Incidental Mutation 'R1743:Lrrc9'
ID 200531
Institutional Source Beutler Lab
Gene Symbol Lrrc9
Ensembl Gene ENSMUSG00000021090
Gene Name leucine rich repeat containing 9
Synonyms 4921529O18Rik, 4930432K16Rik
MMRRC Submission 039775-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.154) question?
Stock # R1743 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 72481391-72561269 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 72502891 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Phenylalanine at position 287 (L287F)
Ref Sequence ENSEMBL: ENSMUSP00000152125 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000161284] [ENSMUST00000162159] [ENSMUST00000221360]
AlphaFold Q8CDN9
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160394
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161195
Predicted Effect probably benign
Transcript: ENSMUST00000161284
AA Change: L287F

PolyPhen 2 Score 0.169 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000124602
Gene: ENSMUSG00000021090
AA Change: L287F

DomainStartEndE-ValueType
Pfam:LRR_4 77 118 2.8e-11 PFAM
LRR 119 140 8.49e1 SMART
LRR 141 164 2.27e1 SMART
LRR 165 187 2.09e2 SMART
LRRcap 210 228 6.12e1 SMART
low complexity region 373 384 N/A INTRINSIC
low complexity region 424 436 N/A INTRINSIC
LRR 706 727 1.41e2 SMART
LRR 728 749 6.78e1 SMART
LRR 750 773 7.17e1 SMART
LRRcap 793 811 2.26e2 SMART
LRR 943 966 2.67e-1 SMART
LRR 967 992 1.22e1 SMART
LRRcap 1031 1049 4.37e0 SMART
low complexity region 1109 1120 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161957
Predicted Effect possibly damaging
Transcript: ENSMUST00000162159
AA Change: L287F

PolyPhen 2 Score 0.796 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000124394
Gene: ENSMUSG00000021090
AA Change: L287F

DomainStartEndE-ValueType
LRR 53 74 5.39e2 SMART
LRR 75 96 1.14e2 SMART
LRR 97 118 7.9e-4 SMART
LRR 119 140 2.75e-3 SMART
LRR 141 164 2.27e1 SMART
LRR 164 185 1.87e1 SMART
LRRcap 210 228 6.12e1 SMART
low complexity region 373 384 N/A INTRINSIC
low complexity region 424 436 N/A INTRINSIC
LRR 705 726 1.41e2 SMART
LRR 727 748 6.78e1 SMART
LRR 749 771 1.37e1 SMART
LRRcap 792 810 2.26e2 SMART
LRR 898 919 2.62e1 SMART
LRR 920 941 5.17e1 SMART
LRR 942 965 2.67e-1 SMART
LRR 966 991 1.22e1 SMART
LRR 1013 1032 4.42e2 SMART
LRRcap 1030 1048 4.37e0 SMART
low complexity region 1108 1119 N/A INTRINSIC
LRR 1128 1150 2.4e1 SMART
LRR 1191 1209 5.7e2 SMART
LRR 1215 1236 1.03e-2 SMART
LRR 1237 1260 8.48e0 SMART
LRR 1283 1304 2.67e-1 SMART
Blast:LRR 1308 1333 4e-6 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162179
Predicted Effect probably damaging
Transcript: ENSMUST00000221360
AA Change: L287F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.1%
  • 20x: 91.7%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aff4 T A 11: 53,259,522 (GRCm39) M11K possibly damaging Het
Ank2 T C 3: 126,722,324 (GRCm39) D88G probably damaging Het
Arhgap32 A G 9: 32,170,727 (GRCm39) E1169G probably benign Het
Atp7b A T 8: 22,496,403 (GRCm39) V865E probably damaging Het
Bcl2l13 T A 6: 120,825,504 (GRCm39) Y13* probably null Het
Birc6 A G 17: 74,886,751 (GRCm39) Q693R possibly damaging Het
Bub1 T C 2: 127,655,770 (GRCm39) D520G probably damaging Het
