Incidental Mutation 'R4510:Lnx1'
ID 331204
Institutional Source Beutler Lab
Gene Symbol Lnx1
Ensembl Gene ENSMUSG00000029228
Gene Name ligand of numb-protein X 1
Synonyms
MMRRC Submission 041585-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.086) question?
Stock # R4510 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 74753108-74863573 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 74780853 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Asparagine at position 382 (D382N)
Ref Sequence ENSEMBL: ENSMUSP00000113035 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039744] [ENSMUST00000087161] [ENSMUST00000113531] [ENSMUST00000117388] [ENSMUST00000117525] [ENSMUST00000121690] [ENSMUST00000127396] [ENSMUST00000153543]
AlphaFold O70263
Predicted Effect possibly damaging
Transcript: ENSMUST00000039744
AA Change: D282N

PolyPhen 2 Score 0.534 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000040098
Gene: ENSMUSG00000029228
AA Change: D282N

DomainStartEndE-ValueType
low complexity region 4 12 N/A INTRINSIC
Blast:PDZ 57 164 1e-33 BLAST
PDZ 188 263 5.33e-19 SMART
PDZ 295 368 2.27e-13 SMART
PDZ 417 494 8.27e-16 SMART
PDZ 547 624 5.71e-19 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000087161
AA Change: D382N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000084405
Gene: ENSMUSG00000029228
AA Change: D382N

DomainStartEndE-ValueType
RING 45 82 5.82e-6 SMART
low complexity region 97 107 N/A INTRINSIC
Blast:PDZ 157 264 3e-33 BLAST
PDZ 288 363 5.33e-19 SMART
PDZ 395 468 2.27e-13 SMART
PDZ 517 594 8.27e-16 SMART
PDZ 647 724 5.71e-19 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000113531
AA Change: D223N

PolyPhen 2 Score 0.838 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000109159
Gene: ENSMUSG00000029228
AA Change: D223N

DomainStartEndE-ValueType
Blast:PDZ 2 105 2e-32 BLAST
PDZ 129 204 5.33e-19 SMART
PDZ 236 309 2.27e-13 SMART
PDZ 358 435 8.27e-16 SMART
PDZ 488 565 5.71e-19 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000117388
AA Change: D382N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000113035
Gene: ENSMUSG00000029228
AA Change: D382N

DomainStartEndE-ValueType
RING 45 82 5.82e-6 SMART
low complexity region 97 107 N/A INTRINSIC
Blast:PDZ 157 264 3e-33 BLAST
PDZ 288 363 5.33e-19 SMART
PDZ 395 468 2.27e-13 SMART
PDZ 517 594 8.27e-16 SMART
PDZ 647 724 5.71e-19 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000117525
AA Change: D282N

PolyPhen 2 Score 0.534 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000113837
Gene: ENSMUSG00000029228
AA Change: D282N

DomainStartEndE-ValueType
low complexity region 4 12 N/A INTRINSIC
Blast:PDZ 57 164 1e-33 BLAST
PDZ 188 263 5.33e-19 SMART
PDZ 295 368 2.27e-13 SMART
PDZ 417 494 8.27e-16 SMART
PDZ 547 624 5.71e-19 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000121690
AA Change: D272N

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000113565
Gene: ENSMUSG00000029228
AA Change: D272N

DomainStartEndE-ValueType
low complexity region 4 12 N/A INTRINSIC
PDZ 178 253 5.33e-19 SMART
PDZ 285 358 2.27e-13 SMART
PDZ 407 484 8.27e-16 SMART
PDZ 537 614 5.71e-19 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000127396
SMART Domains Protein: ENSMUSP00000120886
Gene: ENSMUSG00000029228

DomainStartEndE-ValueType
low complexity region 4 12 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000140084
AA Change: D65N

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000117935
Gene: ENSMUSG00000029228
AA Change: D65N

DomainStartEndE-ValueType
PDZ 1 47 2.73e-1 SMART
PDZ 79 154 1.51e-9 SMART
PDZ 156 233 8.27e-16 SMART
SCOP:d1qaua_ 274 322 3e-7 SMART
Blast:PDZ 286 322 4e-19 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000153543
AA Change: D223N

PolyPhen 2 Score 0.838 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000121094
Gene: ENSMUSG00000029228
AA Change: D223N

