Incidental Mutation 'R1775:Nedd9'
ID 204359
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
MMRRC Submission 039806-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1775 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 41463392-41640836 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 41471438 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 187 (V187A)
Ref Sequence ENSEMBL: ENSMUSP00000021794 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021794] [ENSMUST00000163623] [ENSMUST00000224803]
AlphaFold O35177
Predicted Effect probably benign
Transcript: ENSMUST00000021794
AA Change: V187A

PolyPhen 2 Score 0.330 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000021794
Gene: ENSMUSG00000021365
AA Change: V187A

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: V187A

PolyPhen 2 Score 0.323 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000125773
Gene: ENSMUSG00000021365
AA Change: V187A

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
AA Change: V181A

PolyPhen 2 Score 0.259 (Sensitivity: 0.91; Specificity: 0.88)
Meta Mutation Damage Score 0.0708 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 97.0%
  • 10x: 95.5%
  • 20x: 92.9%
Validation Efficiency 98% (95/97)
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: 93 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700034J04Rik A G 12: 11,272,143 (GRCm39) S20P unknown Het
4921528I07Rik G A 9: 114,108,386 (GRCm39) noncoding transcript Het
4930562C15Rik G A 16: 4,669,422 (GRCm39) probably null Het
4933427I04Rik A G 4: 123,754,286 (GRCm39) T67A possibly damaging Het
Abcc2 A T 19: 43,786,858 (GRCm39) N160Y possibly damaging Het
Acaca A G 11: 84,191,248 (GRCm39) D155G possibly damaging Het
Afg3l1 G A 8: 124,219,639 (GRCm39) R389Q possibly damaging Het
Ank2 G A 3: 126,728,196 (GRCm39) T799M probably benign Het
Anxa2 T C 9: 69,395,363 (GRCm39) Y202H possibly damaging Het
Arhgef33 A G 17: 80,681,172 (GRCm39) T771A probably benign Het
Atp12a T C 14: 56,610,046 (GRCm39) V182A probably benign Het
Birc6 T C 17: 74,919,281 (GRCm39) L210S probably damaging Het
Car3 A G 3: 14,929,492 (GRCm39) T73A probably benign Het
Cd5l T C 3: 87,275,966 (GRCm39) L312P probably damaging Het
Celf5 A G 10: 81,303,138 (GRCm39) probably benign Het
Cep290 T A 10: 100,332,672 (GRCm39) V257E probably damaging Het
Cntrob T C 11: 69,211,693 (GRCm39) D177G possibly damaging Het
Copg2 A T 6: 30,787,271 (GRCm39) F658I probably damaging Het
Csmd3 T C 15: 47,763,135 (GRCm39) T1234A probably damaging Het
Dhx35 A G 2: 158,648,357 (GRCm39) T72A probably damaging Het
Dmrtc2 A T 7: 24,573,792 (GRCm39) H209L possibly damaging Het
Eml5 G T 12: 98,818,963 (GRCm39) probably null Het
Evpl T C 11: 116,114,486 (GRCm39) E1068G possibly damaging Het
Ezh2 A G 6: 47,553,594 (GRCm39) M41T probably damaging Het
Fmo3 A G 1: 162,796,294 (GRCm39) S93P possibly damaging Het
Gdi2 A G 13: 3,610,018 (GRCm39) Y213C possibly damaging Het
Gpr15 A T 16: 58,538,921 (GRCm39) I56K probably benign Het
Gria2 G T 3: 80,598,645 (GRCm39) S796R probably benign Het
Hectd4 T A 5: 121,429,254 (GRCm39) probably benign Het
Hgfac T C 5: 35,200,194 (GRCm39) probably benign Het
Hspg2 C T 4: 137,247,467 (GRCm39) R1200W probably damaging Het
Ift52 G A 2: 162,867,275 (GRCm39) D78N possibly damaging Het
Iqca1 C A 1: 90,009,138 (GRCm39) W415L probably damaging Het
Ism1 A T 2: 139,587,963 (GRCm39) K236N probably damaging Het
Itgb6 C T 2: 60,502,988 (GRCm39) W43* probably null Het
Kcnk18 T A 19: 59,223,773 (GRCm39) I306N probably damaging Het
Kctd8 T C 5: 69,497,903 (GRCm39) K248E probably damaging Het
Layn T A 9: 50,970,833 (GRCm39) I237F probably benign Het
