Incidental Mutation 'R4796:Nedd9'
ID 369076
Institutional Source Beutler Lab
Gene Symbol Nedd9
Ensembl Gene ENSMUSG00000021365
Gene Name neural precursor cell expressed, developmentally down-regulated gene 9
Synonyms Cas-L, HEF1, CasL, E230025G09Rik
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4796 (G1)
Quality Score 225
Status Not validated
Chromosome 13
Chromosomal Location 41463392-41640836 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 41471376 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Glutamic Acid at position 208 (K208E)
Ref Sequence ENSEMBL: ENSMUSP00000125773 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021794] [ENSMUST00000163623] [ENSMUST00000224803]
AlphaFold O35177
Predicted Effect probably benign
Transcript: ENSMUST00000021794
AA Change: K208E

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000021794
Gene: ENSMUSG00000021365
AA Change: K208E

DomainStartEndE-ValueType
SH3 6 64 3.78e-17 SMART
internal_repeat_1 151 218 1.33e-7 PROSPERO
low complexity region 368 396 N/A INTRINSIC
Pfam:Serine_rich 403 561 3.2e-66 PFAM
Pfam:DUF3513 611 828 1.4e-91 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163623
AA Change: K208E

PolyPhen 2 Score 0.117 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000125773
Gene: ENSMUSG00000021365
AA Change: K208E

DomainStartEndE-ValueType
SH3 6 64 3.78e-17 SMART
internal_repeat_1 151 218 1.42e-7 PROSPERO
low complexity region 368 396 N/A INTRINSIC
Pfam:Serine_rich 403 559 2.7e-60 PFAM
Pfam:DUF3513 618 827 1e-81 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000224803
Meta Mutation Damage Score 0.0661 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.8%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the CRK-associated substrates family. Members of this family are adhesion docking molecules that mediate protein-protein interactions for signal transduction pathways. This protein is a focal adhesion protein that acts as a scaffold to regulate signaling complexes important in cell attachment, migration and invasion as well as apoptosis and the cell cycle. This protein has also been reported to have a role in cancer metastasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
PHENOTYPE: Mice homozygous for one null allele exhibit impaired lymphocyte trafficking and a deficit of splenic marginal zone B cells. Mice homozygous for another null allele display impaired spatial learning and decreased hippocampal dendritic spine densities. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 97 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrv1 C T 13: 81,303,350 (GRCm39) W132* probably null Het
Atp8b3 A G 10: 80,360,188 (GRCm39) V961A probably damaging Het
Bglap A C 3: 88,291,712 (GRCm39) I4S unknown Het
Bmp1 T C 14: 70,729,513 (GRCm39) probably null Het
Brd10 G A 19: 29,731,018 (GRCm39) H665Y probably benign Het
Btaf1 T C 19: 36,933,828 (GRCm39) L152P possibly damaging Het
