Incidental Mutation 'R5230:Loxl3'
ID |
403710 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Loxl3
|
Ensembl Gene |
ENSMUSG00000000693 |
Gene Name |
lysyl oxidase-like 3 |
Synonyms |
Lor2 |
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.940)
|
Stock # |
R5230 (G1)
|
Quality Score |
170 |
Status
|
Not validated
|
Chromosome |
6 |
Chromosomal Location |
83011186-83029547 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 83012775 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Alanine
at position 105
(T105A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000098815
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000000707]
[ENSMUST00000089651]
[ENSMUST00000101257]
[ENSMUST00000149918]
|
AlphaFold |
Q9Z175 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000000707
AA Change: T105A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000000707 Gene: ENSMUSG00000000693 AA Change: T105A
Domain | Start | End | E-Value | Type |
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: ENSMUST00000089651
|
SMART Domains |
Protein: ENSMUSP00000087079 Gene: ENSMUSG00000068335
Domain | Start | End | E-Value | Type |
PH
|
4 |
121 |
1.31e-8 |
SMART |
IRS
|
151 |
254 |
1.21e-45 |
SMART |
PTBI
|
152 |
254 |
3.84e-59 |
SMART |
low complexity region
|
411 |
424 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000101257
AA Change: T105A
PolyPhen 2
Score 0.161 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000098815 Gene: ENSMUSG00000000693 AA Change: T105A
Domain | Start | End | E-Value | Type |
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: ENSMUST00000149918
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152679
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000204318
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000204900
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.6%
|
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: 50 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A2m |
A |
G |
6: 121,651,820 (GRCm39) |
N1296S |
probably damaging |
Het |
Abca5 |
A |
T |
11: 110,210,686 (GRCm39) |
D164E |
probably benign |
Het |
Adamts5 |
T |
C |
16: 85,666,956 (GRCm39) |
D512G |
probably damaging |
Het |
Ankrd11 |
G |
A |
8: 123,617,216 (GRCm39) |
T2191I |
probably benign |
Het |
Anxa3 |
T |
C |
5: 96,986,171 (GRCm39) |
F270S |
possibly damaging |
Het |
Bard1 |
A |
G |
1: 71,092,770 (GRCm39) |
|
probably null |
Het |
Ccdc142 |
T |
C |
6: 83,084,777 (GRCm39) |
V591A |
probably damaging |
Het |
Col6a3 |
C |
T |
1: 90,716,776 (GRCm39) |
E1613K |
unknown |
Het |
Dnah9 |
T |
A |
11: 65,975,492 (GRCm39) |
H1519L |
probably damaging |
Het |
Egf |
T |
C |
3: 129,511,673 (GRCm39) |
D498G |
possibly damaging |
Het |
Enah |
A |
C |
1: 181,763,235 (GRCm39) |
|
probably benign |
Het |
Fat3 |
A |
T |
9: 15,901,856 (GRCm39) |
N3056K |
possibly damaging |
Het |
Gm4846 |
T |
A |
1: 166,317,748 (GRCm39) |
N223Y |
probably benign |
Het |
Gm8104 |
A |
G |
14: 42,958,975 (GRCm39) |
N55S |
probably damaging |
Het |
Gpatch8 |
A |
G |
