Mutagenetix > Incidental Mutations

Incidental Mutation 'R5664:Loxl3'

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

Is this an essential gene?

Probably essential (E-score: 0.905) question?

Stock #

R5664 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

83034173-83052562 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 83049882 bp

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]

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

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: ENSMUST00000092618

SMART Domains

Protein: ENSMUSP00000090281
Gene: ENSMUSG00000068328

Domain	Start	End	E-Value	Type
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

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

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144058

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

noncoding transcript
Transcript: ENSMUST00000154829

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155502

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205152

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203180

Predicted Effect

probably benign
Transcript: ENSMUST00000204343

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204383

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204318

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203339

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204385

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204281

Predicted Effect

probably benign
Transcript: ENSMUST00000204719

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204761

Predicted Effect

probably benign
Transcript: ENSMUST00000203915

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204895

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184661

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610030E20Rik	T	A	6: 72,348,994		probably null	Het
1810032O08Rik	A	T	11: 116,672,664	T27S	possibly damaging	Het
4930432K21Rik	A	T	8: 84,166,659	I152F	probably benign	Het
9430015G10Rik	T	A	4: 156,123,559	L112H	probably damaging	Het
Acaca	T	C	11: 84,243,384	L441P	probably damaging	Het
Ank3	G	A	10: 70,002,565	R1566K	possibly damaging	Het
Arsj	A	T	3: 126,438,657	I351F	probably damaging	Het
Atp6v1b2	A	G	8: 69,107,620	T373A	probably damaging	Het
Atr	C	A	9: 95,905,813	N1486K	probably benign	Het
Avl9	T	C	6: 56,753,839	S583P	probably damaging	Het
Bptf	A	T	11: 107,073,699	D1493E	probably benign	Het
C2cd2l	T	C	9: 44,313,772	E548G	probably damaging	Het
Capn3	G	A	2: 120,477,025	R15Q	probably benign	Het
Ccl3	A	G	11: 83,649,213	F22S	probably benign	Het
Clcf1	T	C	19: 4,222,096	F69S	probably damaging	Het
Col13a1	T	C	10: 61,851,116	E170G	probably damaging	Het
Dhx29	T	A	13: 112,946,879	F489L	probably damaging	Het
Dhx8	A	T	11: 101,740,751	N390I	probably damaging	Het
Dkk1	T	A	19: 30,548,789	Y135F	probably benign	Het
Edil3	G	T	13: 89,319,713	V446F	probably damaging	Het
Epha5	T	A	5: 84,331,866	E93V	probably damaging	Het
Epsti1	C	T	14: 77,963,664	T196I	possibly damaging	Het
Fras1	T	C	5: 96,728,535	S2376P	possibly damaging	Het
Frem2	A	G	3: 53,652,490	V1532A	probably benign	Het
Fsip2	T	A	2: 82,988,095	M4724K	probably benign	Het
Gcat	T	A	15: 79,043,073	L238Q	probably damaging	Het
Gimap6	T	C	6: 48,702,275	K276E	probably benign	Het
Gjb5	T	A	4: 127,355,929	I141F	probably benign	Het
Glt6d1	T	C	2: 25,814,180	I7V	probably benign	Het
Gm37596	A	G	3: 93,692,687	F125S	probably benign	Het
Gm5771	C	T	6: 41,394,671	P17L	probably benign	Het
Gm6169	C	A	13: 97,099,121	L39F	probably damaging	Het
Gtf2h5	G	A	17: 6,084,524	G30R	probably damaging	Het
Herc6	C	A	6: 57,618,684	T449K	probably benign	Het
Hpn	A	T	7: 31,099,262	Y132N	probably damaging	Het
Hpx	A	T	7: 105,595,148	M190K	probably benign	Het
Inf2	A	G	12: 112,611,728	H1151R	unknown	Het
Krt74	A	G	15: 101,760,579		noncoding transcript	Het
Map7	T	A	10: 20,267,359	V418E	unknown	Het
Mrpl37	T	C	4: 107,064,391	N214D	probably benign	Het
Mthfr	T	C	4: 148,055,466	Y656H	probably damaging	Het
Myo9b	A	G	8: 71,359,882	D2099G	probably benign	Het
Nktr	T	A	9: 121,749,417	C825*	probably null	Het
Nomo1	A	G	7: 46,076,157	E1029G	probably benign	Het
Nup133	T	C	8: 123,906,281	D1037G	probably benign	Het
Olfr1271	A	G	2: 90,265,615	F272L	probably damaging	Het
Olfr153	T	C	2: 87,532,834	L267P	probably benign	Het
Pcdhb14	T	A	18: 37,448,996	V385D	possibly damaging	Het
Pik3c2g	T	C	6: 139,737,007	L38P	probably damaging	Het
Pkd1	A	T	17: 24,569,371	D701V	probably damaging	Het
Pnpla6	A	G	8: 3,537,478	T1070A	probably damaging	Het
Ppl	T	C	16: 5,106,055	D185G	probably benign	Het
Prune1	A	T	3: 95,258,178	L261Q	probably damaging	Het
Qser1	A	T	2: 104,778,196	L1444I	probably damaging	Het
Serpina6	A	C	12: 103,654,467	C8G	probably damaging	Het
Sla2	A	T	2: 156,874,999	D180E	probably benign	Het
Slc4a4	C	T	5: 89,028,244	L25F	probably damaging	Het
Tbx3	A	G	5: 119,678,731	K311R	possibly damaging	Het
Thbs2	A	T	17: 14,689,837	C167S	probably damaging	Het
Trak1	T	A	9: 121,472,307	C710S	possibly damaging	Het
Tsks	G	A	7: 44,953,784	E337K	probably damaging	Het
Vcpip1	A	G	1: 9,746,379	I593T	probably damaging	Het
Vmn2r118	A	G	17: 55,592,765	I713T	possibly damaging	Het
Vmn2r23	C	T	6: 123,713,074	T303M	probably damaging	Het
Vmn2r68	A	T	7: 85,233,770	M258K	probably benign	Het
Vmn2r76	A	G	7: 86,245,994		probably null	Het
Wap	A	G	11: 6,638,609	I5T	possibly damaging	Het
Zfp235	A	C	7: 24,142,151	H665P	probably damaging	Het

