Incidental Mutation 'R4795:Slit3'
ID 368959
Institutional Source Beutler Lab
Gene Symbol Slit3
Ensembl Gene ENSMUSG00000056427
Gene Name slit guidance ligand 3
Synonyms Slit1, b2b2362.1Clo
MMRRC Submission 041996-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.871) question?
Stock # R4795 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 35012283-35599334 bp(+) (GRCm39)
Type of Mutation critical splice donor site (1 bp from exon)
DNA Base Change (assembly) G to A at 35542647 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000066857 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000069837] [ENSMUST00000069837]
AlphaFold Q9WVB4
Predicted Effect probably null
Transcript: ENSMUST00000069837
SMART Domains Protein: ENSMUSP00000066857
Gene: ENSMUSG00000056427

DomainStartEndE-ValueType
low complexity region 2 23 N/A INTRINSIC
LRRNT 33 65 2.12e-8 SMART
LRR 59 83 1.37e2 SMART
LRR_TYP 84 107 1.12e-3 SMART
LRR_TYP 108 131 7.78e-3 SMART
LRR_TYP 132 155 5.42e-2 SMART
LRR 156 179 5.88e0 SMART
LRR 180 203 7.55e-1 SMART
LRRCT 215 264 1.33e-6 SMART
LRRNT 279 311 6.79e-7 SMART
LRR 305 329 1.16e2 SMART
LRR 330 353 1.26e1 SMART
LRR_TYP 354 377 2.79e-4 SMART
LRR 378 401 4.05e-1 SMART
LRR 402 425 4.05e-1 SMART
LRRCT 437 486 7.75e-8 SMART
LRRNT 504 536 1.95e-7 SMART
LRR_TYP 556 579 7.49e-5 SMART
LRR 581 603 6.41e1 SMART
LRR_TYP 604 627 2.53e-2 SMART
LRR 628 651 1.76e-1 SMART
LRRCT 663 712 2.52e-7 SMART
LRRNT 724 756 3e-8 SMART
LRR 774 797 2.14e0 SMART
LRR_TYP 798 821 2.95e-3 SMART
LRR_TYP 822 845 2.43e-4 SMART
LRRCT 857 906 1.12e-13 SMART
EGF 919 953 6.86e-4 SMART
EGF 958 994 8.84e-7 SMART
EGF 999 1032 1.13e-4 SMART
EGF 1037 1072 2.3e-5 SMART
EGF_CA 1074 1110 5.92e-8 SMART
EGF 1122 1155 3.79e-6 SMART
LamG 1178 1314 3.16e-34 SMART
EGF 1331 1365 2.19e-2 SMART
EGF 1371 1403 1.13e-4 SMART
EGF 1411 1444 5.57e-4 SMART
CT 1455 1523 4.56e-5 SMART
Predicted Effect probably null
Transcript: ENSMUST00000069837
SMART Domains Protein: ENSMUSP00000066857
Gene: ENSMUSG00000056427

DomainStartEndE-ValueType
low complexity region 2 23 N/A INTRINSIC
LRRNT 33 65 2.12e-8 SMART
LRR 59 83 1.37e2 SMART
LRR_TYP 84 107 1.12e-3 SMART
LRR_TYP 108 131 7.78e-3 SMART
LRR_TYP 132 155 5.42e-2 SMART
LRR 156 179 5.88e0 SMART
LRR 180 203 7.55e-1 SMART
LRRCT 215 264 1.33e-6 SMART
LRRNT 279 311 6.79e-7 SMART
LRR 305 329 1.16e2 SMART
LRR 330 353 1.26e1 SMART
LRR_TYP 354 377 2.79e-4 SMART
LRR 378 401 4.05e-1 SMART
LRR 402 425 4.05e-1 SMART
LRRCT 437 486 7.75e-8 SMART
LRRNT 504 536 1.95e-7 SMART
LRR_TYP 556 579 7.49e-5 SMART
LRR 581 603 6.41e1 SMART
LRR_TYP 604 627 2.53e-2 SMART
LRR 628 651 1.76e-1 SMART
LRRCT 663 712 2.52e-7 SMART
LRRNT 724 756 3e-8 SMART
LRR 774 797 2.14e0 SMART
LRR_TYP 798 821 2.95e-3 SMART
LRR_TYP 822 845 2.43e-4 SMART
LRRCT 857 906 1.12e-13 SMART
EGF 919 953 6.86e-4 SMART
EGF 958 994 8.84e-7 SMART
EGF 999 1032 1.13e-4 SMART
EGF 1037 1072 2.3e-5 SMART
EGF_CA 1074 1110 5.92e-8 SMART
EGF 1122 1155 3.79e-6 SMART
LamG 1178 1314 3.16e-34 SMART
EGF 1331 1365 2.19e-2 SMART
EGF 1371 1403 1.13e-4 SMART
EGF 1411 1444 5.57e-4 SMART
CT 1455 1523 4.56e-5 SMART
Meta Mutation Damage Score 0.9494 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.7%
Validation Efficiency 98% (123/125)