Ccdc15 A T 9: 37,188,773 (GRCm39) Y770* probably null Het
Cenpf T C 1: 189,386,460 (GRCm39) E1940G probably benign Het
Cep295 C T 9: 15,252,179 (GRCm39) E397K probably damaging Het
Cmya5 A G 13: 93,233,825 (GRCm39) V421A probably benign Het
Cnnm1 A T 19: 43,460,352 (GRCm39) Y698F possibly damaging Het
Cnst C T 1: 179,437,957 (GRCm39) T507I probably benign Het
Coq8a T C 1: 180,009,794 (GRCm39) M4V probably benign Het
Csmd3 A G 15: 48,485,485 (GRCm39) L140P probably damaging Het
Cul2 A T 18: 3,426,851 (GRCm39) I431F probably damaging Het
Dnah8 G T 17: 30,988,625 (GRCm39) E3198D probably benign Het
Dnai3 C A 3: 145,803,017 (GRCm39) R58L possibly damaging Het
Epn2 T A 11: 61,437,237 (GRCm39) I112F possibly damaging Het
Ext2 T C 2: 93,560,570 (GRCm39) E532G probably damaging Het
Fndc3a A T 14: 72,889,521 (GRCm39) V37E probably damaging Het
Gabbr2 A G 4: 46,677,603 (GRCm39) F759S possibly damaging Het
Ghr G A 15: 3,349,723 (GRCm39) P485L probably benign Het
Glipr1l2 G T 10: 111,928,470 (GRCm39) V122L probably benign Het
Gm10608 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 9: 118,989,784 (GRCm39) probably benign Het
Gm6871 G T 7: 41,195,876 (GRCm39) T287K probably damaging Het
Gm7275 A G 16: 47,894,120 (GRCm39) noncoding transcript Het
Hephl1 C T 9: 15,001,364 (GRCm39) V254I probably damaging Het
Hnf4a C A 2: 163,408,259 (GRCm39) Q362K possibly damaging Het
Kcne3 C T 7: 99,833,631 (GRCm39) R83C probably damaging Het
Klb C A 5: 65,533,204 (GRCm39) N504K probably damaging Het
Loxl2 T A 14: 69,929,851 (GRCm39) I743N possibly damaging Het
Mcm3ap C T 10: 76,320,508 (GRCm39) P822L possibly damaging Het
Nacc2 T C 2: 25,950,155 (GRCm39) N527S probably benign Het
Ncam1 G T 9: 49,468,445 (GRCm39) P338H probably damaging Het
Nfkbiz G T 16: 55,636,757 (GRCm39) Q515K possibly damaging Het
Nipsnap2 T C 5: 129,834,149 (GRCm39) L263P probably damaging Het
Nlrp1a A T 11: 71,015,032 (GRCm39) S73T probably benign Het
Nomo1 G A 7: 45,719,461 (GRCm39) probably null Het
Nos3 G A 5: 24,582,310 (GRCm39) G594D probably benign Het
Oprm1 A G 10: 6,780,105 (GRCm39) I256V probably damaging Het
Or10ak16 A G 4: 118,750,723 (GRCm39) T148A probably benign Het
Or10n1 A T 9: 39,524,916 (GRCm39) T18S possibly damaging Het
Or2b2 A G 13: 21,887,620 (GRCm39) I150V probably benign Het
Oxct2a A T 4: 123,217,309 (GRCm39) L24Q possibly damaging Het
Pcdhb14 T G 18: 37,581,231 (GRCm39) S112R probably benign Het
Polr2a A G 11: 69,630,329 (GRCm39) I1246T probably damaging Het
Ppil4 A T 10: 7,683,145 (GRCm39) K327N probably damaging Het
Pramel30 T C 4: 144,059,575 (GRCm39) S429P probably benign Het
Pstpip1 T C 9: 56,033,214 (GRCm39) Y249H probably damaging Het
Qrsl1 A T 10: 43,757,511 (GRCm39) V369E probably damaging Het
Ranbp10 G T 8: 106,506,610 (GRCm39) P237T probably damaging Het
Rapgef6 A G 11: 54,567,110 (GRCm39) N1097S probably damaging Het
Repin1 T A 6: 48,574,684 (GRCm39) S538T probably damaging Het
Rims2 A T 15: 39,543,046 (GRCm39) M1151L probably benign Het
Rin3 T A 12: 102,356,355 (GRCm39) D965E possibly damaging Het
Sdc2 A G 15: 33,028,224 (GRCm39) D114G probably benign Het
Slc25a30 C A 14: 76,012,523 (GRCm39) A42S probably benign Het
Sphkap G A 1: 83,255,236 (GRCm39) R838* probably null Het
