Incidental Mutation 'R1992:Slitrk3'
ID 223571
Institutional Source Beutler Lab
Gene Symbol Slitrk3
Ensembl Gene ENSMUSG00000048304
Gene Name SLIT and NTRK-like family, member 3
Synonyms ST3
MMRRC Submission 040003-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.715) question?
Stock # R1992 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 72954598-72965136 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 72957104 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 556 (V556A)
Ref Sequence ENSEMBL: ENSMUSP00000141236 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059407] [ENSMUST00000192477]
AlphaFold Q810B9
Predicted Effect possibly damaging
Transcript: ENSMUST00000059407
AA Change: V556A

PolyPhen 2 Score 0.802 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000088561
Gene: ENSMUSG00000048304
AA Change: V556A

DomainStartEndE-ValueType
signal peptide 1 29 N/A INTRINSIC
Blast:LRRNT 44 79 3e-11 BLAST
LRR 101 124 2.08e1 SMART
LRR 125 148 6.05e0 SMART
LRR 149 172 3.97e0 SMART
LRR_TYP 173 196 1.67e-2 SMART
LRR 197 220 2.69e2 SMART
LRRCT 233 283 4.56e-5 SMART
low complexity region 332 350 N/A INTRINSIC
LRRNT 373 411 4.17e0 SMART
LRR 432 455 1.62e0 SMART
LRR_TYP 456 479 2.61e-4 SMART
LRR 480 503 2.82e0 SMART
LRR_TYP 504 527 6.99e-5 SMART
LRRCT 563 613 3.22e-5 SMART
transmembrane domain 658 680 N/A INTRINSIC
low complexity region 713 724 N/A INTRINSIC
low complexity region 836 843 N/A INTRINSIC
low complexity region 846 858 N/A INTRINSIC
low complexity region 870 888 N/A INTRINSIC
Blast:LRRCT 906 943 2e-16 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000192477
AA Change: V556A

PolyPhen 2 Score 0.802 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000141236
Gene: ENSMUSG00000048304
AA Change: V556A

DomainStartEndE-ValueType
signal peptide 1 29 N/A INTRINSIC
Blast:LRRNT 44 79 3e-11 BLAST
LRR 101 124 2.08e1 SMART
LRR 125 148 6.05e0 SMART
LRR 149 172 3.97e0 SMART
LRR_TYP 173 196 1.67e-2 SMART
LRR 197 220 2.69e2 SMART
LRRCT 233 283 4.56e-5 SMART
low complexity region 332 350 N/A INTRINSIC
LRRNT 373 411 4.17e0 SMART
LRR 432 455 1.62e0 SMART
LRR_TYP 456 479 2.61e-4 SMART
LRR 480 503 2.82e0 SMART
LRR_TYP 504 527 6.99e-5 SMART
LRRCT 563 613 3.22e-5 SMART
transmembrane domain 658 680 N/A INTRINSIC
low complexity region 713 724 N/A INTRINSIC
low complexity region 836 843 N/A INTRINSIC
low complexity region 846 858 N/A INTRINSIC
low complexity region 870 888 N/A INTRINSIC
Blast:LRRCT 906 943 2e-16 BLAST
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.4%
  • 20x: 92.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Slitrk family of structurally related transmembrane proteins that are involved in controlling neurite outgrowth. The encoded protein contains two leucine-rich repeat (LRR) domains and a C-terminal domain that is partially similar to Trk neurotrophin receptor protein. Enhanced expression of this gene was found in tissue from several different types of tumors. Alternative splicing results in multiple transcript variants, all encoding the same protein. [provided by RefSeq, Jan 2016]
