Incidental Mutation 'R5664:Loxl3'
ID 444257
Institutional Source Beutler Lab
Gene Symbol Loxl3
Ensembl Gene ENSMUSG00000000693
Gene Name lysyl oxidase-like 3
Synonyms Lor2
MMRRC Submission 043307-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.940) question?
Stock # R5664 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 83011186-83029547 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 83026863 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Asparagine at position 564 (S564N)
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 benign
Transcript: ENSMUST00000000707
AA Change: S564N

PolyPhen 2 Score 0.121 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000000707
Gene: ENSMUSG00000000693
AA Change: S564N

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
SMART Domains Protein: ENSMUSP00000098815
Gene: ENSMUSG00000000693

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: ENSMUST00000203180
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155502
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154829
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144058
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203339
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204281
Predicted Effect probably benign
Transcript: ENSMUST00000203915
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184661
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: 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 probably benign
Transcript: ENSMUST00000132099
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 noncoding transcript
Transcript: ENSMUST00000205152
Predicted Effect probably benign
Transcript: ENSMUST00000204343
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204383
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204318
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204385
Predicted Effect probably benign
Transcript: ENSMUST00000204719
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204761
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204895
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.6%
  • 20x: 96.0%
Validation Efficiency
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610030E20Rik T A 6: 72,325,977 (GRCm39) probably null Het
9430015G10Rik T A 4: 156,208,016 (GRCm39) L112H probably damaging Het
Acaca T C 11: 84,134,210 (GRCm39) L441P probably damaging Het
Ank3 G A 10: 69,838,395 (GRCm39) R1566K possibly damaging Het
Arsj A T 3: 126,232,306 (GRCm39) I351F probably damaging Het
Atp6v1b2 A G 8: 69,560,272 (GRCm39) T373A probably damaging Het
Atr C A 9: 95,787,866 (GRCm39) N1486K probably benign Het
Avl9 T C 6: 56,730,824 (GRCm39) S583P probably damaging Het
Bptf A T 11: 106,964,525 (GRCm39) D1493E probably benign Het
Brme1 A T 8: 84,893,288 (GRCm39) I152F probably benign Het
C2cd2l T C 9: 44,225,069 (GRCm39) E548G probably damaging Het
Capn3 G A 2: 120,307,506 (GRCm39) R15Q probably benign Het
Ccl3 A G 11: 83,540,039 (GRCm39) F22S probably benign Het
Clcf1 T C 19: 4,272,150 (GRCm39) F69S probably damaging Het
Col13a1 T C 10: 61,686,895 (GRCm39) E170G probably damaging Het
Dhx29 T A 13: 113,083,413 (GRCm39) F489L probably damaging Het
Dhx8 A T 11: 101,631,577 (GRCm39) N390I probably damaging Het
Dkk1 T A 19: 30,526,189 (GRCm39) Y135F probably benign Het