DomainStartEndE-ValueType
Blast:PDZ 2 105 9e-37 BLAST
Blast:PDZ 129 159 1e-12 BLAST
Meta Mutation Damage Score 0.1896 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 96% (50/52)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a membrane-bound protein that is involved in signal transduction and protein interactions. The encoded product is an E3 ubiquitin-protein ligase, which mediates ubiquitination and subsequent proteasomal degradation of proteins containing phosphotyrosine binding (PTB) domains. This protein may play an important role in tumorogenesis. Alternatively spliced transcript variants encoding distinct isoforms have been described. A pseudogene, which is located on chromosome 17, has been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a targeted mutation exhibit an increased percentage of B1-like B cells in peritoneal lavage when compared with that of controls. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9330159F19Rik T A 10: 29,100,819 (GRCm39) D397E probably benign Het
Abcc10 A G 17: 46,618,136 (GRCm39) F1005L probably damaging Het
Ackr4 T C 9: 103,975,930 (GRCm39) E339G probably benign Het
Adam39 G T 8: 41,279,328 (GRCm39) C573F probably damaging Het
Anks1b A G 10: 90,346,652 (GRCm39) T651A probably benign Het
Aoc1 C A 6: 48,884,740 (GRCm39) H594Q probably damaging Het
Arid1a A C 4: 133,423,010 (GRCm39) probably benign Het
Atp4a G T 7: 30,423,678 (GRCm39) E928* probably null Het
Atp5pf T C 16: 84,624,862 (GRCm39) D104G probably benign Het
Atp8b5 A G 4: 43,320,629 (GRCm39) T206A probably damaging Het
Atrn G A 2: 130,777,497 (GRCm39) W182* probably null Het
Bltp2 T C 11: 78,168,154 (GRCm39) S1530P possibly damaging Het
Cacna1e G A 1: 154,437,579 (GRCm39) T257I probably damaging Het
Caskin1 G A 17: 24,725,602 (GRCm39) S1296N probably benign Het
Crebrf A G 17: 26,961,938 (GRCm39) Y345C probably benign Het
Cyp26b1 G A 6: 84,551,473 (GRCm39) R248W probably damaging Het
Dclk3 C A 9: 111,297,060 (GRCm39) H201Q probably benign Het
Ddx17 A T 15: 79,422,793 (GRCm39) V315E probably damaging Het
Dhrs11 T C 11: 84,716,342 (GRCm39) *51W probably null Het
Fgfr4 C A 13: 55,309,328 (GRCm39) P455Q possibly damaging Het
Gabbr1 A G 17: 37,380,103 (GRCm39) K697E probably damaging Het
Gcnt1 G A 19: 17,307,641 (GRCm39) T28I probably benign Het
Gga2 G A 7: 121,620,301 (GRCm39) T4M unknown Het
Gm12185 T A 11: 48,799,305 (GRCm39) H396L possibly damaging Het
Gm21976 A G 13: 98,441,839 (GRCm39) R123G probably benign Het
Hecw1 A C 13: 14,531,776 (GRCm39) V166G probably damaging Het
Hpx A G 7: 105,241,295 (GRCm39) V372A possibly damaging Het
Igkv2-109 A G 6: 68,279,962 (GRCm39) Y61C probably damaging Het
Igsf1 A G X: 48,875,050 (GRCm39) F789S probably damaging Het
Il4ra A G 7: 125,175,280 (GRCm39) D496G possibly damaging Het
Ilf3 A G 9: 21,310,511 (GRCm39) T547A possibly damaging Het
Insrr C A 3: 87,715,978 (GRCm39) P558T possibly damaging Het
Ints9 A G 14: 65,266,381 (GRCm39) D411G possibly damaging Het
Irak3 T A 10: 119,981,813 (GRCm39) H393L probably damaging Het
Isx G A 8: 75,600,298 (GRCm39) M10I probably benign Het
Itga11 A G 9: 62,668,870 (GRCm39) D709G probably damaging Het
