Incidental Mutation 'R8065:Ndc1'
ID 619939
Institutional Source Beutler Lab
Gene Symbol Ndc1
Ensembl Gene ENSMUSG00000028614
Gene Name NDC1 transmembrane nucleoporin
Synonyms sks, Tmem48, 2810475A17Rik
MMRRC Submission 067501-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.947) question?
Stock # R8065 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 107367784-107416346 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to A at 107390398 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 468 (S468T)
Ref Sequence ENSEMBL: ENSMUSP00000120365 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030357] [ENSMUST00000125342] [ENSMUST00000139560] [ENSMUST00000149366]
AlphaFold Q8VCB1
Predicted Effect probably benign
Transcript: ENSMUST00000030357
Predicted Effect probably benign
Transcript: ENSMUST00000125342
Predicted Effect probably benign
Transcript: ENSMUST00000139560
AA Change: S468T

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000120365
Gene: ENSMUSG00000028614
AA Change: S468T

DomainStartEndE-ValueType
Pfam:Ndc1_Nup 20 666 1.7e-137 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000149366
AA Change: S468T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000137180
Gene: ENSMUSG00000028614
AA Change: S468T

DomainStartEndE-ValueType
Pfam:Ndc1_Nup 19 511 3.7e-136 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (47/47)
MGI Phenotype PHENOTYPE: Mutations in this gene produce background sensitive growth rates and skeletal anomalies. Both females and males are sterile. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Cap2 T C 13: 46,637,861 (GRCm38) V280A probably damaging Het
Cbx7 A T 15: 79,933,898 (GRCm38) V1D unknown Het
Chodl A T 16: 78,946,713 (GRCm38) L229F probably damaging Het
Depdc5 C A 5: 32,895,908 (GRCm38) N197K possibly damaging Het
Diaph3 A T 14: 87,037,495 (GRCm38) L175Q probably damaging Het
Dlat A T 9: 50,657,849 (GRCm38) M218K possibly damaging Het
Dnaic1 T A 4: 41,614,258 (GRCm38) D311E probably damaging Het
Dpp10 A G 1: 123,352,660 (GRCm38) S646P probably benign Het
Ebf1 G A 11: 44,620,547 (GRCm38) V90M probably benign Het
Efhd1 C T 1: 87,264,591 (GRCm38) P48S probably benign Het
Fbxl16 G A 17: 25,817,983 (GRCm38) V313I probably damaging Het
Flrt2 A G 12: 95,780,774 (GRCm38) T629A probably benign Het
Gpr87 T A 3: 59,179,887 (GRCm38) I66F probably damaging Het
Hmmr G A 11: 40,721,672 (GRCm38) S206F probably damaging Het
Hsd17b4 A T 18: 50,170,752 (GRCm38) I431F possibly damaging Het
Iba57 T C 11: 59,163,260 (GRCm38) probably benign Het
Ibtk A C 9: 85,720,863 (GRCm38) S696R probably benign Het
Igkv11-125 C A 6: 67,913,830 (GRCm38) T44N probably benign Het
Itih2 T A 2: 10,123,483 (GRCm38) I136F probably damaging Het
Itpr3 T A 17: 27,110,862 (GRCm38) D1543E probably benign Het
Ldlr T A 9: 21,737,945 (GRCm38) C339S probably damaging Het
Myh2 G A 11: 67,181,344 (GRCm38) E633K probably null Het
Myl10 G C 5: 136,697,971 (GRCm38) V70L probably benign Het
Mylk A T 16: 34,972,019 (GRCm38) E1570V probably benign Het
Myo15b G A 11: 115,887,943 (GRCm38) probably null Het
N4bp2 T A 5: 65,807,296 (GRCm38) L896H probably damaging Het
Naip2 A T 13: 100,189,222 (GRCm38) S59R probably damaging Het
Ndst3 T C 3: 123,601,445 (GRCm38) N512S probably damaging Het
Olfr1138 T A 2: 87,737,803 (GRCm38) I174F probably damaging Het
Olfr65 A G 7: 103,906,403 (GRCm38) probably benign Het
Plekhn1 T C 4: 156,228,240 (GRCm38) I54V possibly damaging Het