Lce3f C T 3: 92,900,248 (GRCm39) P23L unknown Het
Lct A G 1: 128,228,038 (GRCm39) F1152L probably damaging Het
Mettl25b A G 3: 87,831,124 (GRCm39) S404P probably damaging Het
Mxra8 T C 4: 155,927,531 (GRCm39) I413T probably damaging Het
Net1 A G 13: 3,937,642 (GRCm39) L207P probably damaging Het
Neurod1 G T 2: 79,284,781 (GRCm39) P201T probably benign Het
Nlrp1b A G 11: 71,052,647 (GRCm39) F927S probably damaging Het
Ntrk3 T A 7: 78,005,789 (GRCm39) H524L possibly damaging Het
Nup98 A C 7: 101,784,144 (GRCm39) S1063A probably benign Het
Or10ak11 T A 4: 118,687,065 (GRCm39) M191L probably benign Het
Or11h4b G T 14: 50,918,623 (GRCm39) P156Q possibly damaging Het
Or56b1 G A 7: 104,285,366 (GRCm39) V162I probably benign Het
Or5b97 C A 19: 12,878,599 (GRCm39) V182F probably benign Het
Or5m9b G A 2: 85,905,104 (GRCm39) V7I possibly damaging Het
Or6d15 T C 6: 116,559,925 (GRCm39) probably benign Het
Pdzd2 G A 15: 12,592,546 (GRCm39) R33W probably damaging Het
Phf21a G A 2: 92,160,860 (GRCm39) V243I probably damaging Het
Ppp1r12b A G 1: 134,821,086 (GRCm39) probably null Het
Rexo5 T C 7: 119,444,634 (GRCm39) V703A probably benign Het
Rgs4 A G 1: 169,572,847 (GRCm39) S30P probably benign Het
Rxra C A 2: 27,646,256 (GRCm39) D340E probably damaging Het
Samhd1 A G 2: 156,949,467 (GRCm39) V473A probably benign Het
Scn3a T A 2: 65,302,686 (GRCm39) K1253N probably damaging Het
Scn7a T C 2: 66,511,299 (GRCm39) N1207S probably benign Het
Sec24d T A 3: 123,130,166 (GRCm39) I443N probably damaging Het
Sema4g T A 19: 44,987,681 (GRCm39) probably null Het
Sema5b A G 16: 35,480,694 (GRCm39) K787R probably benign Het
Serpinc1 A G 1: 160,817,217 (GRCm39) N104D probably benign Het
Sfn T C 4: 133,328,542 (GRCm39) H180R probably damaging Het
Slc22a6 G T 19: 8,596,471 (GRCm39) probably null Het
Slc9a8 T C 2: 167,299,278 (GRCm39) S217P probably benign Het
Smc6 A G 12: 11,359,270 (GRCm39) N965D probably benign Het
Sod2 T A 17: 13,233,919 (GRCm39) I177N probably damaging Het
Sp4 A T 12: 118,263,335 (GRCm39) I237K probably damaging Het
Sulf2 T C 2: 165,921,532 (GRCm39) K697R probably benign Het
Svs4 A T 2: 164,119,005 (GRCm39) D110E unknown Het
Tas1r1 T A 4: 152,122,675 (GRCm39) R57* probably null Het
Tlr5 T C 1: 182,801,287 (GRCm39) I197T probably damaging Het
Tmc3 T C 7: 83,261,740 (GRCm39) V606A probably benign Het
Tmem241 T A 18: 12,251,469 (GRCm39) L37F probably damaging Het
Tmem59l A T 8: 70,938,903 (GRCm39) N90K probably damaging Het
Tram1 A C 1: 13,646,680 (GRCm39) probably benign Het
Trim15 T A 17: 37,176,061 (GRCm39) H162L probably benign Het
Ttc28 T A 5: 111,424,677 (GRCm39) Y1501N probably benign Het
Ttc34 T C 4: 154,946,671 (GRCm39) V857A probably benign Het
Tulp4 A G 17: 6,189,321 (GRCm39) T48A probably damaging Het
Usp9y T C Y: 1,368,089 (GRCm39) E939G probably damaging Het
Utp20 A G 10: 88,606,670 (GRCm39) I1634T probably benign Het
Vmn2r72 T C 7: 85,387,378 (GRCm39) M729V probably benign Het
Vps13c C T 9: 67,788,729 (GRCm39) T334M probably damaging Het
Wnk4 C G 11: 101,167,166 (GRCm39) probably benign Het
Xpo1 A G 11: 23,221,193 (GRCm39) N97D probably benign Het
Xpo4 A T 14: 57,841,129 (GRCm39) F518Y probably benign Het
Zfp668 C T 7: 127,465,778 (GRCm39) V469I possibly damaging Het
Zfp85 C A 13: 67,897,823 (GRCm39) C83F probably damaging 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
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
R4796: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'- AACTGCCATTCTTGTTTTATCCCAA -3'
(R):5'- AGAGCAGATAGTTCACGTAAGATTG -3'

Sequencing Primer
(F):5'- GCCATTCTTGTTTTATCCCAATAAAC -3'
(R):5'- ACCTAAATCAAAGAATCCAAGAGTC -3'
Posted On 2014-06-23