Incidental Mutation 'R5434:Lrrc9'
ID 428223
Institutional Source Beutler Lab
Gene Symbol Lrrc9
Ensembl Gene ENSMUSG00000021090
Gene Name leucine rich repeat containing 9
Synonyms 4921529O18Rik, 4930432K16Rik
MMRRC Submission 042999-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.209) question?
Stock # R5434 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 72481391-72561269 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 72500862 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Tyrosine at position 196 (C196Y)
Ref Sequence ENSEMBL: ENSMUSP00000124394 (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: C196Y

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000124602
Gene: ENSMUSG00000021090
AA Change: C196Y

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 probably damaging
Transcript: ENSMUST00000162159
AA Change: C196Y

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000124394
Gene: ENSMUSG00000021090
AA Change: C196Y

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: C196Y

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)
Meta Mutation Damage Score 0.0714 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
Validation Efficiency 100% (57/57)
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Angptl6 G T 9: 20,786,821 (GRCm39) Q301K probably damaging Het
Ankfn1 T C 11: 89,344,013 (GRCm39) Y323C probably damaging Het
Arid5b T A 10: 67,932,719 (GRCm39) H818L possibly damaging Het
Atg13 G T 2: 91,515,110 (GRCm39) probably null Het
Bltp1 A C 3: 36,929,665 (GRCm39) D94A probably damaging Het
Bop1 T C 15: 76,339,611 (GRCm39) M245V probably benign Het
Ces2a T A 8: 105,464,041 (GRCm39) F224L probably damaging Het
Cntnap5b A G 1: 99,999,926 (GRCm39) H228R probably benign Het
Col9a2 A T 4: 120,898,162 (GRCm39) R25* probably null Het
Dcaf12 G T 4: 41,302,744 (GRCm39) T137N probably benign Het
Dennd4c A G 4: 86,729,693 (GRCm39) N765S probably benign Het
Dnah12 A G 14: 26,581,256 (GRCm39) Y3162C probably damaging Het
Dpf1 G T 7: 29,010,756 (GRCm39) C123F possibly damaging Het
Flvcr1 C A 1: 190,758,206 (GRCm39) A29S probably benign Het
Frmd3 A T 4: 74,106,033 (GRCm39) I560F probably damaging Het
Galnt15 G A 14: 31,771,800 (GRCm39) V282I possibly damaging Het
Gm14412 A T 2: 177,006,405 (GRCm39) C497S probably damaging Het
Gm20830 A T Y: 6,916,464 (GRCm39) Y218* probably null Het
Hmcn2 C A 2: 31,310,375 (GRCm39) T3323N probably damaging Het
Idh1 T A 1: 65,214,495 (GRCm39) Q6L probably benign Het
Kansl2-ps A G 7: 72,322,813 (GRCm39) noncoding transcript Het
Kcnj10 T A 1: 172,197,047 (GRCm39) V187E probably damaging Het
Khnyn A G 14: 56,124,957 (GRCm39) T404A probably damaging Het
Lrp1b T A 2: 41,660,880 (GRCm39) N76I probably damaging Het
Ltbr G A 6: 125,289,757 (GRCm39) R146W probably damaging Het
Mgp T A 6: 136,849,772 (GRCm39) N62I probably benign Het
Ms4a6c T A 19: 11,448,588 (GRCm39) H40Q probably benign Het
Necab3 A G 2: 154,389,379 (GRCm39) S121P probably damaging Het
Nfkb1 T A 3: 135,332,372 (GRCm39) K128* probably null Het
Nr4a3 A T 4: 48,067,861 (GRCm39) R486W probably damaging Het
Nwd2 A G 5: 63,964,991 (GRCm39) K1525R probably benign Het
Odad2 T C 18: 7,222,550 (GRCm39) K573R probably benign Het
Pbrm1 G T 14: 30,806,968 (GRCm39) D1085Y probably damaging Het
R3hdm4 C T 10: 79,748,292 (GRCm39) E162K possibly damaging Het
Rbm15 A G 3: 107,237,783 (GRCm39) S872P possibly damaging Het
Retsat A G 6: 72,578,518 (GRCm39) I77V probably damaging Het
Rpl32 A G 6: 115,783,996 (GRCm39) F77L probably benign Het
Ryr3 A T 2: 112,624,814 (GRCm39) V2202D probably damaging Het
Sars2 G A 7: 28,449,716 (GRCm39) R387Q probably null Het
Serpinb3d G T 1: 107,006,263 (GRCm39) T275N probably benign Het
Sf3a1 C A 11: 4,124,041 (GRCm39) P296Q probably damaging Het
Sh3bgr A G 16: 96,025,744 (GRCm39) probably benign Het
St3gal3 A G 4: 117,797,247 (GRCm39) L332P probably damaging Het
Ston1 A G 17: 88,952,739 (GRCm39) probably benign Het
Syne2 T A 12: 76,018,649 (GRCm39) S3383T probably damaging Het
Tektl1 A T 10: 78,584,484 (GRCm39) L346* probably null Het
Tnfsf14 A G 17: 57,499,592 (GRCm39) S87P probably benign Het
Trap1 T C 16: 3,862,529 (GRCm39) D583G probably benign Het
Ube3d A T 9: 86,309,460 (GRCm39) I212N possibly damaging Het
Usp34 T A 11: 23,362,271 (GRCm39) D1572E probably damaging Het
Vmn1r179 A T 7: 23,628,387 (GRCm39) T193S probably benign Het
Vmn2r111 C A 17: 22,767,470 (GRCm39) V676L probably damaging Het
Wee1 TCCCC TCCC 7: 109,723,776 (GRCm39) probably null Het
Wls C T 3: 159,639,976 (GRCm39) R536C probably damaging Het
Zfhx3 A G 8: 109,519,031 (GRCm39) D51G 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
R1743:Lrrc9 UTSW 12 72,502,891 (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
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'- TCACTGTAGCACGCGTACTC -3'
(R):5'- CTGTGTCTTAACAGCCACATGAG -3'

Sequencing Primer
(F):5'- TAGCACGCGTACTCAGGAGTG -3'
(R):5'- TTAACTATGCAAACTCGAGTCACAG -3'
Posted On 2016-09-01