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 secreted, likely interacting with roundabout homolog receptors to effect cell migration. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
PHENOTYPE: Mice homozygous for a gene trap allele show congenital diaphragmatic hernia (CDH), variable renal defects and enlarged heart right ventricles. Mice homozygous for either of two reporter alleles show diaphragm dysgenesis and die prematurely; those with end-stage CDH show dyspnea and lung congestion. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 105 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca4 T G 3: 121,969,772 (GRCm39) L2259R probably damaging Het
Acd A G 8: 106,427,647 (GRCm39) S2P possibly damaging Het
Acsf3 A G 8: 123,506,896 (GRCm39) Y63C possibly damaging Het
Adam21 T C 12: 81,607,748 (GRCm39) I5V probably benign Het
Adamts6 C A 13: 104,580,636 (GRCm39) S783* probably null Het
Adamtsl1 T C 4: 86,162,006 (GRCm39) probably null Het
Adck2 T A 6: 39,553,327 (GRCm39) S313T probably benign Het
Adgb A G 10: 10,233,616 (GRCm39) I1285T probably benign Het
Angptl1 T A 1: 156,688,153 (GRCm39) M485K possibly damaging Het
Ank3 G A 10: 69,694,095 (GRCm39) V289I probably benign Het
Atp13a4 A G 16: 29,308,826 (GRCm39) probably null Het
Atp1a1 A G 3: 101,491,091 (GRCm39) L648P probably benign Het
Atp2a3 A G 11: 72,863,855 (GRCm39) I194V probably benign Het
Bglap A C 3: 88,291,712 (GRCm39) I4S unknown Het
Cacna1b T A 2: 24,527,499 (GRCm39) T1621S possibly damaging Het
Ccdc112 T A 18: 46,420,739 (GRCm39) Q337L probably benign Het
Ccdc121rt3 A G 5: 112,503,165 (GRCm39) S180P possibly damaging Het
Cd34 T G 1: 194,633,319 (GRCm39) S194A probably damaging Het
Cdh20 A G 1: 104,868,989 (GRCm39) D160G probably damaging Het
Clock T C 5: 76,413,763 (GRCm39) K44R probably damaging Het
Commd9 A G 2: 101,729,241 (GRCm39) N116D probably benign Het
Dab2 C A 15: 6,459,092 (GRCm39) P335T probably benign Het
Epb41l3 T A 17: 69,555,714 (GRCm39) probably null Het
Epha2 A G 4: 141,049,727 (GRCm39) probably null 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
Fkbpl G A 17: 34,864,303 (GRCm39) A24T probably benign Het
Glyr1 A C 16: 4,865,622 (GRCm39) V44G probably benign Het
Gm1527 A G 3: 28,974,812 (GRCm39) I542V possibly damaging Het
Gm18856 C A 13: 14,139,793 (GRCm39) probably benign Het
Gm44501 A G 17: 40,889,605 (GRCm39) K40E probably benign Het
Hdhd5 T C 6: 120,500,407 (GRCm39) H97R probably benign Het
Hmcn1 A G 1: 150,629,362 (GRCm39) V965A probably benign Het
Hsf5 A G 11: 87,526,446 (GRCm39) M373V probably benign Het
Igbp1b C T 6: 138,634,803 (GRCm39) E214K probably benign Het
Iigp1 T A 18: 60,522,964 (GRCm39) F27L probably benign 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
Kbtbd3 G A 9: 4,331,073 (GRCm39) W482* probably null Het
Kcnq1 A G 7: 142,736,494 (GRCm39) T168A probably benign Het
Lrch3 A G 16: 32,826,074 (GRCm39) N631S probably damaging Het
Lrrk1 T A 7: 65,912,413 (GRCm39) I1716F possibly damaging Het
Ly75 T C 2: 60,180,284 (GRCm39) E631G probably benign Het
Map4 T C 9: 109,864,331 (GRCm39) S519P probably benign Het
Mroh2a A G 1: 88,186,386 (GRCm39) S64G probably benign Het
Mrtfa C T 15: 80,901,234 (GRCm39) S419N probably damaging Het
