Incidental Mutation 'R5769:Loxl3'
ID 446435
Institutional Source Beutler Lab
Gene Symbol Loxl3
Ensembl Gene ENSMUSG00000000693
Gene Name lysyl oxidase-like 3
Synonyms Lor2
MMRRC Submission 043369-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.940) question?
Stock # R5769 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 83011186-83029547 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 83027581 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 708 (T708A)
Ref Sequence ENSEMBL: ENSMUSP00000000707 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000707] [ENSMUST00000089645] [ENSMUST00000092618] [ENSMUST00000101257] [ENSMUST00000113962] [ENSMUST00000113963] [ENSMUST00000122955] [ENSMUST00000134606]
AlphaFold Q9Z175
Predicted Effect probably damaging
Transcript: ENSMUST00000000707
AA Change: T708A

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000000707
Gene: ENSMUSG00000000693
AA Change: T708A

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
SR 45 146 2.1e-50 SMART
SR 170 283 1.09e-25 SMART
SR 308 408 3.72e-51 SMART
SR 418 526 8.5e-37 SMART
Pfam:Lysyl_oxidase 530 730 3.9e-103 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000089645
SMART Domains Protein: ENSMUSP00000087073
Gene: ENSMUSG00000068329

DomainStartEndE-ValueType
low complexity region 28 39 N/A INTRINSIC
transmembrane domain 106 125 N/A INTRINSIC
low complexity region 128 143 N/A INTRINSIC
Pfam:Trypsin 170 341 1.1e-14 PFAM
Pfam:Trypsin_2 182 320 1.2e-34 PFAM
PDZ 371 445 2.86e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000092618
SMART Domains Protein: ENSMUSP00000090281
Gene: ENSMUSG00000068328

DomainStartEndE-ValueType
low complexity region 10 40 N/A INTRINSIC
transmembrane domain 52 74 N/A INTRINSIC
PlsC 119 222 1.04e-1 SMART
low complexity region 307 322 N/A INTRINSIC
CUE 325 366 1.3e-9 SMART
low complexity region 378 392 N/A INTRINSIC
low complexity region 421 439 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000101257
AA Change: T426A

PolyPhen 2 Score 0.399 (Sensitivity: 0.89; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000098815
Gene: ENSMUSG00000000693
AA Change: T426A

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
SR 45 146 2.1e-50 SMART
SR 170 283 1.09e-25 SMART
SR 308 396 5.46e-17 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000113962
SMART Domains Protein: ENSMUSP00000109595
Gene: ENSMUSG00000068329

DomainStartEndE-ValueType
low complexity region 28 39 N/A INTRINSIC
transmembrane domain 106 125 N/A INTRINSIC
low complexity region 128 143 N/A INTRINSIC
Pfam:Trypsin_2 182 237 2.7e-12 PFAM
Pfam:Trypsin 212 277 4.5e-6 PFAM
PDZ 285 348 4.89e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000113963
SMART Domains Protein: ENSMUSP00000109596
Gene: ENSMUSG00000068329

DomainStartEndE-ValueType
low complexity region 28 39 N/A INTRINSIC
transmembrane domain 106 125 N/A INTRINSIC
low complexity region 128 143 N/A INTRINSIC
Pfam:Trypsin 170 342 6.8e-15 PFAM
Pfam:Trypsin_2 182 320 7.1e-24 PFAM
PDZ 350 413 4.89e-1 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155502
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154829
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184661
Predicted Effect probably benign
Transcript: ENSMUST00000203915
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204209
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203180
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144058
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203339
Predicted Effect probably benign
Transcript: ENSMUST00000132099
Predicted Effect probably benign
Transcript: ENSMUST00000122955
SMART Domains Protein: ENSMUSP00000138153
Gene: ENSMUSG00000068329

DomainStartEndE-ValueType
low complexity region 28 39 N/A INTRINSIC
transmembrane domain 106 125 N/A INTRINSIC
low complexity region 128 143 N/A INTRINSIC
Pfam:Trypsin 170 321 2.1e-10 PFAM
Pfam:Trypsin_2 182 317 9.5e-21 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000134606
SMART Domains Protein: ENSMUSP00000115547
Gene: ENSMUSG00000068329

DomainStartEndE-ValueType
Pfam:Trypsin 7 180 2.7e-15 PFAM
Pfam:Trypsin_2 20 158 3.1e-24 PFAM
PDZ 209 283 2.86e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000150217
SMART Domains Protein: ENSMUSP00000118234
Gene: ENSMUSG00000068329