Ssh2 T A 11: 77,328,582 (GRCm39) F383I probably damaging Het
St8sia1 A T 6: 142,774,742 (GRCm39) V279E probably damaging Het
Tacc2 C A 7: 130,228,328 (GRCm39) S1690* probably null Het
Taf1b A G 12: 24,597,177 (GRCm39) D372G possibly damaging Het
Timm21 G C 18: 84,967,387 (GRCm39) L130V probably damaging Het
Tmem165 G T 5: 76,355,673 (GRCm39) G272C probably damaging Het
Tsc22d2 TCAGTTAACACCTATGAACAGT TCAGT 3: 58,324,960 (GRCm39) probably null Het
Tssk4 C A 14: 55,888,488 (GRCm39) A119D probably damaging Het
Usp9y A G Y: 1,316,727 (GRCm39) Y1941H probably damaging Het
Vmn2r42 A T 7: 8,187,264 (GRCm39) M786K probably benign Het
Wdfy3 G T 5: 101,991,931 (GRCm39) T3470K probably benign Het
Zc3h14 T C 12: 98,745,448 (GRCm39) V479A probably benign Het
Zfp821 G A 8: 110,450,796 (GRCm39) R263Q probably damaging Het
Other mutations in Lrrc9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00092:Lrrc9 APN 12 72,533,017 (GRCm39) missense possibly damaging 0.63
IGL00843:Lrrc9 APN 12 72,510,191 (GRCm39) missense possibly damaging 0.78
IGL01923:Lrrc9 APN 12 72,557,186 (GRCm39) missense possibly damaging 0.93
IGL02027:Lrrc9 APN 12 72,517,108 (GRCm39) splice site probably benign
IGL02271:Lrrc9 APN 12 72,557,155 (GRCm39) missense probably benign 0.06
IGL02398:Lrrc9 APN 12 72,513,677 (GRCm39) missense probably benign
IGL02795:Lrrc9 APN 12 72,525,542 (GRCm39) missense probably damaging 1.00
IGL02931:Lrrc9 APN 12 72,500,923 (GRCm39) missense probably damaging 1.00
IGL03257:Lrrc9 APN 12 72,496,542 (GRCm39) missense probably benign
BB006:Lrrc9 UTSW 12 72,533,071 (GRCm39) missense possibly damaging 0.92
BB016:Lrrc9 UTSW 12 72,533,071 (GRCm39) missense possibly damaging 0.92
IGL02799:Lrrc9 UTSW 12 72,553,178 (GRCm39) missense probably damaging 1.00
R0172:Lrrc9 UTSW 12 72,510,260 (GRCm39) missense possibly damaging 0.50
R0315:Lrrc9 UTSW 12 72,502,802 (GRCm39) missense probably damaging 0.96
R0492:Lrrc9 UTSW 12 72,525,537 (GRCm39) missense possibly damaging 0.47
R0617:Lrrc9 UTSW 12 72,529,788 (GRCm39) missense probably damaging 1.00
R0639:Lrrc9 UTSW 12 72,533,062 (GRCm39) missense probably damaging 1.00
R0987:Lrrc9 UTSW 12 72,557,156 (GRCm39) missense probably benign 0.00
R1325:Lrrc9 UTSW 12 72,543,878 (GRCm39) missense probably damaging 0.99
R1465:Lrrc9 UTSW 12 72,547,533 (GRCm39) missense probably benign 0.05
R1465:Lrrc9 UTSW 12 72,547,533 (GRCm39) missense probably benign 0.05
R1479:Lrrc9 UTSW 12 72,507,599 (GRCm39) nonsense probably null
R1564:Lrrc9 UTSW 12 72,533,827 (GRCm39) missense probably damaging 1.00
R1626:Lrrc9 UTSW 12 72,542,435 (GRCm39) splice site probably null
R1632:Lrrc9 UTSW 12 72,506,794 (GRCm39) splice site probably null
R1715:Lrrc9 UTSW 12 72,524,073 (GRCm39) missense probably damaging 1.00
R1779:Lrrc9 UTSW 12 72,502,772 (GRCm39) nonsense probably null
R1866:Lrrc9 UTSW 12 72,543,912 (GRCm39) missense probably damaging 0.97
R1878:Lrrc9 UTSW 12 72,522,938 (GRCm39) critical splice donor site probably null
R1990:Lrrc9 UTSW 12 72,544,635 (GRCm39) missense probably damaging 0.99
R2361:Lrrc9 UTSW 12 72,510,244 (GRCm39) missense possibly damaging 0.52
R3752:Lrrc9 UTSW 12 72,507,580 (GRCm39) nonsense probably null
R3833:Lrrc9 UTSW 12 72,529,765 (GRCm39) missense probably damaging 1.00