Muc5b A G 7: 141,403,304 (GRCm39) E755G unknown 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
Necab1 G T 4: 15,111,208 (GRCm39) D73E possibly damaging Het
Nedd9 T C 13: 41,471,376 (GRCm39) K208E probably benign Het
Nfyb A T 10: 82,588,202 (GRCm39) probably benign Het
Nol4 T C 18: 23,054,944 (GRCm39) Q162R probably damaging Het
Nwd2 G A 5: 63,962,776 (GRCm39) D787N probably benign Het
Olfr908 T A 9: 38,427,799 (GRCm39) M157K probably damaging Het
Or10a5 A T 7: 106,636,121 (GRCm39) Y253F probably benign Het
Or11g7 A C 14: 50,690,874 (GRCm39) M122L probably damaging Het
Or13a22 A G 7: 140,072,920 (GRCm39) D123G probably damaging Het
Or5ac23 C T 16: 59,149,213 (GRCm39) V220I probably benign Het
Or6a2 C T 7: 106,600,542 (GRCm39) G175D probably damaging Het
Or6e1 A G 14: 54,520,004 (GRCm39) M116T probably damaging Het
Orai3 T C 7: 127,373,060 (GRCm39) V187A probably benign Het
Parn T C 16: 13,424,066 (GRCm39) T444A probably benign Het
Pcdh11x A C X: 119,309,937 (GRCm39) N460T probably damaging Het
Pcnt C T 10: 76,205,858 (GRCm39) R2516H probably benign Het
Pde4d T A 13: 110,074,705 (GRCm39) probably benign Het
Pdgfra A G 5: 75,349,972 (GRCm39) N952S probably benign Het
Pgm2 A G 5: 64,261,217 (GRCm39) Y237C probably damaging Het
Plcb2 A G 2: 118,541,605 (GRCm39) V975A probably benign Het
Polk T C 13: 96,625,764 (GRCm39) T347A probably benign Het
Ppp6r1 C T 7: 4,644,053 (GRCm39) V430M possibly damaging Het
Ptges2 C A 2: 32,286,334 (GRCm39) C16* probably null Het
Relb A T 7: 19,353,764 (GRCm39) I38N probably damaging Het
Runx1t1 T A 4: 13,837,767 (GRCm39) N51K probably damaging Het
Samsn1 A G 16: 75,680,733 (GRCm39) probably benign Het
Scrn1 A G 6: 54,497,754 (GRCm39) V279A possibly damaging Het
Sec31b A G 19: 44,520,185 (GRCm39) S200P probably benign Het
Selp A G 1: 163,972,475 (GRCm39) T705A probably benign Het
Slc2a1 G A 4: 118,989,642 (GRCm39) R61Q probably damaging Het
Smo T A 6: 29,755,573 (GRCm39) V415E probably damaging Het
Spag8 C A 4: 43,652,035 (GRCm39) V350L possibly damaging Het
Tbck T G 3: 132,413,559 (GRCm39) L132R possibly damaging Het
Thnsl1 T A 2: 21,216,856 (GRCm39) C203* probably null Het
Tm9sf2 T A 14: 122,387,252 (GRCm39) probably null Het
Tmem131 A G 1: 36,880,757 (GRCm39) V171A probably damaging Het
Tmem209 T C 6: 30,501,954 (GRCm39) T83A probably benign Het
Tmem63a T C 1: 180,782,416 (GRCm39) Y138H probably damaging Het
Trim80 A G 11: 115,338,769 (GRCm39) Y533C probably damaging Het
Trpv2 A G 11: 62,472,006 (GRCm39) D66G possibly damaging Het
Trrap T A 5: 144,769,298 (GRCm39) I2620N probably benign Het
Ttyh3 A T 5: 140,620,541 (GRCm39) I232N probably damaging Het
Ube2dnl1 G A X: 113,815,482 (GRCm39) C119Y possibly damaging Het
Unc13c T A 9: 73,839,469 (GRCm39) S461C probably damaging Het
Unc80 T G 1: 66,567,100 (GRCm39) I902S probably damaging Het
Usp42 C A 5: 143,709,692 (GRCm39) G170W probably damaging Het
Vldlr T C 19: 27,216,252 (GRCm39) probably null Het
Ywhab A G 2: 163,857,265 (GRCm39) Y180C probably 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
Zdhhc1 CGGGGG CGGGGGG 8: 106,210,376 (GRCm39) probably null Het
Zfp318 A G 17: 46,722,988 (GRCm39) T1664A probably benign Het
Zfp7 T A 15: 76,775,546 (GRCm39) C529* probably null Het
Zfp768 T C 7: 126,942,547 (GRCm39) Q527R possibly damaging Het
