Incidental Mutation 'R6675:Lrig2'
ID 527239
Institutional Source Beutler Lab
Gene Symbol Lrig2
Ensembl Gene ENSMUSG00000032913
Gene Name leucine-rich repeats and immunoglobulin-like domains 2
Synonyms 4632419I10Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6675 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 104361296-104419251 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 104365251 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 634 (N634D)
Ref Sequence ENSEMBL: ENSMUSP00000142373 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046316] [ENSMUST00000198332] [ENSMUST00000199070]
AlphaFold Q52KR2
Predicted Effect probably benign
Transcript: ENSMUST00000046316
AA Change: N999D

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000035999
Gene: ENSMUSG00000032913
AA Change: N999D

DomainStartEndE-ValueType
signal peptide 1 39 N/A INTRINSIC
low complexity region 68 82 N/A INTRINSIC
LRR 118 141 3.56e2 SMART
LRR 142 165 1.81e2 SMART
LRR 167 188 1.31e0 SMART
LRR 213 236 1.41e0 SMART
LRR 237 260 4.98e-1 SMART
LRR 261 284 1.49e1 SMART
LRR 285 308 1.62e0 SMART
LRR 309 332 2.14e0 SMART
LRR_TYP 333 356 2.2e-2 SMART
LRR 357 383 9.22e0 SMART
LRR 384 407 2.17e-1 SMART
LRR_TYP 408 431 3.95e-4 SMART
LRRCT 442 492 3.62e-8 SMART
IG 503 598 2.19e-9 SMART
IGc2 613 681 1.94e-10 SMART
IGc2 707 772 3.2e-11 SMART
transmembrane domain 805 827 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196518
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197018
Predicted Effect probably benign
Transcript: ENSMUST00000198332
AA Change: N992D

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000142540
Gene: ENSMUSG00000032913
AA Change: N992D

DomainStartEndE-ValueType
signal peptide 1 39 N/A INTRINSIC
low complexity region 68 82 N/A INTRINSIC
LRR 118 141 3.56e2 SMART
LRR 142 165 1.81e2 SMART
LRR 167 188 1.31e0 SMART
LRR 213 236 1.41e0 SMART
LRR 237 260 4.98e-1 SMART
LRR 261 284 1.49e1 SMART
LRR 285 308 1.62e0 SMART
LRR 309 332 2.14e0 SMART
LRR_TYP 333 356 2.2e-2 SMART
LRR 357 383 9.22e0 SMART
LRR 384 407 2.17e-1 SMART
LRR_TYP 408 431 3.95e-4 SMART
LRRCT 442 492 3.62e-8 SMART
IG 503 598 2.19e-9 SMART
IGc2 613 681 1.94e-10 SMART
IGc2 707 772 3.2e-11 SMART
transmembrane domain 805 827 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000199070
AA Change: N634D

PolyPhen 2 Score 0.349 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000142373
Gene: ENSMUSG00000032913
AA Change: N634D