Kcng2 G T 18: 80,338,930 (GRCm39) R453S probably benign Het
Kif5b A G 18: 6,214,011 (GRCm39) V664A probably benign Het
Lalba A G 15: 98,380,422 (GRCm39) L44P probably benign Het
Ldlrad1 T G 4: 107,066,715 (GRCm39) F17V probably benign Het
Lrp1 T C 10: 127,429,717 (GRCm39) Y451C probably damaging Het
Lrp2 A T 2: 69,310,406 (GRCm39) N2722K possibly damaging Het
Mctp1 G A 13: 76,973,391 (GRCm39) V431I probably benign Het
Mmrn2 T C 14: 34,125,016 (GRCm39) F866L possibly damaging Het
Mylk2 A G 2: 152,759,330 (GRCm39) E367G probably damaging Het
Nfatc1 A G 18: 80,678,794 (GRCm39) S865P probably damaging Het
Nol6 G C 4: 41,123,526 (GRCm39) T74R probably damaging Het
Notch2 T C 3: 98,053,637 (GRCm39) M2100T probably benign Het
Parp1 A G 1: 180,418,841 (GRCm39) K667R possibly damaging Het
Phlda3 A G 1: 135,694,400 (GRCm39) T72A probably damaging Het
Polg T C 7: 79,105,270 (GRCm39) Q758R probably benign Het
Polq G A 16: 36,868,925 (GRCm39) R765H probably damaging Het
Pramel19 A T 4: 101,798,757 (GRCm39) M243L probably benign Het
Prkd1 T C 12: 50,439,762 (GRCm39) D355G possibly damaging Het
Prpf8 T C 11: 75,382,652 (GRCm39) Y398H probably damaging Het
Ripk1 T C 13: 34,210,731 (GRCm39) Y309H probably damaging Het
Rngtt A T 4: 33,339,032 (GRCm39) Q279L possibly damaging Het
Rusf1 A T 7: 127,875,312 (GRCm39) F319Y probably damaging Het
Samd4 T A 14: 47,315,042 (GRCm39) V114D probably benign Het
Sec23ip G A 7: 128,380,900 (GRCm39) E956K probably damaging Het
Slc4a1ap A T 5: 31,684,747 (GRCm39) T128S probably benign Het
Slc5a11 A T 7: 122,834,858 (GRCm39) I6F probably benign Het
Slc6a19 A C 13: 73,832,094 (GRCm39) L494R probably damaging Het
Slc6a21 A G 7: 44,936,713 (GRCm39) D189G probably damaging Het
Slc7a1 G T 5: 148,277,372 (GRCm39) A381D probably damaging Het
Smc4 T A 3: 68,923,980 (GRCm39) probably null Het
Stk19 T C 17: 35,051,504 (GRCm39) E17G probably damaging Het
Tekt5 A C 16: 10,175,877 (GRCm39) V556G probably benign Het
Tenm4 T C 7: 96,544,070 (GRCm39) F2029L probably benign Het
Thnsl1 T C 2: 21,217,236 (GRCm39) V330A probably damaging Het
Tnfrsf21 A G 17: 43,375,910 (GRCm39) D432G probably damaging Het
Tnip1 T A 11: 54,817,616 (GRCm39) S244C probably benign Het
Tnrc6c A T 11: 117,633,784 (GRCm39) N1294I possibly damaging Het
Trpm3 A G 19: 22,965,381 (GRCm39) I1625M probably benign Het
Ttn A T 2: 76,575,773 (GRCm39) V25040E probably damaging Het
Vwa5a A G 9: 38,633,853 (GRCm39) N19D possibly damaging Het
Washc2 A T 6: 116,197,517 (GRCm39) D250V probably damaging Het
Xpo1 A G 11: 23,237,401 (GRCm39) T755A possibly damaging Het
Zfp462 C T 4: 55,008,934 (GRCm39) T300I possibly damaging Het
Zfp937 A C 2: 150,080,431 (GRCm39) T154P probably damaging Het
Zzef1 A G 11: 72,778,996 (GRCm39) D1819G probably benign Het
Other mutations in Lnx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00965:Lnx1 APN 5 74,846,378 (GRCm39) missense probably benign 0.00
IGL01538:Lnx1 APN 5 74,780,816 (GRCm39) missense possibly damaging 0.50
IGL02351:Lnx1 APN 5 74,788,027 (GRCm39) missense probably damaging 0.97
IGL02358:Lnx1 APN 5 74,788,027 (GRCm39) missense probably damaging 0.97
IGL03011:Lnx1 APN 5 74,846,420 (GRCm39) missense probably benign 0.02