Edil3 G T 13: 89,467,832 (GRCm39) V446F probably damaging Het
Epha5 T A 5: 84,479,725 (GRCm39) E93V probably damaging Het
Epsti1 C T 14: 78,201,104 (GRCm39) T196I possibly damaging Het
Fras1 T C 5: 96,876,394 (GRCm39) S2376P possibly damaging Het
Frem2 A G 3: 53,559,911 (GRCm39) V1532A probably benign Het
Fsip2 T A 2: 82,818,439 (GRCm39) M4724K probably benign Het
Gcat T A 15: 78,927,273 (GRCm39) L238Q probably damaging Het
Gimap6 T C 6: 48,679,209 (GRCm39) K276E probably benign Het
Gjb5 T A 4: 127,249,722 (GRCm39) I141F probably benign Het
Glt6d1 T C 2: 25,704,192 (GRCm39) I7V probably benign Het
Gtf2h5 G A 17: 6,134,799 (GRCm39) G30R probably damaging Het
Herc6 C A 6: 57,595,669 (GRCm39) T449K probably benign Het
Hpn A T 7: 30,798,687 (GRCm39) Y132N probably damaging Het
Hpx A T 7: 105,244,355 (GRCm39) M190K probably benign Het
Inf2 A G 12: 112,578,162 (GRCm39) H1151R unknown Het
Krt74 A G 15: 101,669,014 (GRCm39) noncoding transcript Het
Map7 T A 10: 20,143,105 (GRCm39) V418E unknown Het
Mrpl37 T C 4: 106,921,588 (GRCm39) N214D probably benign Het
Mthfr T C 4: 148,139,923 (GRCm39) Y656H probably damaging Het
Myo9b A G 8: 71,812,526 (GRCm39) D2099G probably benign Het
Nktr T A 9: 121,578,483 (GRCm39) C825* probably null Het
Nomo1 A G 7: 45,725,581 (GRCm39) E1029G probably benign Het
Nup133 T C 8: 124,633,020 (GRCm39) D1037G probably benign Het
Or4b12 A G 2: 90,095,959 (GRCm39) F272L probably damaging Het
Or5w22 T C 2: 87,363,178 (GRCm39) L267P probably benign Het
Pcdhb14 T A 18: 37,582,049 (GRCm39) V385D possibly damaging Het
Pik3c2g T C 6: 139,682,733 (GRCm39) L38P probably damaging Het
Pkd1 A T 17: 24,788,345 (GRCm39) D701V probably damaging Het
Pnpla6 A G 8: 3,587,478 (GRCm39) T1070A probably damaging Het
Ppl T C 16: 4,923,919 (GRCm39) D185G probably benign Het
Prp2rt C A 13: 97,235,629 (GRCm39) L39F probably damaging Het
Prss1l C T 6: 41,371,605 (GRCm39) P17L probably benign Het
Prune1 A T 3: 95,165,489 (GRCm39) L261Q probably damaging Het
Qser1 A T 2: 104,608,541 (GRCm39) L1444I probably damaging Het
Serpina6 A C 12: 103,620,726 (GRCm39) C8G probably damaging Het
Sla2 A T 2: 156,716,919 (GRCm39) D180E probably benign Het
Slc4a4 C T 5: 89,176,103 (GRCm39) L25F probably damaging Het
Snhg16 A T 11: 116,563,490 (GRCm39) T27S possibly damaging Het
Tbx3 A G 5: 119,816,796 (GRCm39) K311R possibly damaging Het
Tdpoz6 A G 3: 93,599,994 (GRCm39) F125S probably benign Het
Thbs2 A T 17: 14,910,099 (GRCm39) C167S probably damaging Het
Trak1 T A 9: 121,301,373 (GRCm39) C710S possibly damaging Het
Tsks G A 7: 44,603,208 (GRCm39) E337K probably damaging Het
Vcpip1 A G 1: 9,816,604 (GRCm39) I593T probably damaging Het
Vmn2r118 A G 17: 55,899,765 (GRCm39) I713T possibly damaging Het
Vmn2r23 C T 6: 123,690,033 (GRCm39) T303M probably damaging Het
Vmn2r68 A T 7: 84,882,978 (GRCm39) M258K probably benign Het
Vmn2r76 A G 7: 85,895,202 (GRCm39) probably null Het
Wap A G 11: 6,588,609 (GRCm39) I5T possibly damaging Het
Zfp235 A C 7: 23,841,576 (GRCm39) H665P probably 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
R5769:Loxl3 UTSW 6 83,027,581 (GRCm39) missense probably damaging 0.98
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'- CTGTGATCTGCCTCGAGAGAAG -3'
(R):5'- CTGAATCCCAACAGGCTTGTTAC -3'

Sequencing Primer
(F):5'- TCGAGAGAAGCCAGTCTCC -3'
(R):5'- ACAGGCTTGTTACACCCCTGAG -3'
Posted On 2016-11-09