Incidental Mutation 'R1473:Nde1'
ID 165957
Institutional Source Beutler Lab
Gene Symbol Nde1
Ensembl Gene ENSMUSG00000022678
Gene Name nudE neurodevelopment protein 1
Synonyms mNudE, 2810027M15Rik
MMRRC Submission 039526-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.866) question?
Stock # R1473 (G1)
Quality Score 225
Status Validated
Chromosome 16
Chromosomal Location 13981139-14010792 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 14003728 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Valine at position 71 (F71V)
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
AA Change: F232V

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000023359
Gene: ENSMUSG00000022678
AA Change: F232V

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
AA Change: F232V

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000111461
Gene: ENSMUSG00000022678
AA Change: F232V

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
AA Change: F232V

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000112817
Gene: ENSMUSG00000022678
AA Change: F232V

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
AA Change: F71V

PolyPhen 2 Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000119355
Gene: ENSMUSG00000022678
AA Change: F71V

DomainStartEndE-ValueType
Pfam:NUDE_C 1 167 8.6e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156041
Meta Mutation Damage Score 0.3266 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.2%
Validation Efficiency 98% (88/90)
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: 89 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ablim1 T C 19: 57,056,668 (GRCm39) D342G probably damaging Het
Acad8 T C 9: 26,890,337 (GRCm39) T293A probably benign Het
Adamts13 C A 2: 26,871,765 (GRCm39) Y310* probably null Het
Adcy6 T A 15: 98,490,624 (GRCm39) Y1102F probably damaging Het
Ahctf1 G A 1: 179,603,673 (GRCm39) T791M probably benign Het
Ahctf1 A G 1: 179,626,844 (GRCm39) V18A probably damaging Het
Ahcyl T A 16: 45,975,182 (GRCm39) E65V probably damaging Het
Ampd3 T G 7: 110,404,142 (GRCm39) S564R probably damaging Het
Anapc1 A T 2: 128,459,617 (GRCm39) I1814K possibly damaging Het
Arl4c A T 1: 88,629,331 (GRCm39) L19Q probably damaging Het
Atp6v0e2 T C 6: 48,516,198 (GRCm39) Y49H probably damaging Het
Ccdc121rt3 T C 5: 112,502,415 (GRCm39) T430A probably benign Het
Ccdc24 G T 4: 117,727,101 (GRCm39) probably benign Het
Ceacam23 A G 7: 17,639,016 (GRCm39) noncoding transcript Het
Clcn6 A C 4: 148,108,613 (GRCm39) F139V possibly damaging Het
Col2a1 A G 15: 97,880,789 (GRCm39) probably benign Het
Crip2 T A 12: 113,107,120 (GRCm39) C29S probably damaging Het
Cyp2a4 A C 7: 26,014,188 (GRCm39) N455T probably benign Het
Dhcr7 T C 7: 143,400,805 (GRCm39) Y323H probably damaging Het
Dhcr7 A G 7: 143,395,105 (GRCm39) D113G probably damaging Het
Dnah7a A C 1: 53,535,173 (GRCm39) S2696A probably benign Het
Dnajc12 A G 10: 63,233,023 (GRCm39) T55A probably benign Het
Drosha G A 15: 12,912,606 (GRCm39) E1075K probably benign Het
Duox2 A G 2: 122,117,602 (GRCm39) S911P possibly damaging Het
Ephb2 G A 4: 136,421,369 (GRCm39) A327V possibly damaging Het
Espl1 C T 15: 102,228,878 (GRCm39) T1711I possibly damaging Het
Fmnl2 A G 2: 52,748,219 (GRCm39) K22R possibly damaging Het
Fzd6 T C 15: 38,894,358 (GRCm39) F175L probably damaging Het
Gm6526 A G 14: 43,986,303 (GRCm39) I76M probably damaging Het
Gm9881 A T 16: 90,967,623 (GRCm39) F34I unknown Het
Gm9892 T C 8: 52,649,649 (GRCm39) D148G possibly damaging Het
Grb10 C T 11: 11,884,249 (GRCm39) V486I probably damaging Het
Gtf3c3 C T 1: 54,456,937 (GRCm39) A488T probably damaging Het