Cacna1b T A 2: 24,527,499 (GRCm39) T1621S possibly damaging Het
Capn3 A T 2: 120,333,479 (GRCm39) N621I probably damaging Het
Ccdc121rt3 A G 5: 112,503,165 (GRCm39) S180P possibly damaging Het
Ccdc59 T C 10: 105,677,429 (GRCm39) S23P probably benign Het
Cd22 A T 7: 30,572,381 (GRCm39) probably null Het
Cdh20 A G 1: 104,868,989 (GRCm39) D160G probably damaging Het
Cep112 T C 11: 108,377,818 (GRCm39) probably null Het
Clock T C 5: 76,413,763 (GRCm39) K44R probably damaging Het
Coq10b A G 1: 55,110,957 (GRCm39) T242A probably damaging Het
Cstdc2 A G 2: 148,692,658 (GRCm39) F48S probably damaging Het
Ctnnd1 G T 2: 84,450,270 (GRCm39) R317S probably damaging Het
Dlg5 G A 14: 24,194,451 (GRCm39) H1674Y probably damaging Het
Drc3 C A 11: 60,254,354 (GRCm39) N75K probably damaging Het
Efna4 T C 3: 89,242,555 (GRCm39) E113G probably damaging Het
Egr3 C A 14: 70,315,024 (GRCm39) A44D probably benign Het
Ercc3 T C 18: 32,381,363 (GRCm39) F393S probably damaging Het
Evi2 T A 11: 79,406,273 (GRCm39) probably benign Het
Fam78b T C 1: 166,906,216 (GRCm39) V125A probably benign Het
Fars2 A T 13: 36,721,400 (GRCm39) E448V probably damaging Het
Farsb A T 1: 78,401,833 (GRCm39) *590R probably null Het
Fat3 A G 9: 15,911,028 (GRCm39) M1658T probably benign Het
Fhod3 G T 18: 25,118,358 (GRCm39) V232F probably damaging Het
Fkbpl G A 17: 34,864,303 (GRCm39) A24T probably benign Het
Fzd3 A G 14: 65,472,607 (GRCm39) V387A possibly damaging Het
Gm1527 A G 3: 28,974,812 (GRCm39) I542V possibly damaging Het
Gm7964 A G 7: 83,405,109 (GRCm39) probably null Het
Hbs1l G T 10: 21,218,405 (GRCm39) G301C probably damaging Het
Hipk4 A G 7: 27,227,995 (GRCm39) H247R probably benign Het
Hmcn1 A G 1: 150,629,362 (GRCm39) V965A probably benign Het
Hoxa5 C T 6: 52,180,943 (GRCm39) A130T probably benign Het
Igf2r C T 17: 12,903,013 (GRCm39) V2346I possibly damaging Het
Igsf8 T C 1: 172,143,889 (GRCm39) V14A probably benign Het
Impg1 G A 9: 80,301,377 (GRCm39) P183L probably damaging Het
Isl1 T C 13: 116,441,966 (GRCm39) N89S probably benign Het
Itga1 C A 13: 115,171,921 (GRCm39) W61C probably damaging Het
Itga5 T C 15: 103,256,187 (GRCm39) R922G probably benign Het
Itgb5 T C 16: 33,705,391 (GRCm39) V227A possibly damaging Het
Jph4 G T 14: 55,347,165 (GRCm39) P461T probably damaging Het
Kcnab1 T A 3: 65,211,586 (GRCm39) probably null Het
Klrc1 T A 6: 129,654,725 (GRCm39) probably null Het
Lonrf2 A T 1: 38,855,119 (GRCm39) L92Q probably benign Het
Ly75 T C 2: 60,180,284 (GRCm39) E631G probably benign Het
Mapk13 T C 17: 28,994,528 (GRCm39) Y140H probably damaging Het
Meak7 A T 8: 120,495,093 (GRCm39) S222T probably benign Het
Mgat4d A G 8: 84,084,749 (GRCm39) E164G probably damaging Het
Mrtfa C T 15: 80,901,234 (GRCm39) S419N probably damaging Het
Mtcl2 A G 2: 156,862,172 (GRCm39) S1586P probably benign Het
Mthfs A T 9: 89,122,078 (GRCm39) H188L probably benign Het
Muc5b T A 7: 141,417,983 (GRCm39) M3643K possibly damaging Het
