Mutagenetix > Incidental Mutation

Incidental Mutation 'R1840:Lingo1'

205712

Institutional Source

Beutler Lab

Gene Symbol

Lingo1

Ensembl Gene

ENSMUSG00000049556

Gene Name

leucine rich repeat and Ig domain containing 1

Synonyms

UNQ201, 4930471K13Rik, Lrrn6a, LINGO-1, LERN1

MMRRC Submission

039866-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.228) question?

Stock #

R1840 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

56525759-56703752 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 56527842 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 249 (M249T)

Ref Sequence

ENSEMBL: ENSMUSP00000148179 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000053568] [ENSMUST00000114247] [ENSMUST00000114256] [ENSMUST00000210032]

AlphaFold

Q9D1T0

Predicted Effect

probably benign
Transcript: ENSMUST00000053568
AA Change: M249T

PolyPhen 2 Score 0.384 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000059050
Gene: ENSMUSG00000049556
AA Change: M249T

Domain	Start	End	E-Value	Type
low complexity region	21	32	N/A	INTRINSIC
LRRNT	35	69	1.6e-3	SMART
LRR	88	111	6.22e0	SMART
LRR_TYP	112	135	5.81e-2	SMART
LRR	136	159	6.57e-1	SMART
LRR	160	183	3.02e0	SMART
LRR	184	207	1.51e0	SMART
LRR	208	231	1.81e2	SMART
LRR	280	303	8.26e1	SMART
LRR	304	327	9.24e1	SMART
LRR	328	351	1.43e-1	SMART
LRRCT	363	416	4.15e-2	SMART
IGc2	431	498	1.58e-10	SMART
transmembrane domain	554	576	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000114247
AA Change: M249T

PolyPhen 2 Score 0.384 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000109885
Gene: ENSMUSG00000049556
AA Change: M249T

Domain	Start	End	E-Value	Type
low complexity region	21	32	N/A	INTRINSIC
LRRNT	35	69	1.6e-3	SMART
LRR	88	111	6.22e0	SMART
LRR_TYP	112	135	5.81e-2	SMART
LRR	136	159	6.57e-1	SMART
LRR	160	183	3.02e0	SMART
LRR	184	207	1.51e0	SMART
LRR	208	231	1.81e2	SMART
LRR	280	303	8.26e1	SMART
LRR	304	327	9.24e1	SMART
LRR	328	351	1.43e-1	SMART
LRRCT	363	416	4.15e-2	SMART
IGc2	431	498	1.58e-10	SMART
transmembrane domain	554	576	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000114256
AA Change: M255T

PolyPhen 2 Score 0.384 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000109894
Gene: ENSMUSG00000049556
AA Change: M255T

Domain	Start	End	E-Value	Type
low complexity region	27	38	N/A	INTRINSIC
LRRNT	41	75	1.6e-3	SMART
LRR	94	117	6.22e0	SMART
LRR_TYP	118	141	5.81e-2	SMART
LRR	142	165	6.57e-1	SMART
LRR	166	189	3.02e0	SMART
LRR	190	213	1.51e0	SMART
LRR	214	237	1.81e2	SMART
LRR	286	309	8.26e1	SMART
LRR	310	333	9.24e1	SMART
LRR	334	357	1.43e-1	SMART
LRRCT	369	422	4.15e-2	SMART
IGc2	437	504	1.58e-10	SMART
transmembrane domain	560	582	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000210032
AA Change: M249T

PolyPhen 2 Score 0.384 (Sensitivity: 0.90; Specificity: 0.89)

Coding Region Coverage

1x: 97.5%
3x: 96.8%
10x: 95.2%
20x: 92.2%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit early-onset CNS myelination. [provided by MGI curators]

Allele List at MGI

All alleles(1) : Targeted, knock-out(1)