H2bc18 G T 3: 96,177,388 (GRCm39) L107F probably damaging Het
Hdac4 T C 1: 91,957,690 (GRCm39) H108R possibly damaging Het
Hmcn1 G A 1: 150,648,303 (GRCm39) T661I probably benign Het
Icam1 T A 9: 20,939,172 (GRCm39) I515N probably damaging Het
Ifi208 A G 1: 173,523,220 (GRCm39) R497G possibly damaging Het
Igsf10 A T 3: 59,226,188 (GRCm39) V2495E probably damaging Het
Iqgap1 T C 7: 80,383,759 (GRCm39) M1102V probably benign Het
Itgb4 A T 11: 115,874,873 (GRCm39) N410I probably benign Het
Jup T C 11: 100,270,427 (GRCm39) H360R possibly damaging Het
Kif20b T A 19: 34,951,896 (GRCm39) S1685T possibly damaging Het
Lins1 T C 7: 66,361,794 (GRCm39) probably null Het
Lrig1 T A 6: 94,584,294 (GRCm39) T917S probably benign Het
Mast2 A G 4: 116,169,152 (GRCm39) S814P probably damaging Het
Mast4 T C 13: 102,909,027 (GRCm39) T483A probably damaging Het
Mcpt1 T C 14: 56,256,990 (GRCm39) M176T probably benign Het
Mettl22 A G 16: 8,291,825 (GRCm39) Q38R probably damaging Het
Mrm2 T C 5: 140,314,443 (GRCm39) T131A probably benign Het
Mtcl2 A T 2: 156,862,368 (GRCm39) Y1520* probably null Het
Nxn C T 11: 76,154,013 (GRCm39) G274D possibly damaging Het
Or4c123 A T 2: 89,127,250 (GRCm39) Y121* probably null Het
Or5h17 A T 16: 58,820,275 (GRCm39) T76S probably benign Het
Or6k14 G T 1: 173,927,315 (GRCm39) C97F probably damaging Het
Or6p1 T A 1: 174,258,209 (GRCm39) W72R probably damaging Het
Osbp2 T C 11: 3,667,175 (GRCm39) probably null Het
Otud7a C A 7: 63,404,377 (GRCm39) probably benign Het
Phf3 G A 1: 30,845,021 (GRCm39) L1313F probably damaging Het
Pkhd1 A T 1: 20,593,207 (GRCm39) D1635E probably benign Het
Plpp1 A G 13: 112,996,198 (GRCm39) H171R probably damaging Het
Pofut1 A G 2: 153,103,166 (GRCm39) M172V probably damaging Het
Prmt5 A G 14: 54,746,372 (GRCm39) F580L probably damaging Het
Rab11fip3 A T 17: 26,210,296 (GRCm39) L987Q probably damaging Het
Retnlb T A 16: 48,639,028 (GRCm39) C76* probably null Het
Rnf38 T C 4: 44,131,584 (GRCm39) N399S probably benign Het
Sbk1 A G 7: 125,891,424 (GRCm39) E286G possibly damaging Het
Scin T A 12: 40,127,501 (GRCm39) T430S probably benign Het
Sgsm1 T A 5: 113,411,123 (GRCm39) T868S probably benign Het
Sipa1l1 G A 12: 82,387,885 (GRCm39) R37H probably damaging Het
Smchd1 A T 17: 71,668,832 (GRCm39) probably benign Het
Sned1 G A 1: 93,209,376 (GRCm39) V830M possibly damaging Het
Stk32c C T 7: 138,705,095 (GRCm39) R23Q probably damaging Het
Sult1d1 A G 5: 87,712,598 (GRCm39) M82T probably benign Het
Tat T C 8: 110,723,550 (GRCm39) L346P probably damaging Het
Tenm3 C A 8: 48,763,660 (GRCm39) G789V probably damaging Het
Thsd7a C T 6: 12,338,621 (GRCm39) S1203N probably benign Het
Tmem191 G A 16: 17,095,826 (GRCm39) probably null Het
Tmem268 A G 4: 63,498,575 (GRCm39) T239A probably damaging Het
Tmem82 A C 4: 141,343,589 (GRCm39) L227R possibly damaging Het
Ttn A T 2: 76,557,376 (GRCm39) I29906N probably damaging Het
Txndc15 T C 13: 55,869,387 (GRCm39) probably benign Het
Ubqln4 A G 3: 88,473,152 (GRCm39) I536V probably benign Het
Unc80 C T 1: 66,560,740 (GRCm39) H823Y possibly damaging Het
Vmn2r102 A T 17: 19,914,843 (GRCm39) I803F probably benign Het
Vmn2r6 G T 3: 64,445,579 (GRCm39) Y715* probably null Het
Vmn2r74 A T 7: 85,610,618 (GRCm39) C25S probably damaging Het
Wdr38 A G 2: 38,890,991 (GRCm39) T261A probably benign Het
Zfp653 T C 9: 21,969,516 (GRCm39) E250G possibly 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
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
Predicted Primers PCR Primer
(F):5'- TGGCTGCATCCTCACCCAAAAG -3'
(R):5'- CACCAGGTTCTTACCAGGGCAAAC -3'

Sequencing Primer
(F):5'- AGCAAGGACTCACATTCTGG -3'
(R):5'- tccttctttctttccttctctcc -3'
Posted On 2014-03-28