PHENOTYPE: Mice homozygous for a knock-out mice exhibit reduced inhibitory synapse density, decreased miniature inhibitory postsynaptic current frequency and increased susceptibility to spontaneous and pharmacologically-induced seizures. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 123 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310009B15Rik T C 1: 138,781,380 (GRCm39) T90A probably damaging Het
A930011G23Rik T C 5: 99,381,784 (GRCm39) D326G possibly damaging Het
Abcc2 A T 19: 43,795,581 (GRCm39) I446F probably damaging Het
Adam34l T C 8: 44,080,176 (GRCm39) K16R probably benign Het
Adamts14 A G 10: 61,034,439 (GRCm39) Y1150H probably benign Het
Adgrl2 A G 3: 148,522,880 (GRCm39) I217T possibly damaging Het
Afap1l1 A T 18: 61,874,842 (GRCm39) Y446* probably null Het
Aimp2 G A 5: 143,843,548 (GRCm39) A14V probably damaging Het
Akap8 G A 17: 32,535,586 (GRCm39) H143Y probably damaging Het
Aldh2 A T 5: 121,714,026 (GRCm39) V207E possibly damaging Het
Aoc1l2 T A 6: 48,907,703 (GRCm39) H234Q probably damaging Het
Armc3 T C 2: 19,297,953 (GRCm39) Y575H probably damaging Het
Arpp21 T C 9: 111,986,861 (GRCm39) E230G probably damaging Het
Arrdc3 G A 13: 81,031,808 (GRCm39) D14N probably damaging Het
Atn1 A G 6: 124,722,291 (GRCm39) probably benign Het
Atxn7l1 G A 12: 33,408,743 (GRCm39) D302N probably damaging Het
Bbs1 T A 19: 4,941,736 (GRCm39) H518L probably benign Het
Bltp1 A T 3: 37,054,181 (GRCm39) H3100L probably benign Het
Bmpr1a C A 14: 34,147,050 (GRCm39) G241C probably damaging Het
Cacna1b G A 2: 24,622,318 (GRCm39) P222L probably damaging Het
Calcrl T C 2: 84,200,855 (GRCm39) Y63C probably damaging Het
Cand2 A G 6: 115,762,093 (GRCm39) H173R possibly damaging Het
Cap2 T A 13: 46,791,357 (GRCm39) Y175N possibly damaging Het
Card14 A T 11: 119,212,647 (GRCm39) probably null Het
Cd3d T A 9: 44,896,299 (GRCm39) Y29* probably null Het
Cd4 A G 6: 124,844,651 (GRCm39) V378A possibly damaging Het
Cluh A T 11: 74,550,828 (GRCm39) H318L probably damaging Het
Clvs1 T A 4: 9,281,899 (GRCm39) D114E probably benign Het
Cnot4 T A 6: 35,000,344 (GRCm39) T548S probably benign Het
Col18a1 T C 10: 76,916,988 (GRCm39) I114V unknown Het
Cr2 G A 1: 194,836,458 (GRCm39) P1278S possibly damaging Het
Crebbp A T 16: 3,946,561 (GRCm39) probably null Het
Dnah7a T G 1: 53,621,835 (GRCm39) K1097Q possibly damaging Het
Doc2a T A 7: 126,450,979 (GRCm39) probably null Het
Dpp10 A T 1: 123,832,833 (GRCm39) V48E probably null Het
Dsg2 A G 18: 20,734,530 (GRCm39) K836R probably damaging Het
Egr2 T C 10: 67,375,857 (GRCm39) V164A probably damaging Het
Erbin A T 13: 103,970,221 (GRCm39) S1132T probably benign Het
Espn T A 4: 152,213,012 (GRCm39) probably null Het
Fam83b A G 9: 76,399,304 (GRCm39) S600P probably benign Het
Fanca A T 8: 124,024,551 (GRCm39) N425K possibly damaging Het
Flot2 C T 11: 77,949,445 (GRCm39) L294F probably damaging Het
Frs2 A G 10: 116,910,459 (GRCm39) V301A probably benign Het
Fv1 T A 4: 147,953,618 (GRCm39) N61K possibly damaging Het
Fxr2 A G 11: 69,540,659 (GRCm39) E339G possibly damaging Het
Gck T C 11: 5,856,515 (GRCm39) Y214C probably damaging Het
Golga3 C G 5: 110,340,839 (GRCm39) T551R probably damaging Het
Gorab A G 1: 163,224,625 (GRCm39) S59P probably damaging Het
Gsdme C T 6: 50,185,102 (GRCm39) V451M probably damaging Het