Other mutations in this stock

Total: 118 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	T	A	16: 21,472,236 (GRCm39)	M85L	probably benign	Het
Aatk	T	G	11: 119,904,558 (GRCm39)	D206A	probably damaging	Het
Agap3	A	G	5: 24,705,229 (GRCm39)	D719G	probably damaging	Het
Agrn	G	A	4: 156,251,872 (GRCm39)	R1797C	probably damaging	Het
Ascc3	T	A	10: 50,566,257 (GRCm39)	M734K	probably benign	Het
Asph	T	A	4: 9,601,340 (GRCm39)	M136L	possibly damaging	Het
Atm	A	T	9: 53,367,830 (GRCm39)	V2431E	probably damaging	Het
Atp2b1	A	G	10: 98,858,791 (GRCm39)	H1158R	probably benign	Het
Atxn7l1	A	G	12: 33,421,032 (GRCm39)		probably null	Het
BC024139	G	T	15: 76,004,842 (GRCm39)	S611R	probably benign	Het
Becn1	C	T	11: 101,186,392 (GRCm39)	G105S	probably damaging	Het
Bud13	A	G	9: 46,197,706 (GRCm39)	E70G	probably damaging	Het
Cacul1	A	T	19: 60,522,688 (GRCm39)	L282*	probably null	Het
Catspere2	A	G	1: 177,830,581 (GRCm39)	D30G	possibly damaging	Het
Ccar1	T	A	10: 62,599,289 (GRCm39)	K614M	probably damaging	Het
Cd96	T	C	16: 45,919,455 (GRCm39)	T189A	probably benign	Het
Cdh5	C	A	8: 104,853,248 (GRCm39)	Y189*	probably null	Het
Chka	A	G	19: 3,936,460 (GRCm39)	N284S	probably benign	Het
Cntn6	A	T	6: 104,751,441 (GRCm39)	I366F	probably damaging	Het
Csmd3	C	T	15: 47,470,560 (GRCm39)	G3372E	probably damaging	Het
Cyp4f16	T	C	17: 32,761,980 (GRCm39)		probably null	Het
Dcaf6	A	G	1: 165,227,317 (GRCm39)	V270A	probably damaging	Het
Ddx60	T	A	8: 62,422,587 (GRCm39)	I608N	probably damaging	Het
Dnah9	A	T	11: 65,725,024 (GRCm39)	C1849*	probably null	Het
Eci3	C	A	13: 35,144,024 (GRCm39)	V34L	probably benign	Het
Eif1ad9	T	C	12: 88,296,181 (GRCm39)	V53A	probably benign	Het
Entrep2	C	A	7: 64,408,943 (GRCm39)	V484L	probably benign	Het
Epha1	C	T	6: 42,340,522 (GRCm39)	R583H	probably damaging	Het
Erbin	A	T	13: 103,971,455 (GRCm39)	N720K	probably benign	Het
Eya1	T	A	1: 14,299,728 (GRCm39)	R346*	probably null	Het
Fhdc1	G	A	3: 84,353,128 (GRCm39)	T699I	possibly damaging	Het
Flvcr2	T	C	12: 85,849,995 (GRCm39)	V427A	possibly damaging	Het
Frey1	T	C	2: 92,213,554 (GRCm39)	S36P	probably benign	Het
Fzd9	T	A	5: 135,278,425 (GRCm39)	T487S	probably benign	Het
Gas2l3	T	C	10: 89,258,113 (GRCm39)	Y160C	possibly damaging	Het
Gm10269	T	C	18: 20,815,866 (GRCm39)	K52R	probably damaging	Het
Gm8674	A	T	13: 50,055,801 (GRCm39)		noncoding transcript	Het
Gpr61	A	G	3: 108,057,797 (GRCm39)	V288A	possibly damaging	Het
Gramd4	T	C	15: 86,014,393 (GRCm39)		probably null	Het
Gtpbp4	A	G	13: 9,029,500 (GRCm39)	L403P	probably benign	Het
H6pd	A	T	4: 150,066,507 (GRCm39)	D626E	possibly damaging	Het
Herc6	T	A	6: 57,635,091 (GRCm39)	L769*	probably null	Het
Hes5	A	G	4: 155,045,711 (GRCm39)	K58R	probably damaging	Het
Heyl	A	G	4: 123,135,183 (GRCm39)	I59V	probably damaging	Het
Hpca	A	G	4: 129,012,393 (GRCm39)	F48L	probably damaging	Het
Ice1	C	T	13: 70,754,337 (GRCm39)	R583Q	probably benign	Het
Ints2	C	T	11: 86,123,911 (GRCm39)	G626R	probably damaging	Het
Kansl1l	T	A	1: 66,817,191 (GRCm39)	I390F	probably damaging	Het
Kat5	C	T	19: 5,659,266 (GRCm39)	V95M	possibly damaging	Het
Kcnh4	T	A	11: 100,636,167 (GRCm39)	I827F	possibly damaging	Het
Kif1b	C	T	4: 149,272,589 (GRCm39)	R138Q	probably damaging	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Lats1	T	A	10: 7,586,703 (GRCm39)	L955*	probably null	Het
Ldlrad2	A	C	4: 137,299,495 (GRCm39)	C110G	possibly damaging	Het
Lgi3	G	A	14: 70,772,216 (GRCm39)		probably null	Het
Lrig3	A	T	10: 125,849,258 (GRCm39)	R993*	probably null	Het
Lsm14b	T	A	2: 179,668,521 (GRCm39)	I74N	probably damaging	Het
Lyplal1	T	A	1: 185,832,414 (GRCm39)	I114F	probably damaging	Het