Other mutations in Loxl3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00957:Loxl3	APN	6	83048766	unclassified	probably benign
IGL01370:Loxl3	APN	6	83049487	missense	probably damaging	1.00
IGL02126:Loxl3	APN	6	83048647	missense	probably damaging	1.00
IGL02128:Loxl3	APN	6	83050583	missense	probably damaging	1.00
R0241:Loxl3	UTSW	6	83050133	missense	probably damaging	1.00
R0241:Loxl3	UTSW	6	83050133	missense	probably damaging	1.00
R1725:Loxl3	UTSW	6	83035593	missense	probably benign	0.00
R1771:Loxl3	UTSW	6	83049909	missense	probably damaging	1.00
R2017:Loxl3	UTSW	6	83048977	missense	probably damaging	0.99
R2291:Loxl3	UTSW	6	83037488	missense	probably benign	0.07
R3731:Loxl3	UTSW	6	83050671	critical splice donor site	probably null
R4179:Loxl3	UTSW	6	83037584	missense	probably benign	0.00
R5230:Loxl3	UTSW	6	83035794	missense	probably benign	0.16
R5385:Loxl3	UTSW	6	83050612	missense	probably damaging	0.99
R5591:Loxl3	UTSW	6	83048037	missense	probably damaging	1.00
R5769:Loxl3	UTSW	6	83050600	missense	probably damaging	0.98
R5771:Loxl3	UTSW	6	83035799	splice site	probably null
R5802:Loxl3	UTSW	6	83049289	missense	possibly damaging	0.67
R5831:Loxl3	UTSW	6	83049018	missense	probably benign	0.01
R5945:Loxl3	UTSW	6	83037511	missense	probably damaging	1.00
R6542:Loxl3	UTSW	6	83048166	missense	probably benign	0.00
R6687:Loxl3	UTSW	6	83050664	missense	probably damaging	1.00
R7961:Loxl3	UTSW	6	83050809	missense	possibly damaging	0.88
R8009:Loxl3	UTSW	6	83050809	missense	possibly damaging	0.88
R8122:Loxl3	UTSW	6	83049259	missense	probably damaging	1.00
R8278:Loxl3	UTSW	6	83048716	missense	probably damaging	1.00
R8373:Loxl3	UTSW	6	83048891	missense	possibly damaging	0.89
R8411:Loxl3	UTSW	6	83050624	missense	probably damaging	1.00
R8539:Loxl3	UTSW	6	83049526	missense	probably benign
V1024:Loxl3	UTSW	6	83035738	missense	probably damaging	1.00
X0009:Loxl3	UTSW	6	83038480	missense	probably damaging	1.00
Z1177:Loxl3	UTSW	6	83038578	nonsense	probably null
Z1177:Loxl3	UTSW	6	83048160	missense	probably benign	0.00

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