H2-T13 A C 17: 36,391,938 (GRCm39) I216S probably damaging Het
Herc4 T A 10: 63,081,743 (GRCm39) V22E possibly damaging Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Hoxa2 A T 6: 52,141,576 (GRCm39) S17T probably damaging Het
Hs3st5 A G 10: 36,708,882 (GRCm39) Y139C probably damaging Het
Ism1 G A 2: 139,587,937 (GRCm39) V221I probably benign Het
Kalrn T G 16: 33,796,108 (GRCm39) L1222F probably damaging Het
Katnip A G 7: 125,419,261 (GRCm39) N476S probably benign Het
Kdm4c A G 4: 74,261,631 (GRCm39) D602G possibly damaging Het
Ktn1 A G 14: 47,932,978 (GRCm39) K711E probably damaging Het
Lce1k A T 3: 92,714,125 (GRCm39) C20S unknown Het
Macf1 A G 4: 123,350,488 (GRCm39) S3792P probably damaging Het
Maml3 C T 3: 51,598,178 (GRCm39) M189I probably benign Het
Mcc C A 18: 44,624,382 (GRCm39) E213* probably null Het
Mep1a T G 17: 43,813,573 (GRCm39) I13L probably benign Het
Mkrn2 G T 6: 115,586,562 (GRCm39) C16F probably damaging Het
Mlh1 C T 9: 111,057,631 (GRCm39) A727T probably damaging Het
Muc21 A T 17: 35,929,600 (GRCm39) S1529T probably benign Het
Naa16 T C 14: 79,593,931 (GRCm39) Y344C probably damaging Het
Nebl T A 2: 17,457,321 (GRCm39) I80F probably damaging Het
Nlrc4 T A 17: 74,752,628 (GRCm39) Y585F probably benign Het
Nrcam A G 12: 44,587,753 (GRCm39) K149R probably damaging Het
Nufip1 T A 14: 76,372,287 (GRCm39) I467N probably damaging Het
Nup133 A G 8: 124,632,960 (GRCm39) I1057T possibly damaging Het
Obscn A T 11: 58,886,653 (GRCm39) probably benign Het
Or10ag52 T A 2: 87,043,588 (GRCm39) C117* probably null Het
Or5k1 A G 16: 58,617,309 (GRCm39) V300A probably benign Het
Or5k14 A C 16: 58,692,874 (GRCm39) I213R probably benign Het
Pi4k2a A T 19: 42,104,377 (GRCm39) I380F probably damaging Het
Piezo2 A T 18: 63,207,733 (GRCm39) L1426Q probably null Het
Pik3cg A T 12: 32,254,024 (GRCm39) D654E possibly damaging Het
Poli G T 18: 70,642,058 (GRCm39) P714Q probably damaging Het
Polr3f A G 2: 144,378,230 (GRCm39) N201D probably benign Het
Prorp A G 12: 55,384,991 (GRCm39) D89G probably damaging Het
Ptprz1 A T 6: 22,959,747 (GRCm39) K81N probably benign Het
Rbm19 T C 5: 120,271,948 (GRCm39) probably null Het
Sec24a C T 11: 51,627,190 (GRCm39) V241I probably benign Het
Sgk3 A G 1: 9,950,567 (GRCm39) T160A possibly damaging Het
Slc1a4 A G 11: 20,254,375 (GRCm39) I497T probably benign Het
Slc26a9 A T 1: 131,690,532 (GRCm39) D512V probably damaging Het
Slc43a3 C T 2: 84,788,084 (GRCm39) R489C probably damaging Het
Slc5a12 T A 2: 110,452,089 (GRCm39) F327L probably benign Het
Spata6l A G 19: 28,926,024 (GRCm39) F130L probably damaging Het
Spib T C 7: 44,178,281 (GRCm39) E180G probably benign Het
Spint2 T A 7: 28,958,833 (GRCm39) N128Y probably damaging Het
Spx G A 6: 142,364,245 (GRCm39) G102E probably benign Het
Spz1 T A 13: 92,712,166 (GRCm39) E103D possibly damaging Het
Sstr2 T C 11: 113,515,495 (GRCm39) I138T probably benign Het
Sytl3 T A 17: 7,000,448 (GRCm39) I206N possibly damaging Het
Tcaf2 T C 6: 42,606,791 (GRCm39) T388A probably benign Het
Tdpoz8 G T 3: 92,981,344 (GRCm39) A121S probably benign Het
Thap12 T C 7: 98,365,572 (GRCm39) V580A possibly damaging Het
Tlr5 T A 1: 182,801,912 (GRCm39) D405E probably damaging Het
