Incidental Mutation 'R4426:Nde1'
ID 328199
Institutional Source Beutler Lab
Gene Symbol Nde1
Ensembl Gene ENSMUSG00000022678
Gene Name nudE neurodevelopment protein 1
Synonyms mNudE, 2810027M15Rik
MMRRC Submission 041697-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.846) question?
Stock # R4426 (G1)
Quality Score 225
Status Not validated
Chromosome 16
Chromosomal Location 13981139-14010792 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 14006200 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 82 (T82A)
Ref Sequence ENSEMBL: ENSMUSP00000119355 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023359] [ENSMUST00000115795] [ENSMUST00000117958] [ENSMUST00000132316] [ENSMUST00000149232]
AlphaFold Q9CZA6
Predicted Effect possibly damaging
Transcript: ENSMUST00000023359
AA Change: T243A

PolyPhen 2 Score 0.835 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000023359
Gene: ENSMUSG00000022678
AA Change: T243A

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 possibly damaging
Transcript: ENSMUST00000115795
AA Change: T243A

PolyPhen 2 Score 0.835 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000111461
Gene: ENSMUSG00000022678
AA Change: T243A

DomainStartEndE-ValueType
low complexity region 47 56 N/A INTRINSIC
Pfam:NUDE_C 134 317 1.2e-40 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000117958
AA Change: T243A

PolyPhen 2 Score 0.835 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000112817
Gene: ENSMUSG00000022678
AA Change: T243A

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 possibly damaging
Transcript: ENSMUST00000149232
AA Change: T82A

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000119355
Gene: ENSMUSG00000022678
AA Change: T82A