11: 102,370,404 (GRCm39) |
S1045P |
probably damaging |
Het |
Haus4 |
A |
G |
14: 54,781,251 (GRCm39) |
M275T |
probably benign |
Het |
Ighe |
T |
A |
12: 113,235,006 (GRCm39) |
T385S |
unknown |
Het |
Ipo9 |
G |
A |
1: 135,347,808 (GRCm39) |
S78L |
probably damaging |
Het |
Kif21b |
G |
A |
1: 136,099,411 (GRCm39) |
V1473M |
probably damaging |
Het |
Lama1 |
T |
A |
17: 68,052,078 (GRCm39) |
Y345* |
probably null |
Het |
Lgr6 |
C |
T |
1: 134,921,748 (GRCm39) |
A199T |
probably damaging |
Het |
Map4k3 |
A |
G |
17: 80,922,599 (GRCm39) |
S441P |
probably benign |
Het |
Med12l |
C |
T |
3: 59,153,209 (GRCm39) |
T1078I |
probably damaging |
Het |
Mef2c |
T |
A |
13: 83,801,026 (GRCm39) |
M242K |
possibly damaging |
Het |
Morc2b |
A |
G |
17: 33,355,226 (GRCm39) |
Y849H |
probably benign |
Het |
Mroh2b |
T |
A |
15: 4,971,004 (GRCm39) |
V1003E |
probably benign |
Het |
Myo15a |
T |
A |
11: 60,393,674 (GRCm39) |
M1135K |
possibly damaging |
Het |
Nckap1l |
A |
T |
15: 103,392,066 (GRCm39) |
I834F |
probably benign |
Het |
Nrg1 |
T |
A |
8: 32,308,507 (GRCm39) |
Y503F |
probably damaging |
Het |
Numa1 |
T |
C |
7: 101,644,731 (GRCm39) |
S236P |
possibly damaging |
Het |
Or4f61 |
A |
T |
2: 111,922,734 (GRCm39) |
I104N |
probably benign |
Het |
Pcdhga2 |
T |
C |
18: 37,802,795 (GRCm39) |
V213A |
probably benign |
Het |
Pdzd2 |
A |
T |
15: 12,390,119 (GRCm39) |
M826K |
probably damaging |
Het |
Pdzrn3 |
C |
T |
6: 101,130,272 (GRCm39) |
D515N |
probably damaging |
Het |
Rnf38 |
T |
C |
4: 44,149,176 (GRCm39) |
Q57R |
probably benign |
Het |
Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
Serpina6 |
T |
C |
12: 103,618,157 (GRCm39) |
T219A |
probably benign |
Het |
Spata31d1c |
T |
A |
13: 65,183,248 (GRCm39) |
N263K |
probably benign |
Het |
Spef2 |
T |
G |
15: 9,667,316 (GRCm39) |
I791L |
possibly damaging |
Het |
Sv2a |
T |
C |
3: 96,092,776 (GRCm39) |
C159R |
probably damaging |
Het |
Tbc1d31 |
T |
A |
15: 57,824,315 (GRCm39) |
L859Q |
probably damaging |
Het |
Tecta |
C |
A |
9: 42,306,239 (GRCm39) |
R63L |
probably damaging |
Het |
Tex52 |
A |
G |
6: 128,361,779 (GRCm39) |
E252G |
probably damaging |
Het |
Tnfsf13b |
A |
G |
8: 10,081,608 (GRCm39) |
I257V |
possibly damaging |
Het |
Tpk1 |
A |
G |
6: 43,400,653 (GRCm39) |
L172P |
probably damaging |
Het |
Trim3 |
T |
G |
7: 105,268,720 (GRCm39) |
N78T |
possibly damaging |
Het |
Try5 |
A |
G |
6: 41,289,312 (GRCm39) |
V88A |
probably benign |
Het |
Vmn1r222 |
T |
G |
13: 23,417,172 (GRCm39) |
M14L |
probably benign |
Het |
Wdr90 |
A |
T |
17: 26,074,277 (GRCm39) |
V678E |
probably benign |
Het |
Zan |
A |
G |
5: 137,452,340 (GRCm39) |
L1543P |
unknown |
Het |
|
Other mutations in Loxl3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
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 |
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'- TTCTATCAGCCCAGAGAAGAAGG -3'
(R):5'- TAGCTTCAGGTCACATGGCC -3'
Sequencing Primer
(F):5'- CTGAGGTTCCGGCTGGCTG -3'
(R):5'- TCAGGTCACATGGCCCTGAAATTAG -3'
|
Posted On |
2016-07-22 |