Incidental Mutation 'IGL02988:Slit3'
ID 453503
Institutional Source Beutler Lab
Gene Symbol Slit3
Ensembl Gene ENSMUSG00000056427
Gene Name slit guidance ligand 3
Synonyms Slit1, b2b2362.1Clo
Accession Numbers
Essential gene? Probably essential (E-score: 0.897) question?
Stock # IGL02988 (G1)
Quality Score 170
Status Validated
Chromosome 11
Chromosomal Location 35012283-35599334 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 35598890 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 1498 (V1498D)
Ref Sequence ENSEMBL: ENSMUSP00000066857 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000069837]
AlphaFold Q9WVB4
Predicted Effect probably damaging
Transcript: ENSMUST00000069837
AA Change: V1498D

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000066857
Gene: ENSMUSG00000056427
AA Change: V1498D

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 0.0910 question?
Coding Region Coverage
  • 1x: 0.0%
  • 3x: 0.0%
  • 10x: 0.0%
  • 20x: 0.0%
Validation Efficiency 99% (71/72)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933416I08Rik TCC TCCC X: 52,692,862 (GRCm39) noncoding transcript Het
Aadacl4fm5 T A 4: 144,513,100 (GRCm39) probably benign Het
Adgrd1 G A 5: 129,221,074 (GRCm39) A488T probably benign Het
Ano3 T C 2: 110,605,355 (GRCm39) S284G probably damaging Het
Aox1 G T 1: 58,376,509 (GRCm39) V897L probably benign Het
Arl6 T A 16: 59,434,209 (GRCm39) probably null Het
Blnk G A 19: 40,917,660 (GRCm39) T441M probably damaging Het
Casp8ap2 C T 4: 32,644,590 (GRCm39) T1221I probably benign Het
Cbll1 A T 12: 31,542,171 (GRCm39) F63L possibly damaging Het
Cdk14 A G 5: 5,086,484 (GRCm39) Y279H probably damaging Het
Cflar A T 1: 58,780,190 (GRCm39) I265F possibly damaging Het
Cilp TGGG TGG 9: 65,187,412 (GRCm39) probably null Het
Crb1 CG C 1: 139,164,824 (GRCm39) probably null Het
Cyp3a13 A T 5: 137,897,272 (GRCm39) Y347* probably null Het
Defa27 T C 8: 21,805,583 (GRCm39) S8P probably damaging Het
Depdc5 A C 5: 33,113,511 (GRCm39) probably null Het
Dlg5 A G 14: 24,216,323 (GRCm39) F573S probably damaging Het
Fam20c A T 5: 138,741,749 (GRCm39) E120V probably benign Het
Fam53a T C 5: 33,764,819 (GRCm39) K296E probably damaging Het
Fcna G C 2: 25,520,693 (GRCm39) probably benign Het
Fndc1 T C 17: 7,972,355 (GRCm39) T1526A possibly damaging Het
Gm14325 A C 2: 177,476,042 (GRCm39) probably null Het
Gm7582 G A 1: 85,019,588 (GRCm39) noncoding transcript Het
Golga7b A C 19: 42,255,239 (GRCm39) Y63S probably damaging Het
Hexb A G 13: 97,334,729 (GRCm39) L14P unknown Het
Hsd17b3 A C 13: 64,236,914 (GRCm39) L10R probably damaging Het
Il6st T C 13: 112,635,420 (GRCm39) F611L probably damaging Het
Ints13 T A 6: 146,457,646 (GRCm39) T411S possibly damaging Het
Kif18b C A 11: 102,799,146 (GRCm39) C685F probably damaging Het
Kif5c A G 2: 49,509,729 (GRCm39) N19S probably damaging Het
Lmbr1 G T 5: 29,497,221 (GRCm39) probably null Het
Minar1 A G 9: 89,484,792 (GRCm39) S202P probably benign Het
Mmp1a TG TGG 9: 7,465,083 (GRCm38) probably null Het
Mrc2 G A 11: 105,216,397 (GRCm39) R62Q probably benign Het
Myo1g T C 11: 6,458,183 (GRCm39) probably benign Het
Myo5a A T 9: 75,037,423 (GRCm39) probably benign Het
Nobox G A 6: 43,282,095 (GRCm39) S326L possibly damaging Het
Nsl1 C A 1: 190,795,300 (GRCm39) S22* probably null Het
Or5b3 A C 19: 13,388,826 (GRCm39) K298Q possibly damaging Het
Or5j3 T C 2: 86,128,823 (GRCm39) I221T probably damaging Het
Pdia3 T A 2: 121,260,037 (GRCm39) L192Q probably damaging Het
Pkd2 A T 5: 104,651,471 (GRCm39) R940* probably null Het
Plcd3 T A 11: 102,967,568 (GRCm39) Q458L probably benign Het
Polm T A 11: 5,786,343 (GRCm39) T75S probably benign Het
Pon3 T A 6: 5,232,330 (GRCm39) D230V possibly damaging Het
Pxdn A T 12: 30,053,113 (GRCm39) K917* probably null Het
Rad54l2 A G 9: 106,577,784 (GRCm39) S1046P probably benign Het
Rb1cc1 T C 1: 6,318,035 (GRCm39) probably null Het
Rnf215 A G 11: 4,086,785 (GRCm39) E194G probably damaging Het
Rorb A T 19: 18,915,336 (GRCm39) F441I probably damaging Het
Sel1l2 C A 2: 140,090,508 (GRCm39) G378V probably damaging Het
Sema6a G T 18: 47,431,281 (GRCm39) A139D probably damaging Het
Serpinb3d A T 1: 107,006,266 (GRCm39) M274K probably benign Het
Siglec15 A C 18: 78,092,462 (GRCm39) L32R probably damaging Het
Siglecg A T 7: 43,067,476 (GRCm39) D681V probably damaging Het
Slc6a13 G T 6: 121,303,066 (GRCm39) probably benign Het
Slc9b2 G T 3: 135,024,179 (GRCm39) A77S probably benign Het
Snorc A G 1: 87,402,926 (GRCm39) probably null Het
Speer4c1 A C 5: 15,919,214 (GRCm39) probably benign Het
Stxbp2 T C 8: 3,683,267 (GRCm39) probably benign Het
Tbc1d9b T C 11: 50,042,773 (GRCm39) S482P possibly damaging Het
Tec A G 5: 72,926,090 (GRCm39) S321P possibly damaging Het
Tenm3 A G 8: 48,688,381 (GRCm39) M2402T probably damaging Het
Thrap3 G A 4: 126,059,335 (GRCm39) probably null Het
Tm4sf1 A T 3: 57,200,537 (GRCm39) probably null Het
Tmcc1 T C 6: 116,019,889 (GRCm39) E306G probably damaging Het
Traf3ip3 A T 1: 192,877,182 (GRCm39) probably null Het
Utf1 C T 7: 139,523,875 (GRCm39) P30L possibly damaging Het
Wdfy3 A T 5: 102,077,847 (GRCm39) C880S probably damaging 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
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
R4795:Slit3 UTSW 11 35,542,647 (GRCm39) critical splice donor site probably null
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'- ACAGTTATCTCCTGGGAGCC -3'
(R):5'- CCTTCGTTCTGAATCTCAAAGAGG -3'

Sequencing Primer
(F):5'- TTACCACCAGAGTCCTAACATTATC -3'
(R):5'- ATCTCAAAGAGGTTCCATGTGGC -3'
Posted On 2017-02-08