Mylk3 T C 8: 86,077,014 (GRCm39) Y474C probably damaging Het
Myo5b A G 18: 74,877,701 (GRCm39) T1567A possibly damaging Het
Ncaph2 T G 15: 89,255,010 (GRCm39) V478G probably damaging Het
Ncbp1 A G 4: 46,152,967 (GRCm39) R247G possibly damaging Het
Nxph2 C T 2: 23,289,870 (GRCm39) T74M probably benign Het
Ogdh T A 11: 6,290,570 (GRCm39) M385K probably benign Het
Or10a5 A T 7: 106,636,121 (GRCm39) Y253F probably benign Het
Or3a1c A T 11: 74,046,417 (GRCm39) I146F probably benign Het
Or4a2 T C 2: 89,248,235 (GRCm39) H174R probably damaging Het
Or6a2 C T 7: 106,600,542 (GRCm39) G175D probably damaging Het
Or7g18 T C 9: 18,787,475 (GRCm39) V284A probably damaging Het
Or8b54 T A 9: 38,686,670 (GRCm39) F40I probably benign Het
Pcsk2 A C 2: 143,655,345 (GRCm39) I510L probably benign Het
Pdgfra A G 5: 75,349,972 (GRCm39) N952S probably benign Het
Pex26 T C 6: 121,170,516 (GRCm39) F287S probably damaging Het
Pick1 G C 15: 79,139,810 (GRCm39) probably benign Het
Plxnb1 G T 9: 108,943,663 (GRCm39) V1917L probably damaging Het
Polk T C 13: 96,625,764 (GRCm39) T347A probably benign Het
Ppp1r10 T G 17: 36,234,979 (GRCm39) I61R probably damaging Het
Prex1 A T 2: 166,434,211 (GRCm39) L503Q probably damaging Het
Ptp4a1 A C 1: 30,983,019 (GRCm39) I133R probably damaging Het
Rassf10 G T 7: 112,553,735 (GRCm39) R112L probably damaging Het
Ripor3 T A 2: 167,823,260 (GRCm39) I884F probably damaging Het
Rnft2 A G 5: 118,339,311 (GRCm39) Y369H probably damaging Het
Rtp3 A T 9: 110,815,522 (GRCm39) V281E probably benign Het
Runx1t1 T A 4: 13,837,767 (GRCm39) N51K probably damaging Het
Selp A G 1: 163,972,475 (GRCm39) T705A probably benign Het
Sgca A T 11: 94,861,553 (GRCm39) probably null Het
Slc22a3 T C 17: 12,642,675 (GRCm39) E514G probably damaging Het
Slc28a2b T A 2: 122,344,940 (GRCm39) I182N probably damaging Het
Slc2a1 G A 4: 118,989,642 (GRCm39) R61Q probably damaging Het
Smarcal1 G A 1: 72,636,599 (GRCm39) V425I probably benign Het
Ssx2ip T C 3: 146,124,114 (GRCm39) V43A probably benign Het
Synpo A G 18: 60,737,386 (GRCm39) S187P probably damaging Het
Thnsl1 T A 2: 21,216,856 (GRCm39) C203* probably null Het
Ttyh3 A T 5: 140,620,541 (GRCm39) I232N probably damaging Het
Upk1b T C 16: 38,607,604 (GRCm39) H41R probably benign Het
Vmn2r76 T C 7: 85,879,652 (GRCm39) D216G possibly damaging Het
Zan A T 5: 137,379,112 (GRCm39) C5329* probably null Het
Zbtb40 C T 4: 136,725,953 (GRCm39) M535I probably benign Het
Zfp383 A C 7: 29,614,263 (GRCm39) T173P possibly damaging Het
Zfp7 T A 15: 76,775,546 (GRCm39) C529* probably null Het
Other mutations in Nedd9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01109:Nedd9 APN 13 41,469,710 (GRCm39) missense probably benign 0.00
IGL01412:Nedd9 APN 13 41,469,262 (GRCm39) nonsense probably null
IGL01669:Nedd9 APN 13 41,492,111 (GRCm39) missense probably damaging 0.99
IGL02543:Nedd9 APN 13 41,470,211 (GRCm39) missense probably damaging 1.00
IGL03302:Nedd9 APN 13 41,492,330 (GRCm39) missense probably damaging 0.99