DomainStartEndE-ValueType
low complexity region 4 11 N/A INTRINSIC
Pfam:Trypsin 41 215 1.6e-11 PFAM
Pfam:Trypsin_2 53 190 1.8e-31 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204383
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204761
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204385
Predicted Effect probably benign
Transcript: ENSMUST00000204719
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205152
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204281
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204895
Predicted Effect probably benign
Transcript: ENSMUST00000204343
Meta Mutation Damage Score 0.1275 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 98% (65/66)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a lysyl oxidase, which likely functions as an amine oxidase and plays a role in the formation of crosslinks in collagens and elastin. Deletion of the related gene in mouse causes neonatal mortality with cleft palate, spine deformity, and defects in collagen organization. A mutation in this gene was found in a family with Stickler syndrome. [provided by RefSeq, Sep 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit lethality shortly after birth, craniofacial and vertebral abnormalities associated with collagen deformities. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A430033K04Rik T A 5: 138,644,595 (GRCm39) V160E possibly damaging Het
Abcb1a A C 5: 8,733,426 (GRCm39) E106A probably benign Het
Acap3 A T 4: 155,986,857 (GRCm39) D371V probably damaging Het
Ahi1 T C 10: 20,835,981 (GRCm39) probably null Het
Coq8a A G 1: 180,006,681 (GRCm39) Y69H probably damaging Het
Defb33 T A 8: 21,387,543 (GRCm39) F27I possibly damaging Het
Dhx29 T A 13: 113,090,251 (GRCm39) L776Q probably damaging Het
Dnah3 G A 7: 119,689,175 (GRCm39) R80* probably null Het
Dtna A T 18: 23,784,611 (GRCm39) D646V probably benign Het
Eml5 T A 12: 98,756,878 (GRCm39) D1964V probably damaging Het
Fbn2 A T 18: 58,238,271 (GRCm39) N575K probably damaging Het
Fbxo38 G A 18: 62,648,036 (GRCm39) P834L probably benign Het
Fyb2 G T 4: 104,870,518 (GRCm39) K706N probably damaging Het
Fyb2 T A 4: 104,872,841 (GRCm39) V738E probably damaging Het
Gcm1 A G 9: 77,972,249 (GRCm39) T397A probably benign Het
Gins1 A T 2: 150,767,918 (GRCm39) E149D probably damaging Het
Gm11595 G A 11: 99,663,381 (GRCm39) R100C unknown Het
Grin2a C T 16: 9,579,390 (GRCm39) R291K possibly damaging Het
Hdac10 T C 15: 89,007,819 (GRCm39) M646V probably benign Het
Hes6 G T 1: 91,340,671 (GRCm39) R38S probably damaging Het
Hipk3 G A 2: 104,265,298 (GRCm39) P667S possibly damaging Het
Jrk T C 15: 74,577,917 (GRCm39) Q456R probably benign Het
Klf18 A C 4: 117,586,162 (GRCm39) probably benign Het
Lyg1 T C 1: 37,989,831 (GRCm39) S19G unknown Het
Magel2 T A 7: 62,027,861 (GRCm39) M255K probably benign Het
Mctp1 A G 13: 76,907,927 (GRCm39) D242G probably damaging Het
Med13 A T 11: 86,236,829 (GRCm39) N109K probably benign Het
Mms19 A G 19: 41,952,825 (GRCm39) F95L probably damaging Het
Nav1 A G 1: 135,379,995 (GRCm39) L1569P probably damaging Het
Nup188 A G 2: 30,220,747 (GRCm39) E940G probably benign Het
Oas1d T C 5: 121,054,917 (GRCm39) F163S probably benign Het
Odf2l A G 3: 144,841,492 (GRCm39) K304R possibly damaging Het
Otud3 T A 4: 138,625,421 (GRCm39) N211I possibly damaging Het
Pabpc6 A T 17: 9,886,772 (GRCm39) L593* probably null Het
Pdcd11 T A 19: 47,091,076 (GRCm39) L350Q possibly damaging Het
Pdia4 A G 6: 47,792,446 (GRCm39) probably benign Het
Pik3cb G A 9: 98,975,212 (GRCm39) Q223* probably null Het
Plb1 G A 5: 32,474,866 (GRCm39) V696M probably benign Het
Ppp2r5a T C 1: 191,104,863 (GRCm39) D61G probably benign Het
Preb G T 5: 31,115,635 (GRCm39) Y87* probably null Het
Rdh16f2 A T 10: 127,712,758 (GRCm39) N252I probably benign Het
Rida T C 15: 34,484,704 (GRCm39) probably benign Het
Rxrb T C 17: 34,251,821 (GRCm39) probably benign Het
Sis T A 3: 72,835,568 (GRCm39) K931N probably damaging Het
Srcap T A 7: 127,158,994 (GRCm39) probably benign Het
