein nudE homolog 1 isoform X4

  6. XM_054380538.1 → XP_054236513.1  nuclear distribution protein nudE homolog 1 isoform X3

  7. XM_054380545.1 → XP_054236520.1  nuclear distribution protein nudE homolog 1 isoform X1

  8. XM_054380541.1 → XP_054236516.1  nuclear distribution protein nudE homolog 1 isoform X6

  9. XM_054380537.1 → XP_054236512.1  nuclear distribution protein nudE homolog 1 isoform X2

  10. XM_054380550.1 → XP_054236525.1  nuclear distribution protein nudE homolog 1 isoform X13

  11. XM_054380551.1 → XP_054236526.1  nuclear distribution protein nudE homolog 1 isoform X15

  12. XM_054380547.1 → XP_054236522.1  nuclear distribution protein nudE homolog 1 isoform X10

  13. XM_054380552.1 → XP_054236527.1  nuclear distribution protein nudE homolog 1 isoform X14

  14. XM_054380553.1 → XP_054236528.1  nuclear distribution protein nudE homolog 1 isoform X16

  15. XM_054380548.1 → XP_054236523.1  nuclear distribution protein nudE homolog 1 isoform X11

    UniProtKB/TrEMBL
    X5DP35

  16. XM_054380546.1 → XP_054236521.1  nuclear distribution protein nudE homolog 1 isoform X9

  17. XM_054380536.1 → XP_054236511.1  nuclear distribution protein nudE homolog 1 isoform X1

  18. XM_054380544.1 → XP_054236519.1  nuclear distribution protein nudE homolog 1 isoform X1

  19. XM_054380554.1 → XP_054236529.1  nuclear distribution protein nudE homolog 1 isoform X19

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXR1.3 GenPept UniProtKB/Swiss-Prot:Q9NXR1

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