DomainStartEndE-ValueType
signal peptide 1 39 N/A INTRINSIC
LRRCT 84 134 1.8e-10 SMART
IG 145 240 9.2e-12 SMART
IGc2 255 323 8.1e-13 SMART
IGc2 349 414 1.3e-13 SMART
transmembrane domain 447 469 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000199180
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200453
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 95.3%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transmembrane protein containing leucine-rich repeats and immunoglobulin-like domains. The encoded protein promotes epidermal growth factor signalling, resulting in increased proliferation. Its expression in the cytoplasm of glioma cells is correlated with poor survival. Mutations in this gene can cause urofacial syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced susceptibility to PDGFB-induced glioma and premature death due to illness with reduced body weight, letahrgy, hackled fur, crouched posture and increased inflammatory response. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca9 T C 11: 110,006,302 (GRCm39) T1268A probably benign Het
Adamts20 A G 15: 94,229,197 (GRCm39) probably null Het
Arhgap45 G T 10: 79,853,938 (GRCm39) D151Y probably null Het
Arhgef40 C A 14: 52,229,098 (GRCm39) L592I probably damaging Het
Ascc3 G T 10: 50,626,659 (GRCm39) E1720* probably null Het
Atp2c1 C T 9: 105,330,732 (GRCm39) probably null Het
Avpi1 G A 19: 42,112,183 (GRCm39) P125L probably benign Het
Cers3 A T 7: 66,435,844 (GRCm39) T232S possibly damaging Het
Cfap53 T C 18: 74,440,447 (GRCm39) probably null Het
Col4a3 T C 1: 82,646,646 (GRCm39) S386P unknown Het
Dhtkd1 A T 2: 5,908,889 (GRCm39) M735K probably damaging Het
Dnah8 G A 17: 30,967,542 (GRCm39) D2585N probably benign Het
Gad2 T C 2: 22,563,997 (GRCm39) V400A possibly damaging Het
Gm10801 TC TCGCC 2: 98,494,151 (GRCm39) probably benign Het
Hmgxb3 T G 18: 61,270,648 (GRCm39) D892A possibly damaging Het
Hsd3b2 G A 3: 98,620,788 (GRCm39) T89I probably benign Het
Iars1 C A 13: 49,873,054 (GRCm39) A713D probably damaging Het
Itih1 G A 14: 30,651,798 (GRCm39) T848I possibly damaging Het
Kcne2 A G 16: 92,093,512 (GRCm39) D13G probably benign Het
Klra17 T A 6: 129,849,286 (GRCm39) N96I probably damaging Het
Mrc2 T A 11: 105,233,906 (GRCm39) probably null Het
Mroh3 A T 1: 136,118,550 (GRCm39) S558T possibly damaging Het
Ncapg2 G T 12: 116,398,281 (GRCm39) K627N possibly damaging Het
Ncstn A T 1: 171,899,095 (GRCm39) D345E probably damaging Het
Nkx1-1 G T 5: 33,591,223 (GRCm39) A33E unknown Het
Or2n1 T A 17: 38,486,905 (GRCm39) M310K probably benign Het
Or51f2 A G 7: 102,526,480 (GRCm39) E51G possibly damaging Het
Osbpl9 G T 4: 108,991,025 (GRCm39) probably null Het
P2rx6 T C 16: 17,380,032 (GRCm39) V52A probably benign Het
Pcdhgb5 C T 18: 37,864,255 (GRCm39) L17F probably damaging Het
Pdk2 T C 11: 94,919,568 (GRCm39) I273V probably benign Het
Pdpr C T 8: 111,828,532 (GRCm39) Q12* probably null Het
Plxdc2 A G 2: 16,716,932 (GRCm39) T339A probably benign Het
Pramel27 G A 4: 143,579,828 (GRCm39) C471Y probably damaging Het
Retsat T C 6: 72,578,672 (GRCm39) V128A probably benign Het
Rnf17 A G 14: 56,697,432 (GRCm39) E442G probably damaging Het
Sec31b T C 19: 44,512,214 (GRCm39) N560S probably benign Het
Slc22a16 C T 10: 40,449,836 (GRCm39) Q91* probably null Het
Slc24a5 G T 2: 124,922,615 (GRCm39) A126S possibly damaging Het
Slc26a4 A T 12: 31,590,512 (GRCm39) D380E possibly damaging Het
Stc2 T A 11: 31,310,307 (GRCm39) D243V probably benign Het
Tshz2 G T 2: 169,727,965 (GRCm39) A385S probably damaging Het
Vmn1r113 G A 7: 20,521,903 (GRCm39) G232S probably benign Het
Vmn1r77 A G 7: 11,775,382 (GRCm39) T53A probably damaging Het
Zeb2 A T 2: 44,887,457 (GRCm39) Y518* probably null Het
Zfp760 T A 17: 21,941,991 (GRCm39) S389T possibly damaging Het
Other mutations in Lrig2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00657:Lrig2 APN 3 104,374,487 (GRCm39) missense probably damaging 0.99
