Incidental Mutation 'R4874:Slit1'
ID 376802
Institutional Source Beutler Lab
Gene Symbol Slit1
Ensembl Gene ENSMUSG00000025020
Gene Name slit guidance ligand 1
Synonyms Slil1
MMRRC Submission 042484-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4874 (G1)
Quality Score 126
Status Validated
Chromosome 19
Chromosomal Location 41588696-41732104 bp(-) (GRCm39)
Type of Mutation critical splice donor site (1 bp from exon)
DNA Base Change (assembly) C to T at 41717493 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000126139 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025993] [ENSMUST00000166496] [ENSMUST00000169141] [ENSMUST00000171586]
AlphaFold Q80TR4
Predicted Effect probably null
Transcript: ENSMUST00000025993
SMART Domains Protein: ENSMUSP00000025993
Gene: ENSMUSG00000025020

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
LRRNT 33 65 5.68e-9 SMART
LRR 59 83 4.58e1 SMART
LRR 84 107 4.7e0 SMART
LRR_TYP 108 131 1.95e-3 SMART
LRR 133 155 6.05e0 SMART
LRR 157 179 3.98e1 SMART
LRR_TYP 180 203 3.44e-4 SMART
LRRCT 215 264 3.51e-6 SMART
LRRNT 281 313 3e-8 SMART
LRR 307 331 6.41e1 SMART
LRR_TYP 332 355 8.22e-2 SMART
LRR_TYP 356 379 9.08e-4 SMART
LRR 380 403 2.82e0 SMART
LRR_TYP 404 427 5.42e-2 SMART
LRRCT 439 488 5.78e-7 SMART
LRRNT 512 544 1.04e-7 SMART
LRR_TYP 564 587 3.39e-3 SMART
LRR 589 611 2.08e1 SMART
LRR_TYP 612 635 1.56e-2 SMART
LRR_TYP 636 659 4.11e-2 SMART
LRRCT 671 720 2.89e-7 SMART
LRRNT 733 765 4.87e-8 SMART
LRR 783 806 1.22e1 SMART
LRR_TYP 807 830 9.73e-4 SMART
LRR_TYP 831 854 9.58e-3 SMART
LRRCT 866 915 5.6e-14 SMART
EGF 928 962 5.08e-7 SMART
EGF 967 1003 1.74e-5 SMART
EGF_CA 1005 1041 1.05e-8 SMART
EGF 1046 1081 1.21e-4 SMART
EGF_CA 1083 1119 3.64e-8 SMART
FOLN 1086 1108 8.44e0 SMART
FOLN 1127 1149 1.4e0 SMART
EGF 1127 1160 1.78e-2 SMART
LamG 1183 1319 4.43e-38 SMART
EGF 1338 1371 6.76e-3 SMART
EGF 1377 1410 3.38e-3 SMART
FOLN 1418 1440 2.25e1 SMART
EGF 1418 1451 1.28e-3 SMART
CT 1462 1531 3.15e-4 SMART
Predicted Effect probably null
Transcript: ENSMUST00000166496
SMART Domains Protein: ENSMUSP00000128381
Gene: ENSMUSG00000025020

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
LRRNT 33 65 5.68e-9 SMART
LRR 59 83 4.58e1 SMART
LRR 84 107 4.7e0 SMART
LRR_TYP 108 131 1.95e-3 SMART
LRR 133 155 6.05e0 SMART
LRR 157 179 3.98e1 SMART
LRR_TYP 180 203 3.44e-4 SMART
LRRCT 215 264 3.51e-6 SMART
LRRNT 281 313 3e-8 SMART
LRR 307 331 6.41e1 SMART
LRR_TYP 332 355 8.22e-2 SMART
LRR_TYP 356 379 9.08e-4 SMART
LRR 380 403 2.82e0 SMART
LRR_TYP 404 427 5.42e-2 SMART
LRRCT 439 488 5.78e-7 SMART
LRRNT 512 544 1.04e-7 SMART
LRR_TYP 564 587 3.39e-3 SMART
LRR 589 611 2.08e1 SMART
LRR_TYP 612 635 1.56e-2 SMART
LRR_TYP 636 659 4.11e-2 SMART
LRRCT 671 720 2.89e-7 SMART
LRRNT 733 765 4.87e-8 SMART
LRR 783 806 1.22e1 SMART
LRR_TYP 807 830 9.73e-4 SMART