Polr3c T C 3: 96,715,652 (GRCm38) E350G probably null Het
Pskh1 T G 8: 105,929,855 (GRCm38) S388A possibly damaging Het
Pum1 T C 4: 130,751,525 (GRCm38) V486A possibly damaging Het
Rin2 T G 2: 145,861,057 (GRCm38) S558A probably damaging Het
Ripk4 A T 16: 97,763,537 (GRCm38) V58D probably damaging Het
Slc17a3 A G 13: 23,858,087 (GRCm38) R491G unknown Het
Smyd3 A G 1: 179,410,463 (GRCm38) M113T possibly damaging Het
Ssh2 A G 11: 77,441,985 (GRCm38) R431G probably damaging Het
Timm22 G A 11: 76,414,105 (GRCm38) D190N probably damaging Het
Ube2g1 G A 11: 72,677,765 (GRCm38) G103D probably benign Het
Zbtb5 A T 4: 44,994,972 (GRCm38) S137R probably benign Het
Zfp105 A G 9: 122,925,129 (GRCm38) T8A probably benign Het
Zfp286 A T 11: 62,753,519 (GRCm38) I192K unknown Het
Zfp942 T C 17: 21,930,410 (GRCm38) Y38C probably damaging Het
Zfpm1 T C 8: 122,335,584 (GRCm38) S461P probably benign Het
Other mutations in Ndc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00927:Ndc1 APN 4 107,384,780 (GRCm38) splice site probably benign
IGL00929:Ndc1 APN 4 107,389,497 (GRCm38) missense probably benign 0.23
IGL01340:Ndc1 APN 4 107,374,147 (GRCm38) missense probably damaging 1.00
IGL01376:Ndc1 APN 4 107,375,197 (GRCm38) missense probably damaging 1.00
IGL01954:Ndc1 APN 4 107,395,804 (GRCm38) missense probably damaging 1.00
IGL02290:Ndc1 APN 4 107,394,995 (GRCm38) splice site probably benign
IGL03251:Ndc1 APN 4 107,380,659 (GRCm38) missense possibly damaging 0.50
R1168:Ndc1 UTSW 4 107,395,812 (GRCm38) missense probably benign 0.02
R1541:Ndc1 UTSW 4 107,371,288 (GRCm38) nonsense probably null
R1605:Ndc1 UTSW 4 107,368,096 (GRCm38) missense probably damaging 0.96
R1612:Ndc1 UTSW 4 107,395,068 (GRCm38) splice site probably benign
R1716:Ndc1 UTSW 4 107,384,795 (GRCm38) missense probably damaging 1.00
R3522:Ndc1 UTSW 4 107,393,158 (GRCm38) missense probably damaging 0.99
R4036:Ndc1 UTSW 4 107,411,072 (GRCm38) missense probably benign 0.22
R4698:Ndc1 UTSW 4 107,411,137 (GRCm38) missense probably benign 0.06
R4794:Ndc1 UTSW 4 107,390,222 (GRCm38) missense probably benign 0.03
R5053:Ndc1 UTSW 4 107,374,218 (GRCm38) missense probably damaging 1.00
R5097:Ndc1 UTSW 4 107,374,161 (GRCm38) missense probably benign 0.01
R5158:Ndc1 UTSW 4 107,375,165 (GRCm38) missense probably damaging 1.00
R5217:Ndc1 UTSW 4 107,389,576 (GRCm38) missense probably benign
R5579:Ndc1 UTSW 4 107,380,704 (GRCm38) missense possibly damaging 0.74
R5666:Ndc1 UTSW 4 107,389,526 (GRCm38) missense possibly damaging 0.52
R5855:Ndc1 UTSW 4 107,383,707 (GRCm38) missense probably damaging 1.00
R6180:Ndc1 UTSW 4 107,411,198 (GRCm38) missense possibly damaging 0.65
R6525:Ndc1 UTSW 4 107,368,107 (GRCm38) missense probably benign 0.01
R8067:Ndc1 UTSW 4 107,390,398 (GRCm38) missense probably benign 0.01
R8100:Ndc1 UTSW 4 107,383,605 (GRCm38) missense possibly damaging 0.94
R8428:Ndc1 UTSW 4 107,368,820 (GRCm38) missense probably benign 0.00
R8952:Ndc1 UTSW 4 107,390,426 (GRCm38) missense probably benign 0.00
R8953:Ndc1 UTSW 4 107,381,693 (GRCm38) missense probably damaging 1.00
R9489:Ndc1 UTSW 4 107,390,666 (GRCm38) critical splice donor site probably null
R9606:Ndc1 UTSW 4 107,389,489 (GRCm38) missense probably damaging 0.97
Z1176:Ndc1 UTSW 4 107,386,602 (GRCm38) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- CTGCTTTTCAGACTCCAAAACC -3'
(R):5'- AGATCACACTGGGCTGTCTC -3'

Sequencing Primer
(F):5'- ACCTAGTCAGACGCCTTCCG -3'
(R):5'- TGTCTTACCCTCAGCAGTAACAGAG -3'
Posted On 2020-01-23