IGL00715:Lrig2 APN 3 104,371,264 (GRCm39) missense probably damaging 1.00
IGL01105:Lrig2 APN 3 104,371,484 (GRCm39) nonsense probably null
IGL01767:Lrig2 APN 3 104,398,861 (GRCm39) missense probably benign 0.12
IGL02080:Lrig2 APN 3 104,371,440 (GRCm39) missense probably damaging 1.00
IGL02088:Lrig2 APN 3 104,374,424 (GRCm39) missense probably damaging 1.00
IGL02967:Lrig2 APN 3 104,401,512 (GRCm39) intron probably benign
IGL03024:Lrig2 APN 3 104,401,389 (GRCm39) missense probably damaging 1.00
IGL03079:Lrig2 APN 3 104,398,287 (GRCm39) missense probably damaging 0.98
IGL03085:Lrig2 APN 3 104,374,575 (GRCm39) missense probably damaging 1.00
IGL03162:Lrig2 APN 3 104,371,613 (GRCm39) missense probably damaging 1.00
Belladonna UTSW 3 104,374,682 (GRCm39) splice site probably benign
R0414:Lrig2 UTSW 3 104,401,372 (GRCm39) critical splice donor site probably null
R0866:Lrig2 UTSW 3 104,371,591 (GRCm39) missense probably benign 0.00
R1184:Lrig2 UTSW 3 104,398,227 (GRCm39) missense possibly damaging 0.94
R1524:Lrig2 UTSW 3 104,371,192 (GRCm39) missense probably benign 0.38
R1606:Lrig2 UTSW 3 104,387,423 (GRCm39) critical splice donor site probably null
R1672:Lrig2 UTSW 3 104,399,128 (GRCm39) missense probably damaging 1.00
R1701:Lrig2 UTSW 3 104,401,993 (GRCm39) missense probably benign 0.02
R1778:Lrig2 UTSW 3 104,374,682 (GRCm39) splice site probably benign
R2034:Lrig2 UTSW 3 104,401,408 (GRCm39) missense probably benign
R2100:Lrig2 UTSW 3 104,418,946 (GRCm39) missense possibly damaging 0.76
R2186:Lrig2 UTSW 3 104,375,914 (GRCm39) missense probably benign 0.00
R3778:Lrig2 UTSW 3 104,365,277 (GRCm39) missense probably benign
R3977:Lrig2 UTSW 3 104,365,160 (GRCm39) missense probably damaging 1.00
R4119:Lrig2 UTSW 3 104,374,511 (GRCm39) missense probably benign 0.00
R4210:Lrig2 UTSW 3 104,374,620 (GRCm39) missense probably benign 0.00
R4612:Lrig2 UTSW 3 104,370,099 (GRCm39) missense probably damaging 1.00
R4872:Lrig2 UTSW 3 104,398,842 (GRCm39) missense possibly damaging 0.66
R5020:Lrig2 UTSW 3 104,365,217 (GRCm39) missense possibly damaging 0.71
R5499:Lrig2 UTSW 3 104,368,873 (GRCm39) missense probably benign 0.00
R5687:Lrig2 UTSW 3 104,371,388 (GRCm39) splice site probably null
R5718:Lrig2 UTSW 3 104,375,931 (GRCm39) nonsense probably null
R5886:Lrig2 UTSW 3 104,370,014 (GRCm39) missense probably benign 0.01
R5921:Lrig2 UTSW 3 104,370,070 (GRCm39) nonsense probably null
R6434:Lrig2 UTSW 3 104,398,863 (GRCm39) missense possibly damaging 0.91
R6468:Lrig2 UTSW 3 104,374,509 (GRCm39) missense probably damaging 1.00
R6513:Lrig2 UTSW 3 104,373,045 (GRCm39) missense probably damaging 1.00
R7243:Lrig2 UTSW 3 104,404,883 (GRCm39) splice site probably null
R7395:Lrig2 UTSW 3 104,404,836 (GRCm39) missense probably benign 0.00
R7444:Lrig2 UTSW 3 104,404,829 (GRCm39) nonsense probably null
R7514:Lrig2 UTSW 3 104,373,076 (GRCm39) missense probably damaging 1.00
R7751:Lrig2 UTSW 3 104,401,985 (GRCm39) nonsense probably null
R8720:Lrig2 UTSW 3 104,418,998 (GRCm39) missense probably damaging 0.99
R8809:Lrig2 UTSW 3 104,368,993 (GRCm39) missense probably benign 0.00
R9019:Lrig2 UTSW 3 104,368,914 (GRCm39) missense probably benign 0.27
R9204:Lrig2 UTSW 3 104,387,438 (GRCm39) missense possibly damaging 0.81
R9215:Lrig2 UTSW 3 104,398,324 (GRCm39) missense probably benign 0.00
R9549:Lrig2 UTSW 3 104,398,191 (GRCm39) missense probably damaging 0.97
R9562:Lrig2 UTSW 3 104,375,924 (GRCm39) missense possibly damaging 0.69
R9664:Lrig2 UTSW 3 104,371,556 (GRCm39) missense probably damaging 1.00
R9773:Lrig2 UTSW 3 104,368,838 (GRCm39) missense probably benign 0.27
Predicted Primers PCR Primer
(F):5'- ATGTGCCCTCAGTACCATCTTG -3'
(R):5'- CGTGTCTTTATCAAGGATGCTG -3'

Sequencing Primer
(F):5'- CTCAGTACCATCTTGAATGATCCGAG -3'
(R):5'- AGTTCCATGAGATCCAGTGC -3'
Posted On 2018-07-23