LRR_TYP 831 854 9.58e-3 SMART
LRRCT 866 915 5.6e-14 SMART
EGF 928 962 5.08e-7 SMART
EGF 967 1003 1.74e-5 SMART
EGF_CA 1005 1041 1.05e-8 SMART
EGF 1046 1081 1.21e-4 SMART
EGF_CA 1083 1119 3.64e-8 SMART
FOLN 1086 1108 8.44e0 SMART
FOLN 1127 1149 1.4e0 SMART
EGF 1127 1160 1.78e-2 SMART
LamG 1183 1319 4.43e-38 SMART
EGF 1338 1371 6.76e-3 SMART
EGF 1377 1410 3.38e-3 SMART
low complexity region 1437 1458 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000169141
SMART Domains Protein: ENSMUSP00000129034
Gene: ENSMUSG00000025020

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
LRRNT 33 65 5.68e-9 SMART
LRR 59 83 4.58e1 SMART
LRR 84 107 4.7e0 SMART
LRR_TYP 108 131 1.95e-3 SMART
LRR 133 155 6.05e0 SMART
LRR 157 179 3.98e1 SMART
LRR_TYP 180 203 3.44e-4 SMART
LRRCT 215 264 3.51e-6 SMART
LRRNT 281 313 3e-8 SMART
LRR 307 331 6.41e1 SMART
LRR_TYP 332 355 8.22e-2 SMART
LRR_TYP 356 379 9.08e-4 SMART
LRR 380 403 2.82e0 SMART
LRR_TYP 404 427 5.42e-2 SMART
LRRCT 439 488 5.78e-7 SMART
LRRNT 512 544 1.04e-7 SMART
LRR_TYP 564 587 3.39e-3 SMART
LRR 589 611 2.08e1 SMART
LRR_TYP 612 635 1.56e-2 SMART
LRR_TYP 636 659 4.11e-2 SMART
LRRCT 671 720 2.89e-7 SMART
LRRNT 733 765 4.87e-8 SMART
LRR 783 806 1.22e1 SMART
LRR_TYP 807 830 9.73e-4 SMART
LRR_TYP 831 854 9.58e-3 SMART
LRRCT 866 915 5.6e-14 SMART
EGF 928 962 5.08e-7 SMART
EGF 967 1003 1.74e-5 SMART
EGF_CA 1005 1041 1.05e-8 SMART
EGF 1046 1081 1.21e-4 SMART
EGF_CA 1083 1119 3.64e-8 SMART
FOLN 1086 1108 8.44e0 SMART
FOLN 1127 1149 1.4e0 SMART
EGF 1127 1160 1.78e-2 SMART
LamG 1183 1319 4.43e-38 SMART
EGF 1338 1371 6.76e-3 SMART
EGF 1377 1410 3.38e-3 SMART
FOLN 1418 1440 2.25e1 SMART
EGF 1418 1451 1.28e-3 SMART
Predicted Effect probably null
Transcript: ENSMUST00000171586
SMART Domains Protein: ENSMUSP00000126139
Gene: ENSMUSG00000025020

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
LRRNT 33 65 5.68e-9 SMART
LRR 59 83 4.58e1 SMART
LRR 84 107 4.7e0 SMART
LRR_TYP 108 131 2.24e-3 SMART
LRR 133 155 3.98e1 SMART
LRR_TYP 156 179 3.44e-4 SMART
LRRCT 191 240 3.51e-6 SMART
LRRNT 257 289 3e-8 SMART
LRR 283 307 6.41e1 SMART
LRR_TYP 308 331 8.22e-2 SMART
LRR_TYP 332 355 9.08e-4 SMART
LRR 356 379 2.82e0 SMART
Meta Mutation Damage Score 0.9479 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.5%
Validation Efficiency 94% (51/54)
MGI Phenotype PHENOTYPE: Mice homozygous for a reporter allele exhibit normal interneuron numbers and morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadat G A 8: 60,969,147 (GRCm39) probably null Het
Adamtsl1 A G 4: 86,260,729 (GRCm39) N988S possibly damaging Het
Aph1b A T 9: 66,697,878 (GRCm39) probably null Het
B4galnt3 C A 6: 120,184,167 (GRCm39) R880L probably damaging Het
Bcam T C 7: 19,503,247 (GRCm39) probably benign Het
Cr2 A T 1: 194,858,878 (GRCm39) I14N possibly damaging Het
