Incidental Mutation 'R5646:Nde1'
ID 441187
Institutional Source Beutler Lab
Gene Symbol Nde1
Ensembl Gene ENSMUSG00000022678
Gene Name nudE neurodevelopment protein 1
Synonyms mNudE, 2810027M15Rik
MMRRC Submission 043294-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.866) question?
Stock # R5646 (G1)
Quality Score 225
Status Not validated
Chromosome 16
Chromosomal Location 13981139-14010792 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 13987378 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 8 (F8L)
Ref Sequence ENSEMBL: ENSMUSP00000112817 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023359] [ENSMUST00000115795] [ENSMUST00000117958] [ENSMUST00000132316]
AlphaFold Q9CZA6
Predicted Effect probably damaging
Transcript: ENSMUST00000023359
AA Change: F8L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000023359
Gene: ENSMUSG00000022678
AA Change: F8L

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 damaging
Transcript: ENSMUST00000115795
AA Change: F8L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000111461
Gene: ENSMUSG00000022678
AA Change: F8L

DomainStartEndE-ValueType
low complexity region 47 56 N/A INTRINSIC
Pfam:NUDE_C 134 317 1.2e-40 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000117958
AA Change: F8L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000112817
Gene: ENSMUSG00000022678
AA Change: F8L

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 damaging
Transcript: ENSMUST00000132316
AA Change: F8L

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000118005
Gene: ENSMUSG00000022678
AA Change: F8L