Zfp975 T A 7: 42,314,570 (GRCm39) probably null Het
Other mutations in Slit3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00731:Slit3 APN 11 35,512,981 (GRCm39) missense probably damaging 1.00
IGL01324:Slit3 APN 11 35,501,529 (GRCm39) missense probably damaging 1.00
IGL01612:Slit3 APN 11 35,591,211 (GRCm39) missense possibly damaging 0.95
IGL02145:Slit3 APN 11 35,520,569 (GRCm39) missense probably damaging 0.99
IGL02146:Slit3 APN 11 35,125,675 (GRCm39) missense possibly damaging 0.71
IGL02430:Slit3 APN 11 35,068,601 (GRCm39) splice site probably null
IGL02528:Slit3 APN 11 35,469,801 (GRCm39) missense probably benign
IGL02530:Slit3 APN 11 35,598,969 (GRCm39) makesense probably null
IGL02640:Slit3 APN 11 35,591,172 (GRCm39) missense probably benign 0.10
IGL02819:Slit3 APN 11 35,062,417 (GRCm39) missense possibly damaging 0.71
IGL02839:Slit3 APN 11 35,539,874 (GRCm39) missense possibly damaging 0.46
IGL03150:Slit3 APN 11 35,399,084 (GRCm39) missense possibly damaging 0.88
IGL03161:Slit3 APN 11 35,591,241 (GRCm39) missense probably benign 0.10
IGL03336:Slit3 APN 11 35,560,928 (GRCm39) missense probably damaging 0.97
Bloated UTSW 11 35,524,779 (GRCm39) missense possibly damaging 0.55
Quellung UTSW 11 35,542,647 (GRCm39) critical splice donor site probably null
IGL02988:Slit3 UTSW 11 35,598,890 (GRCm39) missense probably damaging 0.99
PIT4791001:Slit3 UTSW 11 35,552,072 (GRCm39) missense possibly damaging 0.85
R0013:Slit3 UTSW 11 35,598,745 (GRCm39) missense probably benign
R0013:Slit3 UTSW 11 35,598,745 (GRCm39) missense probably benign
R0334:Slit3 UTSW 11 35,469,928 (GRCm39) missense probably damaging 0.97
R0385:Slit3 UTSW 11 35,591,109 (GRCm39) missense probably damaging 0.98
R0840:Slit3 UTSW 11 35,514,263 (GRCm39) splice site probably benign
R1065:Slit3 UTSW 11 35,012,462 (GRCm39) missense possibly damaging 0.86
R1364:Slit3 UTSW 11 35,560,934 (GRCm39) missense probably benign
R1476:Slit3 UTSW 11 35,577,126 (GRCm39) missense probably damaging 0.97
R1508:Slit3 UTSW 11 35,461,448 (GRCm39) missense probably damaging 1.00
R1665:Slit3 UTSW 11 35,125,733 (GRCm39) missense possibly damaging 0.71
R1692:Slit3 UTSW 11 35,550,171 (GRCm39) missense probably damaging 1.00
R1696:Slit3 UTSW 11 35,566,750 (GRCm39) missense probably damaging 0.99
R1727:Slit3 UTSW 11 35,520,659 (GRCm39) missense probably damaging 1.00
R1752:Slit3 UTSW 11 35,455,480 (GRCm39) missense probably damaging 0.98
R1970:Slit3 UTSW 11 35,521,668 (GRCm39) critical splice acceptor site probably null
R2077:Slit3 UTSW 11 35,435,575 (GRCm39) missense possibly damaging 0.88
R2126:Slit3 UTSW 11 35,579,506 (GRCm39) missense probably damaging 1.00
R2143:Slit3 UTSW 11 35,503,088 (GRCm39) splice site probably null
R2162:Slit3 UTSW 11 35,579,509 (GRCm39) missense probably null 1.00
R2873:Slit3 UTSW 11 35,435,620 (GRCm39) nonsense probably null
R3813:Slit3 UTSW 11 35,566,806 (GRCm39) missense probably damaging 1.00
R3831:Slit3 UTSW 11 35,579,509 (GRCm39) missense probably null 1.00
R3832:Slit3 UTSW 11 35,579,509 (GRCm39) missense probably null 1.00
R3833:Slit3 UTSW 11 35,579,509 (GRCm39) missense probably null 1.00
R3839:Slit3 UTSW 11 35,399,064 (GRCm39) missense probably benign 0.10
R4152:Slit3 UTSW 11 35,589,147 (GRCm39) missense probably damaging 0.98