R4134:Lrrc9 UTSW 12 72,513,740 (GRCm39) missense probably benign 0.00
R4651:Lrrc9 UTSW 12 72,524,160 (GRCm39) missense probably damaging 1.00
R4652:Lrrc9 UTSW 12 72,524,160 (GRCm39) missense probably damaging 1.00
R4659:Lrrc9 UTSW 12 72,517,038 (GRCm39) missense probably damaging 1.00
R4831:Lrrc9 UTSW 12 72,546,453 (GRCm39) missense probably damaging 1.00
R4857:Lrrc9 UTSW 12 72,546,466 (GRCm39) missense possibly damaging 0.94
R5017:Lrrc9 UTSW 12 72,553,099 (GRCm39) missense possibly damaging 0.86
R5163:Lrrc9 UTSW 12 72,496,163 (GRCm39) missense probably damaging 1.00
R5279:Lrrc9 UTSW 12 72,542,368 (GRCm39) missense possibly damaging 0.80
R5434:Lrrc9 UTSW 12 72,500,862 (GRCm39) missense probably damaging 0.98
R5783:Lrrc9 UTSW 12 72,502,827 (GRCm39) missense possibly damaging 0.62
R6021:Lrrc9 UTSW 12 72,516,005 (GRCm39) missense probably damaging 0.97
R6214:Lrrc9 UTSW 12 72,506,627 (GRCm39) missense probably damaging 1.00
R6255:Lrrc9 UTSW 12 72,533,797 (GRCm39) missense probably benign 0.33
R6538:Lrrc9 UTSW 12 72,547,703 (GRCm39) missense probably benign 0.08
R6563:Lrrc9 UTSW 12 72,533,169 (GRCm39) splice site probably null
R6672:Lrrc9 UTSW 12 72,520,710 (GRCm39) missense possibly damaging 0.88
R6919:Lrrc9 UTSW 12 72,553,167 (GRCm39) missense probably benign 0.01
R6929:Lrrc9 UTSW 12 72,497,546 (GRCm39) missense probably benign 0.41
R7092:Lrrc9 UTSW 12 72,510,238 (GRCm39) missense possibly damaging 0.81
R7150:Lrrc9 UTSW 12 72,513,726 (GRCm39) missense probably benign 0.00
R7338:Lrrc9 UTSW 12 72,510,305 (GRCm39) splice site probably null
R7398:Lrrc9 UTSW 12 72,547,590 (GRCm39) missense probably damaging 0.98
R7477:Lrrc9 UTSW 12 72,550,301 (GRCm39) critical splice donor site probably null
R7501:Lrrc9 UTSW 12 72,496,490 (GRCm39) missense probably damaging 1.00
R7542:Lrrc9 UTSW 12 72,553,094 (GRCm39) missense probably damaging 0.96
R7816:Lrrc9 UTSW 12 72,542,466 (GRCm39) missense probably damaging 1.00
R7870:Lrrc9 UTSW 12 72,532,964 (GRCm39) missense probably damaging 0.99
R7929:Lrrc9 UTSW 12 72,533,071 (GRCm39) missense possibly damaging 0.92
R8042:Lrrc9 UTSW 12 72,507,680 (GRCm39) missense probably benign 0.02
R8108:Lrrc9 UTSW 12 72,500,833 (GRCm39) missense probably damaging 1.00
R8192:Lrrc9 UTSW 12 72,496,163 (GRCm39) missense probably damaging 1.00
R8244:Lrrc9 UTSW 12 72,546,384 (GRCm39) missense probably benign 0.22
R8333:Lrrc9 UTSW 12 72,528,317 (GRCm39) missense probably benign 0.38
R9288:Lrrc9 UTSW 12 72,522,858 (GRCm39) missense probably benign 0.01
R9324:Lrrc9 UTSW 12 72,496,171 (GRCm39) missense probably damaging 1.00
R9342:Lrrc9 UTSW 12 72,506,767 (GRCm39) missense probably damaging 1.00
R9557:Lrrc9 UTSW 12 72,532,981 (GRCm39) missense probably benign 0.01
R9624:Lrrc9 UTSW 12 72,497,586 (GRCm39) missense probably benign 0.19
R9677:Lrrc9 UTSW 12 72,497,539 (GRCm39) missense probably damaging 1.00
X0025:Lrrc9 UTSW 12 72,543,834 (GRCm39) missense probably damaging 1.00
Z1176:Lrrc9 UTSW 12 72,524,167 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCCTTTACCTTCAGTCCACAGCAATGA -3'
(R):5'- TAGTCCGCCTTGTCTGCGACAGAG -3'

Sequencing Primer
(F):5'- AGTCCACAGCAATGAAAAAAATAATG -3'
(R):5'- ctgtctctgcttcccagtc -3'
Posted On 2014-05-23