Dcdc5 T C 2: 106,198,451 (GRCm39) noncoding transcript Het
Dll1 A T 17: 15,590,501 (GRCm39) M405K probably benign Het
Dync1h1 C A 12: 110,624,560 (GRCm39) T3700N probably damaging Het
Ern2 T C 7: 121,775,810 (GRCm39) D428G probably benign Het
Esp36 A T 17: 38,727,987 (GRCm39) M98K unknown Het
Foxd2 G T 4: 114,764,768 (GRCm39) H417Q possibly damaging Het
Glrb T C 3: 80,758,349 (GRCm39) N304D possibly damaging Het
Haus3 A G 5: 34,324,972 (GRCm39) V229A probably benign Het
Hpgd A T 8: 56,770,838 (GRCm39) I159F possibly damaging Het
Ighv1-22 T A 12: 114,710,036 (GRCm39) I70F probably benign Het
Il16 A T 7: 83,310,153 (GRCm39) F584L possibly damaging Het
Lamc2 T C 1: 153,030,141 (GRCm39) D167G probably null Het
Megf10 G A 18: 57,426,930 (GRCm39) V1083I probably benign Het
Mertk T C 2: 128,592,079 (GRCm39) S268P probably damaging Het
Mfng C T 15: 78,648,588 (GRCm39) R163H probably benign Het
Mki67 T C 7: 135,310,500 (GRCm39) D132G probably damaging Het
Nbas A G 12: 13,371,756 (GRCm39) N419D probably damaging Het
Negr1 T C 3: 156,565,082 (GRCm39) L56S probably damaging Het
Nup214 A G 2: 31,870,596 (GRCm39) probably null Het
Opn5 C G 17: 42,891,610 (GRCm39) A276P probably damaging Het
Or10j5 A G 1: 172,785,166 (GRCm39) E268G probably benign Het
Or2d3 C T 7: 106,490,642 (GRCm39) V225I probably benign Het
Or5t9 T A 2: 86,659,598 (GRCm39) H167Q probably damaging Het
Papln G T 12: 83,823,917 (GRCm39) V499L probably benign Het
Pgap1 A T 1: 54,569,296 (GRCm39) W357R probably damaging Het
Pibf1 T C 14: 99,377,992 (GRCm39) Y373H probably damaging Het
Pitpnm1 T C 19: 4,162,252 (GRCm39) probably null Het
Prcd T A 11: 116,550,597 (GRCm39) W3R probably null Het
Prkaa1 A G 15: 5,203,838 (GRCm39) N249S probably benign Het
Reg3b T A 6: 78,349,809 (GRCm39) N116K possibly damaging Het
Rpusd2 T C 2: 118,865,360 (GRCm39) L19P probably benign Het
Rufy1 T C 11: 50,297,277 (GRCm39) T392A possibly damaging Het
Sall3 T C 18: 81,017,188 (GRCm39) K247E probably benign Het
Shank1 C T 7: 43,965,497 (GRCm39) T191M unknown Het
Sorl1 A T 9: 41,975,048 (GRCm39) V520E probably damaging Het
Vmn2r115 T A 17: 23,578,825 (GRCm39) F766Y probably damaging Het
Wdr87-ps A G 7: 29,235,608 (GRCm39) noncoding transcript Het
Zfp644 A G 5: 106,783,279 (GRCm39) S1032P probably damaging Het
Other mutations in Slit1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00162:Slit1 APN 19 41,639,274 (GRCm39) missense probably damaging 1.00
IGL00515:Slit1 APN 19 41,612,940 (GRCm39) missense probably damaging 0.97
IGL00909:Slit1 APN 19 41,590,694 (GRCm39) missense possibly damaging 0.89
IGL00953:Slit1 APN 19 41,590,739 (GRCm39) missense probably damaging 1.00
IGL01116:Slit1 APN 19 41,594,824 (GRCm39) missense possibly damaging 0.93
IGL01457:Slit1 APN 19 41,599,483 (GRCm39) missense probably damaging 1.00