R4387:Slit3 UTSW 11 35,574,875 (GRCm39) missense probably benign 0.12
R4910:Slit3 UTSW 11 35,523,549 (GRCm39) missense probably damaging 0.99
R4933:Slit3 UTSW 11 35,579,420 (GRCm39) missense probably damaging 1.00
R5048:Slit3 UTSW 11 35,479,812 (GRCm39) missense probably damaging 1.00
R5106:Slit3 UTSW 11 35,503,194 (GRCm39) missense probably damaging 1.00
R5138:Slit3 UTSW 11 35,479,812 (GRCm39) missense probably damaging 1.00
R5218:Slit3 UTSW 11 35,575,002 (GRCm39) critical splice donor site probably null
R5338:Slit3 UTSW 11 35,512,975 (GRCm39) missense probably benign
R5354:Slit3 UTSW 11 35,566,740 (GRCm39) missense probably damaging 1.00
R5436:Slit3 UTSW 11 35,598,738 (GRCm39) missense probably benign 0.05
R5896:Slit3 UTSW 11 35,598,932 (GRCm39) missense probably damaging 0.99
R5933:Slit3 UTSW 11 35,520,578 (GRCm39) missense probably benign 0.04
R5963:Slit3 UTSW 11 35,591,063 (GRCm39) missense probably damaging 1.00
R5964:Slit3 UTSW 11 35,591,063 (GRCm39) missense probably damaging 1.00
R6125:Slit3 UTSW 11 35,461,560 (GRCm39) critical splice donor site probably null
R6153:Slit3 UTSW 11 35,591,310 (GRCm39) missense possibly damaging 0.69
R6484:Slit3 UTSW 11 35,552,125 (GRCm39) missense probably benign
R6526:Slit3 UTSW 11 35,552,119 (GRCm39) missense probably benign 0.33
R6797:Slit3 UTSW 11 35,524,779 (GRCm39) missense possibly damaging 0.55
R6887:Slit3 UTSW 11 35,435,633 (GRCm39) splice site probably null
R7067:Slit3 UTSW 11 35,399,057 (GRCm39) missense probably benign 0.04
R7150:Slit3 UTSW 11 35,461,546 (GRCm39) missense probably damaging 1.00
R7228:Slit3 UTSW 11 35,490,245 (GRCm39) missense probably damaging 1.00
R7232:Slit3 UTSW 11 35,501,516 (GRCm39) missense possibly damaging 0.87
R7418:Slit3 UTSW 11 35,577,255 (GRCm39) missense possibly damaging 0.64
R7545:Slit3 UTSW 11 35,591,139 (GRCm39) missense possibly damaging 0.52
R7727:Slit3 UTSW 11 35,574,871 (GRCm39) missense probably damaging 1.00
R7820:Slit3 UTSW 11 35,591,235 (GRCm39) missense probably benign 0.23
R8177:Slit3 UTSW 11 35,469,919 (GRCm39) missense probably damaging 0.99
R8179:Slit3 UTSW 11 35,554,903 (GRCm39) missense probably benign 0.31
R8416:Slit3 UTSW 11 35,399,062 (GRCm39) missense probably benign 0.08
R8417:Slit3 UTSW 11 35,501,438 (GRCm39) missense probably damaging 0.99
R8476:Slit3 UTSW 11 35,520,596 (GRCm39) missense possibly damaging 0.70
R8785:Slit3 UTSW 11 35,560,968 (GRCm39) missense probably damaging 0.98
R8955:Slit3 UTSW 11 35,589,207 (GRCm39) missense probably damaging 0.97
R9040:Slit3 UTSW 11 35,594,136 (GRCm39) missense probably damaging 0.98
R9068:Slit3 UTSW 11 35,574,917 (GRCm39) missense probably damaging 1.00
R9088:Slit3 UTSW 11 35,012,463 (GRCm39) missense possibly damaging 0.86
R9266:Slit3 UTSW 11 35,598,808 (GRCm39) missense probably damaging 0.98
R9539:Slit3 UTSW 11 35,589,155 (GRCm39) nonsense probably null
R9636:Slit3 UTSW 11 35,594,088 (GRCm39) missense probably damaging 0.97
X0028:Slit3 UTSW 11 35,455,464 (GRCm39) missense probably damaging 0.99
Z1176:Slit3 UTSW 11 35,598,751 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- AGTAGCAGGAGGTTTCTCTTCTC -3'
(R):5'- ACCTCAGGAATGCCTCACTC -3'

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