IGL03188:Lnx1 APN 5 74,780,924 (GRCm39) missense probably damaging 1.00
bobcat UTSW 5 74,846,351 (GRCm39) missense probably damaging 1.00
Caracal UTSW 5 74,766,710 (GRCm39) missense probably damaging 1.00
R0490:Lnx1 UTSW 5 74,781,008 (GRCm39) critical splice acceptor site probably null
R0714:Lnx1 UTSW 5 74,768,570 (GRCm39) splice site probably benign
R1343:Lnx1 UTSW 5 74,758,040 (GRCm39) missense probably damaging 0.98
R1533:Lnx1 UTSW 5 74,780,678 (GRCm39) missense probably damaging 1.00
R1681:Lnx1 UTSW 5 74,846,071 (GRCm39) missense probably benign
R1714:Lnx1 UTSW 5 74,768,398 (GRCm39) missense probably null 1.00
R1727:Lnx1 UTSW 5 74,768,577 (GRCm39) splice site probably null
R1806:Lnx1 UTSW 5 74,766,710 (GRCm39) missense probably damaging 1.00
R2091:Lnx1 UTSW 5 74,780,727 (GRCm39) missense probably benign 0.25
R2879:Lnx1 UTSW 5 74,780,784 (GRCm39) missense probably benign 0.03
R2984:Lnx1 UTSW 5 74,846,083 (GRCm39) nonsense probably null
R3790:Lnx1 UTSW 5 74,789,027 (GRCm39) splice site probably benign
R3953:Lnx1 UTSW 5 74,766,750 (GRCm39) missense probably benign
R4509:Lnx1 UTSW 5 74,780,853 (GRCm39) missense probably damaging 1.00
R4511:Lnx1 UTSW 5 74,780,853 (GRCm39) missense probably damaging 1.00
R4575:Lnx1 UTSW 5 74,846,204 (GRCm39) missense probably damaging 1.00
R4583:Lnx1 UTSW 5 74,771,457 (GRCm39) missense probably benign 0.16
R4624:Lnx1 UTSW 5 74,821,121 (GRCm39) intron probably benign
R4647:Lnx1 UTSW 5 74,771,457 (GRCm39) missense probably benign 0.16
R4648:Lnx1 UTSW 5 74,771,457 (GRCm39) missense probably benign 0.16
R4877:Lnx1 UTSW 5 74,788,784 (GRCm39) missense probably benign 0.01
R4883:Lnx1 UTSW 5 74,768,530 (GRCm39) missense probably benign
R5256:Lnx1 UTSW 5 74,846,315 (GRCm39) missense probably damaging 1.00
R6169:Lnx1 UTSW 5 74,838,230 (GRCm39) missense probably damaging 1.00
R6185:Lnx1 UTSW 5 74,846,269 (GRCm39) nonsense probably null
R6408:Lnx1 UTSW 5 74,846,307 (GRCm39) missense probably damaging 1.00
R6476:Lnx1 UTSW 5 74,768,541 (GRCm39) missense possibly damaging 0.52
R7083:Lnx1 UTSW 5 74,788,846 (GRCm39) missense possibly damaging 0.94
R7085:Lnx1 UTSW 5 74,788,846 (GRCm39) missense possibly damaging 0.94
R7261:Lnx1 UTSW 5 74,838,175 (GRCm39) nonsense probably null
R7511:Lnx1 UTSW 5 74,780,972 (GRCm39) missense probably benign 0.01
R7574:Lnx1 UTSW 5 74,846,099 (GRCm39) missense probably benign 0.33
R7670:Lnx1 UTSW 5 74,846,351 (GRCm39) missense probably damaging 1.00
R8145:Lnx1 UTSW 5 74,846,060 (GRCm39) missense probably benign 0.22
R9015:Lnx1 UTSW 5 74,780,783 (GRCm39) missense probably benign 0.00
R9224:Lnx1 UTSW 5 74,766,810 (GRCm39) missense probably benign 0.37
R9321:Lnx1 UTSW 5 74,780,991 (GRCm39) missense probably damaging 1.00
R9340:Lnx1 UTSW 5 74,758,584 (GRCm39) missense probably benign 0.01
R9704:Lnx1 UTSW 5 74,780,879 (GRCm39) missense probably benign 0.02
Z1177:Lnx1 UTSW 5 74,788,102 (GRCm39) missense possibly damaging 0.80
Predicted Primers PCR Primer
(F):5'- GCCAAATCGAAGGTCATGCC -3'
(R):5'- TGGCATGGACCTTTTCAGAATGC -3'

Sequencing Primer
(F):5'- CAAATCGAAGGTCATGCCCGTTG -3'
(R):5'- AGTAGGCTTACTCTCAAATGGCC -3'
Posted On 2015-07-21