IGL01688:Slit1 APN 19 41,717,545 (GRCm39) missense probably damaging 1.00
IGL01720:Slit1 APN 19 41,622,653 (GRCm39) missense probably benign 0.01
IGL01925:Slit1 APN 19 41,596,817 (GRCm39) missense probably damaging 0.98
IGL02008:Slit1 APN 19 41,634,579 (GRCm39) missense probably damaging 0.99
IGL02312:Slit1 APN 19 41,590,119 (GRCm39) missense possibly damaging 0.66
IGL02398:Slit1 APN 19 41,590,676 (GRCm39) missense probably damaging 1.00
IGL02542:Slit1 APN 19 41,615,687 (GRCm39) missense probably damaging 1.00
IGL02559:Slit1 APN 19 41,709,524 (GRCm39) missense probably benign 0.01
IGL02609:Slit1 APN 19 41,590,743 (GRCm39) missense probably damaging 0.99
IGL02623:Slit1 APN 19 41,640,122 (GRCm39) missense probably damaging 0.98
IGL02729:Slit1 APN 19 41,591,773 (GRCm39) missense probably damaging 1.00
IGL03230:Slit1 APN 19 41,717,524 (GRCm39) missense probably damaging 1.00
IGL03387:Slit1 APN 19 41,591,881 (GRCm39) missense possibly damaging 0.57
PIT4576001:Slit1 UTSW 19 41,612,988 (GRCm39) missense possibly damaging 0.52
R0366:Slit1 UTSW 19 41,599,470 (GRCm39) missense probably damaging 1.00
R0432:Slit1 UTSW 19 41,731,732 (GRCm39) missense probably damaging 0.98
R0496:Slit1 UTSW 19 41,596,750 (GRCm39) splice site probably benign
R0722:Slit1 UTSW 19 41,596,874 (GRCm39) missense probably damaging 1.00
R1468:Slit1 UTSW 19 41,596,823 (GRCm39) missense probably damaging 1.00
R1468:Slit1 UTSW 19 41,596,823 (GRCm39) missense probably damaging 1.00
R1488:Slit1 UTSW 19 41,596,824 (GRCm39) missense probably damaging 1.00
R1615:Slit1 UTSW 19 41,639,110 (GRCm39) splice site probably benign
R1694:Slit1 UTSW 19 41,626,031 (GRCm39) missense possibly damaging 0.69
R1762:Slit1 UTSW 19 41,591,774 (GRCm39) missense probably damaging 1.00
R1842:Slit1 UTSW 19 41,709,477 (GRCm39) critical splice donor site probably null
R1844:Slit1 UTSW 19 41,614,012 (GRCm39) missense probably damaging 1.00
R1940:Slit1 UTSW 19 41,619,215 (GRCm39) missense probably damaging 1.00
R2087:Slit1 UTSW 19 41,625,922 (GRCm39) missense probably benign 0.00
R2094:Slit1 UTSW 19 41,594,819 (GRCm39) missense probably damaging 0.99
R2095:Slit1 UTSW 19 41,594,819 (GRCm39) missense probably damaging 0.99
R2104:Slit1 UTSW 19 41,590,686 (GRCm39) missense possibly damaging 0.69
R2305:Slit1 UTSW 19 41,599,455 (GRCm39) missense probably benign 0.03
R2972:Slit1 UTSW 19 41,599,455 (GRCm39) missense probably benign 0.03
R2973:Slit1 UTSW 19 41,599,455 (GRCm39) missense probably benign 0.03
R2974:Slit1 UTSW 19 41,599,455 (GRCm39) missense probably benign 0.03
R3159:Slit1 UTSW 19 41,592,812 (GRCm39) missense probably benign
R3752:Slit1 UTSW 19 41,635,406 (GRCm39) critical splice donor site probably null
R4095:Slit1 UTSW 19 41,596,925 (GRCm39) intron probably benign
R4282:Slit1 UTSW 19 41,602,856 (GRCm39) missense probably benign
