Incidental Mutation 'R5338:Slit3'
ID 423644
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: 0.871) question?
Stock # R5338 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 35012283-35599334 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 35512975 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 534 (T534A)
Ref Sequence ENSEMBL: ENSMUSP00000066857 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000069837]
AlphaFold Q9WVB4
Predicted Effect probably benign
Transcript: ENSMUST00000069837
AA Change: T534A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000066857
Gene: ENSMUSG00000056427
AA Change: T534A

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
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
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 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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A4gnt T A 9: 99,502,597 (GRCm39) N252K probably damaging Het
Abhd16a A G 17: 35,313,278 (GRCm39) E132G probably damaging Het
Adgrv1 G A 13: 81,677,165 (GRCm39) R1889W possibly damaging Het
Aftph A T 11: 20,677,203 (GRCm39) D135E probably benign Het
Arf1 A C 11: 59,104,041 (GRCm39) F63V probably damaging Het
Atg14 G A 14: 47,805,656 (GRCm39) R70C probably damaging Het
B3gnt7 T A 1: 86,233,366 (GRCm39) F87Y probably damaging Het
Bcat1 A G 6: 144,953,353 (GRCm39) Y345H possibly damaging Het
Birc2 G T 9: 7,857,360 (GRCm39) T371K probably benign Het
Ccdc175 A T 12: 72,231,745 (GRCm39) S5T probably damaging Het
Ccdc186 A T 19: 56,801,689 (GRCm39) S143T possibly damaging Het
Cct6b A T 11: 82,653,015 (GRCm39) M28K possibly damaging Het
Cers4 C A 8: 4,565,680 (GRCm39) A42D probably damaging Het
Crmp1 G T 5: 37,437,018 (GRCm39) V236L probably benign Het
Ctdspl2 T A 2: 121,811,793 (GRCm39) N212K probably benign Het
Dclk3 T C 9: 111,298,127 (GRCm39) V557A possibly damaging Het
Dnmt1 A T 9: 20,864,015 (GRCm39) H23Q probably benign Het
Dpp8 G T 9: 64,971,206 (GRCm39) E609* probably null Het
Dtx3 C A 10: 127,028,919 (GRCm39) M106I probably benign Het
Ero1b A C 13: 12,589,732 (GRCm39) D45A probably damaging Het
Fcho2 T A 13: 98,867,399 (GRCm39) D688V probably damaging Het
Fhod3 A T 18: 25,161,138 (GRCm39) S557C probably damaging Het
Flnc T C 6: 29,444,063 (GRCm39) S626P possibly damaging Het
Foxi3 G T 6: 70,937,602 (GRCm39) G278V probably damaging Het
Gbp10 A G 5: 105,372,166 (GRCm39) L198P probably damaging Het
Gcn1 A G 5: 115,721,462 (GRCm39) T458A probably benign Het
Gigyf1 C T 5: 137,521,422 (GRCm39) probably benign Het
Gtpbp2 A C 17: 46,478,760 (GRCm39) T526P probably damaging Het
Gys2 A G 6: 142,400,239 (GRCm39) L324S probably damaging Het
Hpn C A 7: 30,802,781 (GRCm39) V119L probably benign Het
Ino80d C A 1: 63,098,098 (GRCm39) V599L probably benign Het
Kcnh3 G T 15: 99,140,275 (GRCm39) G1054* probably null Het
Maml1 A T 11: 50,157,778 (GRCm39) D132E probably benign Het
Mastl A T 2: 23,023,503 (GRCm39) S407T probably benign Het
Mettl1 T C 10: 126,878,954 (GRCm39) W3R probably damaging Het
Mprip A G 11: 59,651,399 (GRCm39) Y1701C probably damaging Het
Mylk3 T C 8: 86,069,350 (GRCm39) N484D probably damaging Het
Nod2 G A 8: 89,399,413 (GRCm39) probably null Het
Nrde2 A T 12: 100,097,037 (GRCm39) F921Y probably damaging Het
Nup88 G T 11: 70,835,734 (GRCm39) T575N probably damaging Het
Nxpe3 T C 16: 55,686,706 (GRCm39) T101A possibly damaging Het
Or1o3 T A 17: 37,574,532 (GRCm39) T8S probably benign Het
Or2r11 A G 6: 42,437,908 (GRCm39) M15T probably benign Het
Or4c109 C T 2: 88,817,809 (GRCm39) V246I possibly damaging Het
Or52e15 A G 7: 104,645,514 (GRCm39) L199S possibly damaging Het
Or8g32 A T 9: 39,305,371 (GRCm39) I92F probably damaging Het
Pcnx3 A T 19: 5,722,624 (GRCm39) L1356Q probably damaging Het
Pkd1 A T 17: 24,813,510 (GRCm39) M4017L probably benign Het
Polg2 A G 11: 106,670,064 (GRCm39) C69R possibly damaging Het
Prr5l T G 2: 101,547,452 (GRCm39) S358R probably benign Het
Ptprg A G 14: 12,154,111 (GRCm38) T611A probably benign Het
Ryk G T 9: 102,774,516 (GRCm39) E417* probably null Het
Sbp T C 17: 24,161,396 (GRCm39) probably benign Het
Sema4a T C 3: 88,358,804 (GRCm39) T155A probably benign Het
Shank3 A G 15: 89,415,914 (GRCm39) probably null Het
Slc35d2 A T 13: 64,245,496 (GRCm39) M294K possibly damaging Het
Slc41a3 A T 6: 90,589,153 (GRCm39) N88I possibly damaging Het
Ssx2ip A G 3: 146,142,296 (GRCm39) probably null Het
Stard13 T C 5: 150,983,063 (GRCm39) K648R probably damaging Het
Tanc1 A T 2: 59,626,178 (GRCm39) T512S probably damaging Het
Tbcc T C 17: 47,202,082 (GRCm39) V156A probably benign Het
Terf1 T G 1: 15,901,787 (GRCm39) I273R possibly damaging Het
Tesc A G 5: 118,197,523 (GRCm39) Y179C probably damaging Het
Ttc3 T G 16: 94,184,900 (GRCm39) V40G probably damaging Het
Tysnd1 T A 10: 61,532,028 (GRCm39) F227I probably damaging Het
Vps53 T C 11: 75,972,034 (GRCm39) E271G probably damaging Het
Wdfy4 C T 14: 32,812,823 (GRCm39) R1650H 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
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
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
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'- GAACCTTGTGCCTGAAAACCG -3'
(R):5'- GAGCAACGCCTGGTTTTATAG -3'

Sequencing Primer
(F):5'- CTTGTGCCTGAAAACCGAAATG -3'
(R):5'- TAGTGAGTGTCCAGAAAGCATTC -3'
Posted On 2016-08-04