DomainStartEndE-ValueType
Pfam:NUDE_C 1 167 8.6e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156041
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Albfm1 G T 5: 90,720,642 (GRCm39) C271F probably damaging Het
Arhgef39 C T 4: 43,497,112 (GRCm39) G293E possibly damaging Het
Atp8a1 A C 5: 67,932,171 (GRCm39) I206S probably benign Het
Cacnb2 A T 2: 14,980,026 (GRCm39) R290* probably null Het
Ccdc137 T C 11: 120,351,074 (GRCm39) S159P probably damaging Het
Chil5 A G 3: 105,926,943 (GRCm39) S231P probably damaging Het
Cic C T 7: 24,993,433 (GRCm39) probably benign Het
Csmd3 A G 15: 47,532,581 (GRCm39) V2434A possibly damaging Het
Csnk1a1 A G 18: 61,718,381 (GRCm39) probably benign Het
Eif4e1b T C 13: 54,932,296 (GRCm39) S49P probably benign Het
Far1 C A 7: 113,149,208 (GRCm39) P194Q probably benign Het
Fut4 T C 9: 14,662,677 (GRCm39) T206A possibly damaging Het
Galnt7 G T 8: 58,005,606 (GRCm39) S209* probably null Het
Gas2l1 A G 11: 5,013,908 (GRCm39) V184A probably benign Het
Herc1 T C 9: 66,403,287 (GRCm39) L4402P probably damaging Het
Hoxa13 C A 6: 52,237,714 (GRCm39) probably benign Het
Ighv1-9 T A 12: 114,547,416 (GRCm39) K42* probably null Het
Kif20a C T 18: 34,764,994 (GRCm39) R743W probably damaging Het
Lama2 G A 10: 27,298,554 (GRCm39) R181C probably damaging Het
Lrp2 G T 2: 69,336,692 (GRCm39) T1360K probably benign Het
Map4k1 G A 7: 28,688,020 (GRCm39) V177I probably damaging Het
Nbea G A 3: 55,989,800 (GRCm39) T352I probably damaging Het
Nes A G 3: 87,883,349 (GRCm39) E536G probably damaging Het
Nms C T 1: 38,978,377 (GRCm39) P4L probably benign Het
Nrip1 T C 16: 76,088,293 (GRCm39) Q1088R possibly damaging Het
Nwd1 A G 8: 73,393,423 (GRCm39) K229E probably damaging Het
Or51f1d T C 7: 102,701,018 (GRCm39) L171P probably damaging Het
Or52ad1 A G 7: 102,995,290 (GRCm39) Y282H probably damaging Het
Pcdhac2 T A 18: 37,277,796 (GRCm39) S259T probably benign Het
Pdcd5 T C 7: 35,345,605 (GRCm39) D102G possibly damaging Het
Pgm1 T C 4: 99,819,337 (GRCm39) V169A probably benign Het
Pitpnm2 C T 5: 124,280,186 (GRCm39) E121K probably benign Het
Plin3 T C 17: 56,593,555 (GRCm39) Y53C probably damaging Het
Poc1b T C 10: 98,991,001 (GRCm39) probably null Het
Polr2c A T 8: 95,590,090 (GRCm39) N232Y probably damaging Het
Ppp1r9b A T 11: 94,892,150 (GRCm39) R188S possibly damaging Het
Rab36 G A 10: 74,880,328 (GRCm39) V63I probably damaging Het
Rab3gap2 G A 1: 184,967,539 (GRCm39) S141N probably damaging Het
Radx T C X: 138,381,645 (GRCm39) V134A possibly damaging Het
Rap1gap2 C A 11: 74,298,148 (GRCm39) A491S possibly damaging Het
Rnf166 A G 8: 123,196,979 (GRCm39) L91P probably damaging Het
Robo2 T A 16: 73,745,154 (GRCm39) M200L probably damaging Het
Rp1 A T 1: 4,418,147 (GRCm39) H988Q probably benign Het
Sbno2 T C 10: 79,908,192 (GRCm39) K69R probably null Het
Sgce G A 6: 4,691,459 (GRCm39) A295V probably damaging Het
Shc3 C G 13: 51,634,130 (GRCm39) probably null Het
Slc44a1 T C 4: 53,563,286 (GRCm39) V671A probably benign Het
Sptbn4 A C 7: 27,123,223 (GRCm39) L233R probably damaging Het
Stx5a A G 19: 8,727,104 (GRCm39) T252A probably benign Het
Timd6 T A 11: 46,475,247 (GRCm39) F147L probably benign Het
Tmem87b C T 2: 128,688,670 (GRCm39) A485V probably benign Het
Tns1 A G 1: 74,024,908 (GRCm39) I403T probably damaging Het
Ttll10 G C 4: 156,133,018 (GRCm39) T22R possibly damaging Het
Uevld A T 7: 46,589,890 (GRCm39) S293T probably benign Het
Utp18 T C 11: 93,757,264 (GRCm39) N467D probably damaging Het
Vmn1r39 A T 6: 66,782,345 (GRCm39) probably null Het
Vmn2r106 A G 17: 20,505,641 (GRCm39) S18P probably benign Het
Vmn2r61 A T 7: 41,950,157 (GRCm39) H859L probably benign Het
Vmn2r61 T C 7: 41,950,159 (GRCm39) S860P probably benign Het
Vmn2r72 G A 7: 85,387,036 (GRCm39) R843* probably null Het
Vwc2 A G 11: 11,104,235 (GRCm39) T256A probably damaging Het
Zfp715 T C 7: 42,960,516 (GRCm39) D25G probably damaging Het
Other mutations in Nde1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03013:Nde1 APN 16 14,009,611 (GRCm39) missense probably benign
A4554:Nde1 UTSW 16 14,006,274 (GRCm39) splice site 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
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
Predicted Primers PCR Primer
(F):5'- CTTGGTGTGTTGTCCAATTAATTCC -3'
(R):5'- TGGACACATGGCTCTCTACAATG -3'

Sequencing Primer
(F):5'- TGTGTTGTCCAATTAATTCCTTACTG -3'
(R):5'- CTCCTATCGAATGAGCTGAAGATGC -3'
Posted On 2015-07-07