R4417:Slit1 UTSW 19 41,602,908 (GRCm39) missense probably damaging 1.00
R4607:Slit1 UTSW 19 41,605,232 (GRCm39) missense probably benign 0.10
R4729:Slit1 UTSW 19 41,635,459 (GRCm39) missense probably damaging 1.00
R4756:Slit1 UTSW 19 41,637,452 (GRCm39) missense probably damaging 1.00
R4764:Slit1 UTSW 19 41,709,483 (GRCm39) nonsense probably null
R4849:Slit1 UTSW 19 41,637,983 (GRCm39) missense probably benign 0.17
R5581:Slit1 UTSW 19 41,605,102 (GRCm39) critical splice donor site probably null
R5699:Slit1 UTSW 19 41,613,959 (GRCm39) critical splice donor site probably null
R5888:Slit1 UTSW 19 41,731,735 (GRCm39) missense probably damaging 1.00
R5906:Slit1 UTSW 19 41,594,813 (GRCm39) missense probably damaging 1.00
R6176:Slit1 UTSW 19 41,626,034 (GRCm39) missense probably damaging 1.00
R6277:Slit1 UTSW 19 41,588,948 (GRCm39) missense possibly damaging 0.81
R6702:Slit1 UTSW 19 41,603,309 (GRCm39) missense possibly damaging 0.95
R6860:Slit1 UTSW 19 41,605,154 (GRCm39) missense probably benign 0.10
R7015:Slit1 UTSW 19 41,618,325 (GRCm39) nonsense probably null
R7172:Slit1 UTSW 19 41,623,105 (GRCm39) missense probably damaging 1.00
R7512:Slit1 UTSW 19 41,589,074 (GRCm39) missense probably damaging 1.00
R7568:Slit1 UTSW 19 41,590,074 (GRCm39) missense probably damaging 1.00
R7614:Slit1 UTSW 19 41,622,639 (GRCm39) missense probably damaging 1.00
R7650:Slit1 UTSW 19 41,618,363 (GRCm39) missense probably damaging 1.00
R7687:Slit1 UTSW 19 41,639,128 (GRCm39) missense probably benign 0.03
R7732:Slit1 UTSW 19 41,592,847 (GRCm39) missense probably benign 0.01
R7947:Slit1 UTSW 19 41,599,248 (GRCm39) missense probably benign
R7947:Slit1 UTSW 19 41,599,247 (GRCm39) missense probably damaging 1.00
R8171:Slit1 UTSW 19 41,715,512 (GRCm39) missense probably damaging 0.97
R8217:Slit1 UTSW 19 41,612,959 (GRCm39) missense possibly damaging 0.60
R8355:Slit1 UTSW 19 41,634,473 (GRCm39) missense probably damaging 1.00
R9025:Slit1 UTSW 19 41,612,968 (GRCm39) missense probably benign 0.01
R9124:Slit1 UTSW 19 41,594,951 (GRCm39) missense probably benign 0.02
R9288:Slit1 UTSW 19 41,613,144 (GRCm39) intron probably benign
R9343:Slit1 UTSW 19 41,615,737 (GRCm39) missense probably damaging 1.00
R9435:Slit1 UTSW 19 41,591,764 (GRCm39) critical splice donor site probably null
R9563:Slit1 UTSW 19 41,596,874 (GRCm39) missense probably damaging 1.00
R9564:Slit1 UTSW 19 41,591,861 (GRCm39) missense probably benign 0.16
R9595:Slit1 UTSW 19 41,637,851 (GRCm39) missense probably damaging 1.00
R9667:Slit1 UTSW 19 41,731,832 (GRCm39) nonsense probably null
X0023:Slit1 UTSW 19 41,590,079 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- TCCCAGAGACAGAAATGGCC -3'
(R):5'- AAGTGATGTGCTGGGCTTCAC -3'

Sequencing Primer
(F):5'- GGAGGCAGTAAGCTCTCTAGATC -3'
(R):5'- TGGGCTTCACCTCACTGG -3'
Posted On 2016-03-17