Mmp15	A	G	8: 96,092,048 (GRCm39)	Y86C	probably damaging	Het
Myh2	A	G	11: 67,077,313 (GRCm39)	E816G	probably benign	Het
Myo5c	A	G	9: 75,157,017 (GRCm39)	N151S	probably damaging	Het
Nckap1	T	A	2: 80,332,594 (GRCm39)	E1082V	possibly damaging	Het
Nrg4	A	C	9: 55,189,890 (GRCm39)		probably benign	Het
Nrp2	T	C	1: 62,777,498 (GRCm39)	L101P	probably damaging	Het
Or14j5	A	T	17: 38,161,639 (GRCm39)	D52V	probably damaging	Het
Or2at1	A	T	7: 99,416,803 (GRCm39)	T145S	probably benign	Het
Or4p19	T	C	2: 88,242,411 (GRCm39)	D197G	probably benign	Het
Or51q1c	A	G	7: 103,653,324 (GRCm39)	I281V	probably benign	Het
Or5ak22	G	A	2: 85,230,512 (GRCm39)	R122C	probably benign	Het
Parp14	T	A	16: 35,683,819 (GRCm39)	E169V	probably damaging	Het
Pcolce2	A	T	9: 95,552,256 (GRCm39)	N130Y	probably benign	Het
Pcolce2	G	A	9: 95,552,170 (GRCm39)	R101H	probably damaging	Het
Plscr1	A	T	9: 92,140,127 (GRCm39)	S5C	unknown	Het
Plxdc2	T	C	2: 16,674,667 (GRCm39)	V338A	probably benign	Het
Psg23	T	A	7: 18,344,363 (GRCm39)	N364I	possibly damaging	Het
Psmg4	A	G	13: 34,362,039 (GRCm39)	E109G	probably damaging	Het
Ptk2	T	C	15: 73,082,733 (GRCm39)	E908G	probably damaging	Het
Ptpn14	G	A	1: 189,519,048 (GRCm39)	R26H	probably damaging	Het
Ranbp2	T	A	10: 58,314,588 (GRCm39)	N1769K	probably benign	Het
Rbm14	C	T	19: 4,851,823 (GRCm39)		probably benign	Het
Rgs7	A	T	1: 174,980,714 (GRCm39)	D103E	probably damaging	Het
Rmnd5a	G	A	6: 71,375,439 (GRCm39)	L80F	probably benign	Het
Rock2	T	A	12: 16,978,990 (GRCm39)	D93E	probably benign	Het
Rps6ka6	A	G	X: 110,330,629 (GRCm39)	I246T	possibly damaging	Het
Rubcn	T	C	16: 32,646,542 (GRCm39)	M803V	possibly damaging	Het
Ryr3	T	C	2: 112,581,165 (GRCm39)	Y2889C	probably damaging	Het
Sall2	T	C	14: 52,551,182 (GRCm39)	N671S	probably damaging	Het
Selplg	T	C	5: 113,957,905 (GRCm39)	T134A	possibly damaging	Het
Sez6	C	A	11: 77,844,543 (GRCm39)	T122N	possibly damaging	Het
Slc9b1	T	A	3: 135,063,229 (GRCm39)	D4E	unknown	Het
Smim18	A	G	8: 34,232,376 (GRCm39)	M81T	probably benign	Het
Snap91	A	T	9: 86,697,518 (GRCm39)	H281Q	probably damaging	Het
Sparc	C	A	11: 55,286,692 (GRCm39)	C302F	probably damaging	Het
Spg11	A	G	2: 121,932,237 (GRCm39)	L535P	probably damaging	Het
Spsb1	G	A	4: 149,991,088 (GRCm39)	T160I	probably damaging	Het
Stra6	A	G	9: 58,047,813 (GRCm39)	N128S	probably benign	Het
Strc	T	C	2: 121,209,777 (GRCm39)	E182G	probably damaging	Het
Sult2a6	A	G	7: 13,988,754 (GRCm39)	M2T	probably benign	Het
Sv2c	T	C	13: 96,118,352 (GRCm39)	N499S	probably benign	Het
Szt2	A	T	4: 118,222,854 (GRCm39)		probably benign	Het
Tbx20	A	T	9: 24,636,972 (GRCm39)	S372T	probably benign	Het
Tcp11l2	T	A	10: 84,440,463 (GRCm39)	S289T	probably damaging	Het
Tdrd1	A	G	19: 56,830,744 (GRCm39)	E259G	probably damaging	Het
Thsd7a	T	A	6: 12,330,973 (GRCm39)	I1390L	probably benign	Het
Tln2	G	A	9: 67,249,325 (GRCm39)	R921W	probably damaging	Het
Tmem126a	C	A	7: 90,102,092 (GRCm39)	G36*	probably null	Het
Tmem245	C	T	4: 56,903,947 (GRCm39)	V606I	probably benign	Het
Trpm6	A	G	19: 18,843,631 (GRCm39)	D1665G	probably benign	Het
Ubac2	T	G	14: 122,231,674 (GRCm39)	V200G	probably benign	Het
Ubr5	G	A	15: 37,981,161 (GRCm39)	A2372V	possibly damaging	Het
Ugcg	C	T	4: 59,219,517 (GRCm39)	P285S	probably damaging	Het
Vmn1r9	T	C	6: 57,048,522 (GRCm39)	V199A	probably damaging	Het
Vmn2r118	T	A	17: 55,917,406 (GRCm39)	K369*	probably null	Het
Xpnpep3	G	T	15: 81,311,554 (GRCm39)	A87S	probably benign	Het
Zc3h7a	C	T	16: 10,978,890 (GRCm39)	R95H	probably damaging	Het
Zdhhc11	A	G	13: 74,122,771 (GRCm39)	N169S	probably damaging	Het
Zfp62	T	A	11: 49,107,215 (GRCm39)	D435E	probably damaging	Het
Zfyve16	T	C	13: 92,648,033 (GRCm39)	D1007G	possibly damaging	Het