Tnxb T C 17: 34,890,878 (GRCm39) V407A probably damaging Het
Tpx2 T A 2: 152,732,544 (GRCm39) M606K probably benign Het
Trim43a T G 9: 88,466,312 (GRCm39) L211R probably damaging Het
Trim46 A T 3: 89,145,008 (GRCm39) Y489N probably damaging Het
Ttc28 C T 5: 111,424,188 (GRCm39) S1485L probably benign Het
Ttll8 T C 15: 88,798,654 (GRCm39) T694A probably benign Het
Txnl1 T C 18: 63,812,585 (GRCm39) T70A probably benign Het
Ube3a C T 7: 58,953,535 (GRCm39) A823V probably damaging Het
Ubqln5 C A 7: 103,778,741 (GRCm39) V28F probably damaging Het
Ulk1 T A 5: 110,935,017 (GRCm39) Q972L probably damaging Het
Unc93b1 T C 19: 3,994,062 (GRCm39) Y398H probably benign Het
Usp1 A G 4: 98,822,531 (GRCm39) D615G probably benign Het
Utp15 A G 13: 98,387,420 (GRCm39) C385R probably benign Het
Vmn2r91 T A 17: 18,356,142 (GRCm39) V603D probably damaging Het
Whamm C T 7: 81,241,519 (GRCm39) R277* probably null Het
Wnt8a A G 18: 34,677,937 (GRCm39) D115G probably damaging Het
Yjefn3 A T 8: 70,341,645 (GRCm39) probably null Het
Ywhab A T 2: 163,853,807 (GRCm39) I95F probably damaging Het
Zfp143 C T 7: 109,660,489 (GRCm39) probably benign Het
Zfp607b C G 7: 27,401,949 (GRCm39) T135R possibly damaging Het
Zfp970 A G 2: 177,166,663 (GRCm39) Q79R possibly damaging Het
Other mutations in Slitrk3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00465:Slitrk3 APN 3 72,958,436 (GRCm39) missense probably damaging 1.00
IGL00857:Slitrk3 APN 3 72,957,174 (GRCm39) missense probably damaging 1.00
IGL00990:Slitrk3 APN 3 72,957,414 (GRCm39) missense probably damaging 1.00
IGL01010:Slitrk3 APN 3 72,956,606 (GRCm39) missense probably benign 0.14
IGL01299:Slitrk3 APN 3 72,956,349 (GRCm39) missense probably benign 0.43
IGL01609:Slitrk3 APN 3 72,957,570 (GRCm39) missense probably damaging 1.00
IGL01881:Slitrk3 APN 3 72,956,639 (GRCm39) missense probably benign 0.00
IGL01941:Slitrk3 APN 3 72,958,404 (GRCm39) missense possibly damaging 0.72
IGL02183:Slitrk3 APN 3 72,957,312 (GRCm39) missense probably damaging 0.97
IGL02187:Slitrk3 APN 3 72,957,605 (GRCm39) missense probably damaging 1.00
IGL02478:Slitrk3 APN 3 72,958,046 (GRCm39) missense probably damaging 0.96
IGL02512:Slitrk3 APN 3 72,957,735 (GRCm39) missense probably benign 0.28
IGL02720:Slitrk3 APN 3 72,958,101 (GRCm39) missense probably damaging 1.00
IGL03113:Slitrk3 APN 3 72,957,723 (GRCm39) missense probably benign 0.00
IGL03224:Slitrk3 APN 3 72,957,263 (GRCm39) missense possibly damaging 0.72
wee UTSW 3 72,958,118 (GRCm39) missense probably damaging 1.00
R0233:Slitrk3 UTSW 3 72,955,910 (GRCm39) missense probably benign 0.00
R0233:Slitrk3 UTSW 3 72,955,910 (GRCm39) missense probably benign 0.00
R0639:Slitrk3 UTSW 3 72,956,982 (GRCm39) missense probably benign 0.02
R1448:Slitrk3 UTSW 3 72,957,674 (GRCm39) missense probably damaging 0.99
R1656:Slitrk3 UTSW 3 72,957,672 (GRCm39) missense probably damaging 0.98
R1713:Slitrk3 UTSW 3 72,957,024 (GRCm39) missense probably benign 0.00
R1999:Slitrk3 UTSW 3 72,957,297 (GRCm39) missense probably benign 0.13
R2359:Slitrk3 UTSW 3 72,956,678 (GRCm39) missense possibly damaging 0.56
R3083:Slitrk3 UTSW 3 72,955,928 (GRCm39) missense probably benign 0.00
