Mutagenetix > Incidental Mutation

Incidental Mutation 'R2017:Loxl3'

223187

Institutional Source

Beutler Lab

Gene Symbol

Loxl3

Ensembl Gene

ENSMUSG00000000693

Gene Name

lysyl oxidase-like 3

Synonyms

Lor2

MMRRC Submission

040026-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.940) question?

Stock #

R2017 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

83011186-83029547 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 83025958 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 402 (D402V)

Ref Sequence

ENSEMBL: ENSMUSP00000000707 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000707] [ENSMUST00000089645] [ENSMUST00000101257] [ENSMUST00000113962] [ENSMUST00000113963] [ENSMUST00000122955] [ENSMUST00000134606]

AlphaFold

Q9Z175

Predicted Effect

probably damaging
Transcript: ENSMUST00000000707
AA Change: D402V

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000000707
Gene: ENSMUSG00000000693
AA Change: D402V

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: ENSMUST00000089645

SMART Domains

Protein: ENSMUSP00000087073
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
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: ENSMUST00000101257

SMART Domains

Protein: ENSMUSP00000098815
Gene: ENSMUSG00000000693

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: ENSMUST00000113962

SMART Domains

Protein: ENSMUSP00000109595
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

probably benign
Transcript: ENSMUST00000122955

SMART Domains

Protein: ENSMUSP00000138153
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
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: ENSMUST00000132099

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203339

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204318

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155502

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204281

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154829

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144058

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184661

Predicted Effect

probably benign
Transcript: ENSMUST00000150217

SMART Domains

Protein: ENSMUSP00000118234
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
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: ENSMUST00000134606

SMART Domains

Protein: ENSMUSP00000115547
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
Pfam:Trypsin	7	180	2.7e-15	PFAM
Pfam:Trypsin_2	20	158	3.1e-24	PFAM
PDZ	209	283	2.86e-10	SMART

