Incidental Mutation 'A4554:Nde1'
ID 106
Institutional Source Beutler Lab
Gene Symbol Nde1
Ensembl Gene ENSMUSG00000022678
Gene Name nudE neurodevelopment protein 1
Synonyms mNudE, 2810027M15Rik
Accession Numbers
Essential gene? Probably essential (E-score: 0.866) question?
Stock # A4554 of strain gemini
Quality Score
Status Validated
Chromosome 16
Chromosomal Location 13981139-14010792 bp(+) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to C at 14006274 bp (GRCm39)
Zygosity Homozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000119355 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023359] [ENSMUST00000115795] [ENSMUST00000117958] [ENSMUST00000132316] [ENSMUST00000149232]
AlphaFold Q9CZA6
Predicted Effect probably benign
Transcript: ENSMUST00000023359
SMART Domains Protein: ENSMUSP00000023359
Gene: ENSMUSG00000022678

DomainStartEndE-ValueType
low complexity region 47 56 N/A INTRINSIC
Pfam:NUDE_C 134 312 1.7e-50 PFAM
low complexity region 324 336 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000115795
SMART Domains Protein: ENSMUSP00000111461
Gene: ENSMUSG00000022678

DomainStartEndE-ValueType
low complexity region 47 56 N/A INTRINSIC
Pfam:NUDE_C 134 317 1.2e-40 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000117958
SMART Domains Protein: ENSMUSP00000112817
Gene: ENSMUSG00000022678

DomainStartEndE-ValueType
low complexity region 47 56 N/A INTRINSIC
Pfam:NUDE_C 134 317 9.8e-41 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127801
Predicted Effect probably benign
Transcript: ENSMUST00000132316
SMART Domains Protein: ENSMUSP00000118005
Gene: ENSMUSG00000022678

DomainStartEndE-ValueType
PDB:2V71|B 8 79 2e-14 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000149232
SMART Domains Protein: ENSMUSP00000119355
Gene: ENSMUSG00000022678

DomainStartEndE-ValueType
Pfam:NUDE_C 1 167 8.6e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156041
Coding Region Coverage
  • 1x: 85.5%
  • 3x: 63.0%
Validation Efficiency 84% (92/109)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] 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 mental retardation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
PHENOTYPE: Homozygous null mutants have a small brain with fewer neurons in the cerebral cortex and very thin superficial cortical layers. [provided by MGI curators]
Allele List at MGI

All alleles(37) : Targeted, knock-out(1) Gene trapped(36)

Other mutations in this stock
Total: 18 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Asap1 T C 15: 63,996,560 (GRCm39) probably benign Het
Bpifb5 A T 2: 154,069,100 (GRCm39) Y139F possibly damaging Homo
Chd2 A C 7: 73,130,716 (GRCm39) V782G probably benign Homo
Chst4 G T 8: 110,756,520 (GRCm39) Q448K probably benign Homo
Dido1 T C 2: 180,317,164 (GRCm39) K8E probably damaging Homo
Evpl A G 11: 116,111,660 (GRCm39) L2010P probably damaging Homo
Fgl2 A G 5: 21,577,776 (GRCm39) E21G probably benign Homo
Greb1l A T 18: 10,532,862 (GRCm39) M919L possibly damaging Homo
Kel T A 6: 41,674,353 (GRCm39) D359V possibly damaging Homo
Lmtk2 A G 5: 144,103,135 (GRCm39) D298G possibly damaging Homo
Masp1 A T 16: 23,273,690 (GRCm39) probably null Homo
Mrgprb8 A T 7: 48,039,156 (GRCm39) I276F probably damaging Homo
Rbck1 G T 2: 152,161,092 (GRCm39) N385K probably damaging Homo
Senp6 G T 9: 80,055,740 (GRCm39) probably benign Het
Tm4sf4 T A 3: 57,345,188 (GRCm39) probably null Homo
Ubn2 A T 6: 38,461,045 (GRCm39) H488L probably damaging Homo
Vmn2r120 A G 17: 57,832,715 (GRCm39) F155L probably benign Homo
Vmn2r65 T A 7: 84,595,791 (GRCm39) T298S probably damaging Homo
Other mutations in Nde1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03013:Nde1 APN 16 14,009,611 (GRCm39) missense probably benign
PIT4515001:Nde1 UTSW 16 13,988,357 (GRCm39) critical splice donor site probably null
R1473:Nde1 UTSW 16 14,003,728 (GRCm39) missense probably benign 0.07
R2014:Nde1 UTSW 16 13,987,321 (GRCm39) start gained probably benign
R2015:Nde1 UTSW 16 13,987,321 (GRCm39) start gained probably benign
R4426:Nde1 UTSW 16 14,006,200 (GRCm39) missense possibly damaging 0.94
R5116:Nde1 UTSW 16 14,001,351 (GRCm39) missense probably benign 0.19
R5646:Nde1 UTSW 16 13,987,378 (GRCm39) missense probably damaging 1.00
R6770:Nde1 UTSW 16 14,006,242 (GRCm39) missense probably damaging 1.00
R7722:Nde1 UTSW 16 14,008,128 (GRCm39) missense unknown
R8856:Nde1 UTSW 16 14,001,446 (GRCm39) missense
R9405:Nde1 UTSW 16 14,006,255 (GRCm39) missense probably damaging 1.00
R9574:Nde1 UTSW 16 13,988,345 (GRCm39) missense probably damaging 0.99
Nature of Mutation

DNA sequencing using the SOLiD technique identified a T to C transition at base pair 14188503 in the Genbank genomic region NC_000082 for the Nde1 gene on chromosome 16 (GTAAGTCTGG ->GTAAGCCTGG). The mutation is located within intron 3, six nucleotides from the previous exon 3 (from the ATG exon). The Nde1 transcript contains 9 total exons. Multiple transcripts of the Nde1 gene are displayed on Ensembl. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).

Protein Function and Prediction
The Nde1 gene encodes a 344 amino acid protein that is required for centrosome duplication, and formation and function of the mitotic spindle. The protein belongs to the nudE family, and is essential for the development of the cerebral cortex (Uniprot Q9CZA6). Homozygous null mutants have a small brain with fewer neurons in the cerebral cortex and very thin superficial cortical layers.
Posted On 2010-03-16