DomainStartEndE-ValueType
PDB:2V71|B 8 79 2e-14 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133249
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
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: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Add1 C A 5: 34,788,024 (GRCm39) A691D probably benign Het
Agap3 C A 5: 24,688,395 (GRCm39) D394E probably benign Het
Arhgef11 T C 3: 87,591,793 (GRCm39) V59A possibly damaging Het
Atp2a1 A G 7: 126,052,277 (GRCm39) V402A probably benign Het
Bbs9 T C 9: 22,490,011 (GRCm39) F261L probably benign Het
Bsn A T 9: 107,987,631 (GRCm39) probably benign Het
Camk1 A G 6: 113,316,301 (GRCm39) V81A probably damaging Het
Cass4 T G 2: 172,258,165 (GRCm39) C54W probably damaging Het
Ccdc39 A T 3: 33,879,699 (GRCm39) F456L probably damaging Het
Cdc42bpa A G 1: 179,933,659 (GRCm39) E766G probably damaging Het
Cdcp2 T C 4: 106,962,339 (GRCm39) C171R probably damaging Het
Cdh9 G A 15: 16,823,371 (GRCm39) E118K probably damaging Het
Col4a2 G A 8: 11,491,281 (GRCm39) G1227R probably damaging Het
Cyp2d9 A G 15: 82,336,665 (GRCm39) T5A probably benign Het
Dlg5 T A 14: 24,208,767 (GRCm39) D813V probably damaging Het
Dmtf1 G A 5: 9,174,515 (GRCm39) S405F possibly damaging Het
Drd2 A G 9: 49,316,212 (GRCm39) K324R probably benign Het
Ergic1 T C 17: 26,833,332 (GRCm39) S29P probably damaging Het
Fmnl1 A G 11: 103,087,338 (GRCm39) probably benign Het
Foxd2 C T 4: 114,765,832 (GRCm39) A63T unknown Het
Gfap T C 11: 102,782,282 (GRCm39) I409M probably benign Het
Gfpt1 A G 6: 87,019,981 (GRCm39) M1V probably null Het
H2-T23 C G 17: 36,342,695 (GRCm39) E148Q possibly damaging Het
Hip1 G A 5: 135,457,595 (GRCm39) R704W probably damaging Het
Kif19a A C 11: 114,670,480 (GRCm39) D130A probably damaging Het
Lin7b T C 7: 45,018,617 (GRCm39) D14G probably damaging Het
Meioc T A 11: 102,566,083 (GRCm39) N510K possibly damaging Het
Mettl5 C A 2: 69,711,663 (GRCm39) G68* probably null Het
Mitf A T 6: 97,990,655 (GRCm39) I184F probably damaging Het
Mmp9 T A 2: 164,790,970 (GRCm39) H119Q probably benign Het
Mycbp2 T A 14: 103,407,346 (GRCm39) H2768L probably benign Het
Myh2 A T 11: 67,079,638 (GRCm39) I1032F probably benign Het
Myo3b T C 2: 70,144,774 (GRCm39) I1110T probably damaging Het
Or10aa3 C T 1: 173,878,853 (GRCm39) Q305* probably null Het
Or2a25 A G 6: 42,888,457 (GRCm39) probably null Het
Or2h2b-ps1 T C 17: 37,480,808 (GRCm39) I244V probably benign Het
Or4f47 T C 2: 111,973,028 (GRCm39) V246A possibly damaging Het
Or51r1 A C 7: 102,228,512 (GRCm39) Y270S possibly damaging Het
Or5ac20 C T 16: 59,104,342 (GRCm39) V173I probably benign Het
Or6c202 T C 10: 128,996,706 (GRCm39) D49G possibly damaging Het
Pcdhga8 A G 18: 37,859,823 (GRCm39) H293R probably benign Het
Pde7a A T 3: 19,287,937 (GRCm39) L244Q probably damaging Het
Pex14 T C 4: 149,045,910 (GRCm39) D340G probably benign Het
Pfkfb4 A T 9: 108,837,489 (GRCm39) I195F probably damaging Het
Pik3c2a C A 7: 116,005,186 (GRCm39) G361W probably damaging Het
Prkcg T A 7: 3,377,597 (GRCm39) M517K probably damaging Het
Prob1 A T 18: 35,787,167 (GRCm39) F362L probably benign Het
Rims4 C T 2: 163,705,937 (GRCm39) W232* probably null Het
Robo2 T C 16: 73,758,707 (GRCm39) D688G probably damaging Het
Sec24c C A 14: 20,729,641 (GRCm39) A73E probably benign Het
Slc15a3 A G 19: 10,820,574 (GRCm39) N64D probably benign Het
Smg1 A T 7: 117,811,782 (GRCm39) N65K probably benign Het
Spata31h1 A G 10: 82,119,610 (GRCm39) S4467P probably damaging Het
Sptb G T 12: 76,634,215 (GRCm39) D2165E probably benign Het
Sptbn5 A T 2: 119,879,292 (GRCm39) noncoding transcript Het
Syt12 A T 19: 4,506,569 (GRCm39) M192K possibly damaging Het
Tas2r107 A G 6: 131,636,671 (GRCm39) V126A probably benign Het
Thbs3 T C 3: 89,126,405 (GRCm39) L242P probably damaging Het
Timp2 A T 11: 118,208,358 (GRCm39) probably null Het
Tmtc1 G A 6: 148,148,329 (GRCm39) A751V probably damaging Het
Tnni2 A T 7: 141,997,650 (GRCm39) D85V probably damaging Het
Ttc39b G A 4: 83,162,307 (GRCm39) P319L probably damaging Het
Ttc6 A T 12: 57,622,805 (GRCm39) K68M probably damaging Het
Usp25 G A 16: 76,847,360 (GRCm39) R156Q probably benign Het
Vill A T 9: 118,900,230 (GRCm39) D365V probably damaging Het
Vmn1r65 T A 7: 6,012,223 (GRCm39) T4S probably benign Het
Vmn2r76 C A 7: 85,875,261 (GRCm39) C572F probably damaging Het
Vps26a A C 10: 62,304,077 (GRCm39) N181K probably damaging Het
Xirp2 T C 2: 67,341,134 (GRCm39) L1125P probably damaging Het
Zbtb41 T G 1: 139,351,501 (GRCm39) S205A probably benign Het
Zfp438 T C 18: 5,214,526 (GRCm39) D144G probably benign Het
Zfp600 T C 4: 146,131,670 (GRCm39) S113P probably damaging Het
Zfp84 C T 7: 29,475,818 (GRCm39) T170M probably benign Het
Zmiz2 T A 11: 6,352,837 (GRCm39) D654E probably damaging Het
Zswim4 A T 8: 84,957,739 (GRCm39) probably null 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
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
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'- TGGGCTGCAACTGAAGGTAG -3'
(R):5'- ACTTCCCAATTGCTCAGGG -3'

Sequencing Primer
(F):5'- CTGCAACTGAAGGTAGGCTAC -3'
(R):5'- CAATTGCTCAGGGGCCTCTTTAG -3'
Posted On 2016-11-08