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.7%

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700025C18Rik	T	C	2: 164,920,946 (GRCm39)	D29G	unknown	Het
Abca13	A	T	11: 9,240,619 (GRCm39)	L827F	probably damaging	Het
Abcc1	T	A	16: 14,279,068 (GRCm39)	V1126E	probably damaging	Het
Abcc12	A	G	8: 87,290,617 (GRCm39)	L41S	probably damaging	Het
Adgrg7	T	C	16: 56,553,169 (GRCm39)	T643A	probably benign	Het
Angpt2	T	C	8: 18,755,747 (GRCm39)	N240S	probably damaging	Het
Apc	A	G	18: 34,446,655 (GRCm39)	T1150A	probably benign	Het
Apob	G	A	12: 8,057,751 (GRCm39)	D2078N	possibly damaging	Het
Apool	T	A	X: 111,274,258 (GRCm39)	S234T	probably benign	Het
Ascc3	C	T	10: 50,566,307 (GRCm39)	P751S	probably benign	Het
Astn2	G	A	4: 65,459,178 (GRCm39)	T1079I	probably damaging	Het
Atp8b1	T	C	18: 64,673,405 (GRCm39)	N989S	probably damaging	Het
B3gnt2	T	C	11: 22,786,621 (GRCm39)	D189G	probably damaging	Het
Bcas1	A	C	2: 170,190,081 (GRCm39)		probably null	Het
Btk	T	C	X: 133,448,350 (GRCm39)	D355G	probably benign	Het
C2cd4c	A	G	10: 79,448,823 (GRCm39)	V108A	possibly damaging	Het
Cbfa2t2	T	C	2: 154,359,727 (GRCm39)	L264P	probably damaging	Het
Cd22	A	T	7: 30,572,205 (GRCm39)	L423Q	probably damaging	Het
Cep128	T	C	12: 91,333,238 (GRCm39)	D9G	probably damaging	Het
Cer1	A	T	4: 82,801,120 (GRCm39)	V181D	probably damaging	Het
Ciita	T	C	16: 10,329,540 (GRCm39)	L584P	probably damaging	Het
Cmss1	T	C	16: 57,136,641 (GRCm39)	D77G	probably damaging	Het
Col4a2	T	C	8: 11,495,086 (GRCm39)	F1515L	probably benign	Het
Cyria	T	A	12: 12,412,362 (GRCm39)	V208D	probably damaging	Het
Dcaf1	T	A	9: 106,716,287 (GRCm39)	D360E	probably benign	Het
Dcaf1	A	G	9: 106,725,122 (GRCm39)	E536G	probably damaging	Het
Dnah2	T	A	11: 69,327,896 (GRCm39)	I3370F	probably damaging	Het
Dsg1c	T	C	18: 20,399,253 (GRCm39)	V119A	possibly damaging	Het
Edn3	A	G	2: 174,620,455 (GRCm39)	E103G	probably benign	Het
Efemp1	G	T	11: 28,871,613 (GRCm39)	R376L	probably damaging	Het
Eid1	A	G	2: 125,515,121 (GRCm39)	M4V	probably benign	Het
Emilin3	G	A	2: 160,751,530 (GRCm39)	R170C	possibly damaging	Het
Epx	T	C	11: 87,765,163 (GRCm39)	D178G	probably damaging	Het
Fkbp10	G	A	11: 100,312,499 (GRCm39)	V252I	possibly damaging	Het
Flnc	G	A	6: 29,443,796 (GRCm39)		probably null	Het
Fsip2	A	G	2: 82,813,076 (GRCm39)	K3132E	possibly damaging	Het
Gla	C	T	X: 133,497,071 (GRCm39)	A39T	probably damaging	Het
Hivep2	C	T	10: 14,006,501 (GRCm39)	T1033M	probably damaging	Het
Hsd17b8	A	T	17: 34,245,187 (GRCm39)	M259K	probably damaging	Het
Ift70a1	A	G	2: 75,811,801 (GRCm39)	L94P	probably benign	Het
Ikzf4	C	T	10: 128,470,026 (GRCm39)	G498D	probably damaging	Het
Impg1	T	C	9: 80,322,720 (GRCm39)	Y95C	probably damaging	Het
Ino80c	T	A	18: 24,244,810 (GRCm39)	K136*	probably null	Het
Iqsec1	A	C	6: 90,666,912 (GRCm39)	H508Q	probably benign	Het
Itgb3	A	G	11: 104,528,788 (GRCm39)	H305R	possibly damaging	Het
Jup	T	A	11: 100,277,167 (GRCm39)	T14S	probably benign	Het
Kcnh8	GAGACCAACGAGCAGCTGATGCTTCAGA	GAGA	17: 53,032,934 (GRCm39)	74	probably benign	Het
Klf12	T	C	14: 100,260,073 (GRCm39)	R219G	possibly damaging	Het
Klhl42	G	T	6: 147,009,291 (GRCm39)	V377L	probably benign	Het
Large1	A	G	8: 73,578,825 (GRCm39)	F460S	probably damaging	Het
Lrrc37a	T	A	11: 103,391,951 (GRCm39)	Y1158F	probably benign	Het
Map2	T	A	1: 66,451,958 (GRCm39)	S365T	probably damaging	Het
Mapk8ip1	A	G	2: 92,221,379 (GRCm39)		probably null	Het
Med26	A	G	8: 73,250,791 (GRCm39)	S103P	probably damaging	Het
Muc4	T	C	16: 32,570,121 (GRCm39)	S394P	possibly damaging	Het
Nle1	G	T	11: 82,796,373 (GRCm39)	P166Q	probably damaging	Het
Obox5	T	C	7: 15,492,807 (GRCm39)	I254T	probably benign	Het
Or1p1c	T	A	11: 74,161,159 (GRCm39)	W315R	probably benign	Het
Or4g7	G	T	2: 111,309,532 (GRCm39)	M134I	probably benign	Het
Or52j3	T	C	7: 102,836,137 (GRCm39)	F110L	probably benign	Het
Or7c19	T	C	8: 85,957,373 (GRCm39)	L83P	possibly damaging	Het
Pacs2	A	T	12: 113,026,077 (GRCm39)	N545Y	probably damaging	Het
Palld	T	C	8: 62,137,799 (GRCm39)	E652G	probably damaging	Het
Pgm5	T	C	19: 24,801,676 (GRCm39)	N184S	probably benign	Het
Pitpnm1	T	C	19: 4,161,873 (GRCm39)	V955A	probably benign	Het
Plcb1	T	A	2: 135,204,340 (GRCm39)	I898N	possibly damaging	Het
Pramel13	A	G	4: 144,121,244 (GRCm39)	V260A	possibly damaging	Het
Prr36	T	A	8: 4,265,205 (GRCm39)	T182S	probably benign	Het
Prss35	A	G	9: 86,637,565 (GRCm39)	S112G	probably benign	Het
Ptprj	C	T	2: 90,294,958 (GRCm39)	V417M	probably damaging	Het
Ptprm	G	T	17: 67,264,148 (GRCm39)		probably null	Het
Rasgrp2	T	C	19: 6,463,195 (GRCm39)	V498A	probably benign	Het
Rfx6	A	G	10: 51,597,700 (GRCm39)	N513S	possibly damaging	Het
Rhbdf1	A	G	11: 32,160,471 (GRCm39)	I693T	probably damaging	Het
Scn9a	T	C	2: 66,345,665 (GRCm39)	T1143A	probably damaging	Het
Spata17	A	G	1: 186,780,650 (GRCm39)	S366P	possibly damaging	Het
Svep1	A	G	4: 58,070,568 (GRCm39)	L2406P	probably benign	Het
Tasor2	A	T	13: 3,626,770 (GRCm39)	I1060K	probably benign	Het
Tgfb2	A	T	1: 186,362,962 (GRCm39)	Y287*	probably null	Het
Trip11	A	T	12: 101,851,619 (GRCm39)	V815E	probably benign	Het
Trp53bp2	G	T	1: 182,276,580 (GRCm39)	V854L	probably benign	Het
Vmn1r78	T	C	7: 11,887,270 (GRCm39)	S294P	possibly damaging	Het
Vmn2r86	T	C	10: 130,282,582 (GRCm39)	K678R	probably benign	Het
Yeats2	T	A	16: 19,977,931 (GRCm39)	N138K	probably benign	Het
Zup1	A	T	10: 33,803,460 (GRCm39)	N541K	possibly damaging	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
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
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'- ACTTCTAGGGGTGCATTCCTTG -3'
(R):5'- CACTGAGTCGGATCTGTAGAG -3'

Sequencing Primer
(F):5'- CATTCCTTGGGAAGGTATGGAGTCC -3'
(R):5'- ACTGAGTCGGATCTGTAGAGGTATAG -3'

Posted On

2014-08-25