Srp68 A G 11: 116,137,495 (GRCm39) S525P probably damaging Het
Susd2 C T 10: 75,473,853 (GRCm39) A581T probably damaging Het
Synj1 A G 16: 90,735,141 (GRCm39) probably benign Het
Syt12 T C 19: 4,501,072 (GRCm39) Y326C probably damaging Het
Tesk2 A G 4: 116,659,512 (GRCm39) probably null Het
Tmem41b G A 7: 109,577,945 (GRCm39) T113I possibly damaging Het
Tmtc2 T C 10: 105,205,907 (GRCm39) I463V probably benign Het
Trak1 A T 9: 121,277,904 (GRCm39) D320V probably damaging Het
Ushbp1 A T 8: 71,838,863 (GRCm39) N570K probably benign Het
Vmn1r33 T A 6: 66,588,817 (GRCm39) I246F possibly damaging Het
Vmn2r54 A C 7: 12,349,209 (GRCm39) L791R possibly damaging Het
Washc1 A T 17: 66,425,111 (GRCm39) T372S probably benign Het
Zfp1005 A G 2: 150,110,198 (GRCm39) E296G possibly damaging Het
Other mutations in Loxl3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00957:Loxl3 APN 6 83,025,747 (GRCm39) unclassified probably benign
IGL01370:Loxl3 APN 6 83,026,468 (GRCm39) missense probably damaging 1.00
IGL02126:Loxl3 APN 6 83,025,628 (GRCm39) missense probably damaging 1.00
IGL02128:Loxl3 APN 6 83,027,564 (GRCm39) missense probably damaging 1.00
R0241:Loxl3 UTSW 6 83,027,114 (GRCm39) missense probably damaging 1.00
R0241:Loxl3 UTSW 6 83,027,114 (GRCm39) missense probably damaging 1.00
R1725:Loxl3 UTSW 6 83,012,574 (GRCm39) missense probably benign 0.00
R1771:Loxl3 UTSW 6 83,026,890 (GRCm39) missense probably damaging 1.00
R2017:Loxl3 UTSW 6 83,025,958 (GRCm39) missense probably damaging 0.99
R2291:Loxl3 UTSW 6 83,014,469 (GRCm39) missense probably benign 0.07
R3731:Loxl3 UTSW 6 83,027,652 (GRCm39) critical splice donor site probably null
R4179:Loxl3 UTSW 6 83,014,565 (GRCm39) missense probably benign 0.00
R5230:Loxl3 UTSW 6 83,012,775 (GRCm39) missense probably benign 0.16
R5385:Loxl3 UTSW 6 83,027,593 (GRCm39) missense probably damaging 0.99
R5591:Loxl3 UTSW 6 83,025,018 (GRCm39) missense probably damaging 1.00
R5664:Loxl3 UTSW 6 83,026,863 (GRCm39) missense probably benign 0.12
R5771:Loxl3 UTSW 6 83,012,780 (GRCm39) splice site probably null
R5802:Loxl3 UTSW 6 83,026,270 (GRCm39) missense possibly damaging 0.67
R5831:Loxl3 UTSW 6 83,025,999 (GRCm39) missense probably benign 0.01
R5945:Loxl3 UTSW 6 83,014,492 (GRCm39) missense probably damaging 1.00
R6542:Loxl3 UTSW 6 83,025,147 (GRCm39) missense probably benign 0.00
R6687:Loxl3 UTSW 6 83,027,645 (GRCm39) missense probably damaging 1.00
R7961:Loxl3 UTSW 6 83,027,790 (GRCm39) missense possibly damaging 0.88
R8009:Loxl3 UTSW 6 83,027,790 (GRCm39) missense possibly damaging 0.88
R8122:Loxl3 UTSW 6 83,026,240 (GRCm39) missense probably damaging 1.00
R8278:Loxl3 UTSW 6 83,025,697 (GRCm39) missense probably damaging 1.00
R8373:Loxl3 UTSW 6 83,025,872 (GRCm39) missense possibly damaging 0.89
R8411:Loxl3 UTSW 6 83,027,605 (GRCm39) missense probably damaging 1.00
R8539:Loxl3 UTSW 6 83,026,507 (GRCm39) missense probably benign
R8684:Loxl3 UTSW 6 83,012,566 (GRCm39) missense probably benign 0.23
R8782:Loxl3 UTSW 6 83,025,051 (GRCm39) missense probably benign
R8801:Loxl3 UTSW 6 83,025,629 (GRCm39) missense probably damaging 1.00
R8859:Loxl3 UTSW 6 83,014,526 (GRCm39) missense probably damaging 1.00
R8864:Loxl3 UTSW 6 83,012,739 (GRCm39) missense probably damaging 0.99
R9031:Loxl3 UTSW 6 83,012,503 (GRCm39) missense probably damaging 1.00
R9081:Loxl3 UTSW 6 83,025,638 (GRCm39) missense possibly damaging 0.67
R9176:Loxl3 UTSW 6 83,026,292 (GRCm39) missense probably damaging 0.99
R9369:Loxl3 UTSW 6 83,027,393 (GRCm39) missense probably benign 0.26
R9634:Loxl3 UTSW 6 83,027,835 (GRCm39) missense probably benign 0.10
V1024:Loxl3 UTSW 6 83,012,719 (GRCm39) missense probably damaging 1.00
X0009:Loxl3 UTSW 6 83,015,461 (GRCm39) missense probably damaging 1.00
Z1177:Loxl3 UTSW 6 83,025,141 (GRCm39) missense probably benign 0.00
Z1177:Loxl3 UTSW 6 83,015,559 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- AGCCAGGAAACTACATTCTTCAGG -3'
(R):5'- GCTTCTTCGCTGAAGGCATC -3'

Sequencing Primer
(F):5'- GGAAACTACATTCTTCAGGTGCCTAG -3'
(R):5'- TCACCTGCAGAATAGACAGGC -3'
Posted On 2016-11-21