hebei UTSW 13 41,492,455 (GRCm39) nonsense probably null
sheep UTSW 13 41,471,438 (GRCm39) missense probably benign 0.33
yanzhao UTSW 13 41,465,270 (GRCm39) missense probably damaging 1.00
R1157:Nedd9 UTSW 13 41,467,979 (GRCm39) splice site probably null
R1611:Nedd9 UTSW 13 41,470,406 (GRCm39) missense probably benign
R1669:Nedd9 UTSW 13 41,465,270 (GRCm39) missense probably damaging 1.00
R1718:Nedd9 UTSW 13 41,492,402 (GRCm39) missense probably damaging 1.00
R1775:Nedd9 UTSW 13 41,471,438 (GRCm39) missense probably benign 0.33
R1971:Nedd9 UTSW 13 41,492,424 (GRCm39) missense probably damaging 1.00
R2107:Nedd9 UTSW 13 41,492,455 (GRCm39) nonsense probably null
R2341:Nedd9 UTSW 13 41,469,987 (GRCm39) missense probably damaging 1.00
R4362:Nedd9 UTSW 13 41,471,429 (GRCm39) missense probably damaging 0.99
R4363:Nedd9 UTSW 13 41,471,429 (GRCm39) missense probably damaging 0.99
R4707:Nedd9 UTSW 13 41,492,051 (GRCm39) critical splice donor site probably null
R4724:Nedd9 UTSW 13 41,470,073 (GRCm39) missense possibly damaging 0.50
R4795:Nedd9 UTSW 13 41,471,376 (GRCm39) missense probably benign 0.12
R4853:Nedd9 UTSW 13 41,469,837 (GRCm39) missense probably benign 0.01
R4934:Nedd9 UTSW 13 41,492,411 (GRCm39) missense probably damaging 1.00
R5020:Nedd9 UTSW 13 41,469,270 (GRCm39) missense probably damaging 1.00
R5070:Nedd9 UTSW 13 41,470,074 (GRCm39) missense probably benign 0.00
R5585:Nedd9 UTSW 13 41,469,950 (GRCm39) missense probably damaging 1.00
R5588:Nedd9 UTSW 13 41,469,437 (GRCm39) missense possibly damaging 0.76
R6310:Nedd9 UTSW 13 41,471,928 (GRCm39) missense probably benign 0.00
R6634:Nedd9 UTSW 13 41,465,584 (GRCm39) missense probably damaging 1.00
R6729:Nedd9 UTSW 13 41,469,278 (GRCm39) missense probably damaging 0.99
R7114:Nedd9 UTSW 13 41,492,099 (GRCm39) missense probably benign
R7172:Nedd9 UTSW 13 41,470,280 (GRCm39) missense probably benign 0.01
R7477:Nedd9 UTSW 13 41,471,956 (GRCm39) missense probably benign 0.02
R7665:Nedd9 UTSW 13 41,469,785 (GRCm39) missense probably benign 0.01
R7672:Nedd9 UTSW 13 41,492,198 (GRCm39) missense possibly damaging 0.69
R7810:Nedd9 UTSW 13 41,465,483 (GRCm39) missense possibly damaging 0.52
R7893:Nedd9 UTSW 13 41,469,265 (GRCm39) missense probably damaging 1.00
R7952:Nedd9 UTSW 13 41,470,431 (GRCm39) missense probably damaging 1.00
R8215:Nedd9 UTSW 13 41,492,319 (GRCm39) missense probably benign 0.14
R8399:Nedd9 UTSW 13 41,471,950 (GRCm39) nonsense probably null
R8959:Nedd9 UTSW 13 41,469,758 (GRCm39) missense probably damaging 0.98
R9039:Nedd9 UTSW 13 41,471,984 (GRCm39) missense probably damaging 1.00
R9236:Nedd9 UTSW 13 41,492,153 (GRCm39) missense possibly damaging 0.86
R9663:Nedd9 UTSW 13 41,469,941 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ATGTCTTCATATTTTCGGGGACTC -3'
(R):5'- ACGACCAAGTCTATGTATGACC -3'

Sequencing Primer
(F):5'- CATATTTTCGGGGACTCAAAATTTG -3'
(R):5'- CGACCAAGTCTATGTATGACCTGATG -3'
Posted On 2016-02-04