R3153:Slitrk3 UTSW 3 72,956,315 (GRCm39) nonsense probably null
R3821:Slitrk3 UTSW 3 72,956,549 (GRCm39) missense possibly damaging 0.94
R4208:Slitrk3 UTSW 3 72,958,490 (GRCm39) missense possibly damaging 0.67
R4323:Slitrk3 UTSW 3 72,958,118 (GRCm39) missense probably damaging 1.00
R4580:Slitrk3 UTSW 3 72,958,539 (GRCm39) missense probably damaging 0.96
R4730:Slitrk3 UTSW 3 72,956,852 (GRCm39) missense probably benign 0.08
R4742:Slitrk3 UTSW 3 72,955,898 (GRCm39) missense probably benign 0.00
R4979:Slitrk3 UTSW 3 72,957,129 (GRCm39) missense possibly damaging 0.95
R5018:Slitrk3 UTSW 3 72,957,845 (GRCm39) missense probably benign 0.31
R5023:Slitrk3 UTSW 3 72,957,981 (GRCm39) missense probably benign 0.24
R5057:Slitrk3 UTSW 3 72,957,981 (GRCm39) missense probably benign 0.24
R5156:Slitrk3 UTSW 3 72,956,592 (GRCm39) missense probably benign
R5500:Slitrk3 UTSW 3 72,957,680 (GRCm39) missense probably damaging 1.00
R5582:Slitrk3 UTSW 3 72,957,737 (GRCm39) missense probably benign 0.09
R5797:Slitrk3 UTSW 3 72,955,962 (GRCm39) missense probably damaging 0.99
R5963:Slitrk3 UTSW 3 72,958,046 (GRCm39) missense probably benign 0.30
R5985:Slitrk3 UTSW 3 72,958,233 (GRCm39) missense probably damaging 1.00
R6123:Slitrk3 UTSW 3 72,957,095 (GRCm39) missense probably damaging 1.00
R6393:Slitrk3 UTSW 3 72,957,247 (GRCm39) missense possibly damaging 0.79
R6529:Slitrk3 UTSW 3 72,958,551 (GRCm39) missense probably benign 0.02
R6584:Slitrk3 UTSW 3 72,956,558 (GRCm39) missense probably damaging 0.99
R6645:Slitrk3 UTSW 3 72,957,194 (GRCm39) missense probably benign 0.13
R7001:Slitrk3 UTSW 3 72,957,942 (GRCm39) nonsense probably null
R7282:Slitrk3 UTSW 3 72,957,798 (GRCm39) missense possibly damaging 0.70
R7534:Slitrk3 UTSW 3 72,957,440 (GRCm39) missense probably damaging 0.98
R7577:Slitrk3 UTSW 3 72,958,448 (GRCm39) missense probably damaging 0.99
R7757:Slitrk3 UTSW 3 72,958,172 (GRCm39) missense probably damaging 1.00
R8251:Slitrk3 UTSW 3 72,956,729 (GRCm39) missense possibly damaging 0.67
R8354:Slitrk3 UTSW 3 72,956,513 (GRCm39) missense probably benign 0.08
R8454:Slitrk3 UTSW 3 72,956,513 (GRCm39) missense probably benign 0.08
R8488:Slitrk3 UTSW 3 72,958,520 (GRCm39) missense probably benign 0.02
R8491:Slitrk3 UTSW 3 72,958,592 (GRCm39) missense possibly damaging 0.89
R8843:Slitrk3 UTSW 3 72,956,164 (GRCm39) missense probably benign 0.04
R9140:Slitrk3 UTSW 3 72,957,792 (GRCm39) missense probably benign 0.02
R9451:Slitrk3 UTSW 3 72,958,616 (GRCm39) missense possibly damaging 0.83
R9511:Slitrk3 UTSW 3 72,958,272 (GRCm39) missense possibly damaging 0.46
R9575:Slitrk3 UTSW 3 72,956,127 (GRCm39) missense probably benign 0.00
R9589:Slitrk3 UTSW 3 72,957,981 (GRCm39) missense probably benign 0.24
R9603:Slitrk3 UTSW 3 72,958,649 (GRCm39) missense probably benign 0.00
X0022:Slitrk3 UTSW 3 72,957,599 (GRCm39) missense probably damaging 1.00
Z1176:Slitrk3 UTSW 3 72,956,103 (GRCm39) missense probably benign 0.09
Z1177:Slitrk3 UTSW 3 72,956,475 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- ATGGTCCAGGTTGGGCAATATG -3'
(R):5'- TCAACGTCATCCGGGAAATC -3'

Sequencing Primer
(F):5'- AATATGCAGCATCTCTGGGC -3'
(R):5'- GTCATCCGGGAAATCCAACCTG -3'
Posted On 2014-08-25