Other mutations in Lingo1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01648:Lingo1	APN	9	56,527,111 (GRCm39)	missense	probably damaging	1.00
IGL02335:Lingo1	APN	9	56,527,365 (GRCm39)	missense	probably damaging	1.00
IGL03093:Lingo1	APN	9	56,526,748 (GRCm39)	missense	possibly damaging	0.90
3-1:Lingo1	UTSW	9	56,527,704 (GRCm39)	missense	probably benign	0.02
R1932:Lingo1	UTSW	9	56,526,934 (GRCm39)	missense	possibly damaging	0.89
R2475:Lingo1	UTSW	9	56,526,910 (GRCm39)	missense	probably benign	0.03
R3439:Lingo1	UTSW	9	56,528,017 (GRCm39)	missense	probably benign	0.23
R3870:Lingo1	UTSW	9	56,527,009 (GRCm39)	missense	probably benign	0.00
R4241:Lingo1	UTSW	9	56,527,386 (GRCm39)	missense	probably damaging	1.00
R4701:Lingo1	UTSW	9	56,527,542 (GRCm39)	missense	probably damaging	1.00
R4757:Lingo1	UTSW	9	56,527,209 (GRCm39)	missense	probably benign	0.14
R5451:Lingo1	UTSW	9	56,527,711 (GRCm39)	missense	probably damaging	1.00
R6190:Lingo1	UTSW	9	56,526,934 (GRCm39)	missense	possibly damaging	0.89
R6254:Lingo1	UTSW	9	56,527,371 (GRCm39)	missense	possibly damaging	0.55
R6836:Lingo1	UTSW	9	56,527,056 (GRCm39)	missense	probably damaging	0.99
R6849:Lingo1	UTSW	9	56,526,900 (GRCm39)	missense	probably damaging	1.00
R6935:Lingo1	UTSW	9	56,527,149 (GRCm39)	missense	probably damaging	1.00
R7051:Lingo1	UTSW	9	56,527,467 (GRCm39)	missense	probably benign	0.35
R7116:Lingo1	UTSW	9	56,527,911 (GRCm39)	missense	probably benign	0.17
R7196:Lingo1	UTSW	9	56,527,903 (GRCm39)	missense	probably damaging	1.00
R7470:Lingo1	UTSW	9	56,527,908 (GRCm39)	missense	probably damaging	1.00
R7471:Lingo1	UTSW	9	56,528,167 (GRCm39)	nonsense	probably null
R7804:Lingo1	UTSW	9	56,526,798 (GRCm39)	missense	probably benign	0.00
R8179:Lingo1	UTSW	9	56,527,134 (GRCm39)	missense	probably damaging	1.00
R8534:Lingo1	UTSW	9	56,528,353 (GRCm39)	missense	probably benign	0.00
R8684:Lingo1	UTSW	9	56,528,106 (GRCm39)	missense	probably damaging	0.98
R9430:Lingo1	UTSW	9	56,527,512 (GRCm39)	missense	probably benign	0.09
R9794:Lingo1	UTSW	9	56,528,592 (GRCm39)	missense	probably benign
X0023:Lingo1	UTSW	9	56,527,312 (GRCm39)	nonsense	probably null
Z1177:Lingo1	UTSW	9	56,528,226 (GRCm39)	missense	possibly damaging	0.87

Predicted Primers

PCR Primer
(F):5'- GTAGTTGAGCCCACGAAAGG -3'
(R):5'- CTGGAGAAATGCAATCTGACCTC -3'

Sequencing Primer
(F):5'- TGGATCTCCTGCAACCGC -3'
(R):5'- GAGAAATGCAATCTGACCTCCATCC -3'

Posted On

2014-06-23