Mutagenetix > Incidental Mutation

Incidental Mutation 'R6254:Lingo1'

505997

Institutional Source

Beutler Lab

Gene Symbol

Lingo1

Ensembl Gene

ENSMUSG00000049556

Gene Name

leucine rich repeat and Ig domain containing 1

Synonyms

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

MMRRC Submission

044371-MU

Accession Numbers

Genbank: NM_181074; MGI: 1915522

Is this an essential gene?

Probably non essential (E-score: 0.242) question?

Stock #

R6254 (G1)

Quality Score

196.009

Status

Validated

Chromosome

Chromosomal Location

56618475-56796468 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 56620087 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 406 (D406V)

Ref Sequence

ENSEMBL: ENSMUSP00000148179 (fasta)

Gene Model

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

AlphaFold

Q9D1T0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000053568
AA Change: D406V

PolyPhen 2 Score 0.546 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000059050
Gene: ENSMUSG00000049556
AA Change: D406V

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

possibly damaging
Transcript: ENSMUST00000114247
AA Change: D406V

PolyPhen 2 Score 0.546 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000109885
Gene: ENSMUSG00000049556
AA Change: D406V

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: D412V

PolyPhen 2 Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000109894
Gene: ENSMUSG00000049556
AA Change: D412V

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

possibly damaging
Transcript: ENSMUST00000210032
AA Change: D406V

PolyPhen 2 Score 0.546 (Sensitivity: 0.88; Specificity: 0.91)

Meta Mutation Damage Score

0.2202

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.4%

Validation Efficiency

100% (82/82)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932443I19Rik	A	G	8: 13,706,043	D26G	possibly damaging	Het
Adam6b	A	T	12: 113,489,570	L2F	probably damaging	Het
Ank2	T	A	3: 126,941,804		probably benign	Het
Anpep	T	G	7: 79,839,233	D369A	probably damaging	Het
App	T	C	16: 84,978,177	E599G	probably damaging	Het
Asphd1	C	T	7: 126,948,868	V88I	probably benign	Het
Atad5	A	T	11: 80,127,389	I1389F	probably damaging	Het
Blm	T	C	7: 80,480,342	N950S	probably benign	Het
Bsn	A	T	9: 108,111,866	M2229K	probably damaging	Het
Cacna2d2	A	G	9: 107,509,216	M181V	probably benign	Het
Cadps2	T	A	6: 23,329,163		probably null	Het
Cdh1	T	A	8: 106,663,798	V590D	probably damaging	Het
Cdk5rap2	G	A	4: 70,364,032	T160M	probably damaging	Het
Chrna5	A	G	9: 55,006,456	M325V	probably benign	Het
Clca3a2	A	G	3: 144,802,134	I116T	probably benign	Het
Cyp2c23	T	C	19: 44,005,463	K488R	probably benign	Het
Edil3	T	A	13: 89,319,729	I451N	probably damaging	Het
Exph5	T	G	9: 53,372,710	S364A	possibly damaging	Het
Fam84b	A	G	15: 60,823,801	I32T	probably damaging	Het
Fam98c	A	G	7: 29,154,517	S209P	probably damaging	Het
Fat3	G	A	9: 15,996,145	L2854F	probably benign	Het
Fbxo38	T	C	18: 62,505,500		probably null	Het
Fermt2	T	C	14: 45,476,059	D205G	probably damaging	Het
Fmnl1	G	A	11: 103,196,315		probably benign	Het
Fn3k	A	G	11: 121,435,068	E27G	probably damaging	Het
Foxj2	A	G	6: 122,838,139	H378R	probably damaging	Het
Fubp1	A	G	3: 152,232,408	K140E	possibly damaging	Het
Gm4788	A	G	1: 139,754,390	I156T	probably damaging	Het
Gm7694	A	T	1: 170,302,534	C98*	probably null	Het
Golgb1	T	C	16: 36,913,978	S1196P	probably damaging	Het
Gpm6a	G	A	8: 55,047,396		probably null	Het
Hltf	T	A	3: 20,063,829	N80K	possibly damaging	Het
Il1rap	G	A	16: 26,695,270	R251H	probably benign	Het
Ipo7	T	A	7: 110,049,060	D688E	probably benign	Het
Itgal	T	A	7: 127,325,203	N897K	probably damaging	Het
Itsn2	A	G	12: 4,624,982		probably null	Het
Kcnk13	A	G	12: 99,965,372		probably benign	Het
Kdm7a	A	G	6: 39,170,269	L248P	probably damaging	Het
Kmt2c	T	C	5: 25,349,874	E1254G	possibly damaging	Het
Ldah	G	A	12: 8,275,912		probably benign	Het
Lrriq1	A	T	10: 103,215,451	V480E	probably benign	Het
Mtcl1	C	T	17: 66,358,134	R1142H	probably benign	Het
Mtmr3	G	A	11: 4,497,381	Q360*	probably null	Het
Muc6	T	C	7: 141,651,115	N252S	probably benign	Het
Naa20	T	C	2: 145,903,320	L4P	probably damaging	Het
Neb	T	A	2: 52,222,961	I4274L	probably benign	Het
Noa1	A	T	5: 77,309,669	F130I	probably benign	Het
Nrg4	G	T	9: 55,236,512	H87N	possibly damaging	Het
Olfr1024	T	A	2: 85,904,505	Y183F	probably damaging	Het
Olfr632	T	A	7: 103,937,534	H51Q	probably benign	Het
P3h3	C	T	6: 124,845,601	E536K	probably damaging	Het
Pcdhb11	T	C	18: 37,421,718	S34P	probably damaging	Het
Pik3r1	T	C	13: 101,689,406	T71A	possibly damaging	Het
Plaur	T	A	7: 24,466,800	C99S	possibly damaging	Het
Plekha5	G	A	6: 140,586,436	G501E	probably damaging	Het
Plxnd1	C	T	6: 115,977,960	V614M	probably benign	Het
Ppp2r3a	T	C	9: 101,148,587	D307G	possibly damaging	Het
Prl3d3	C	T	13: 27,157,470	S28F	possibly damaging	Het
Prpf40a	T	C	2: 53,157,915	M197V	probably benign	Het
Ptk7	C	A	17: 46,572,642	Q832H	probably damaging	Het
Qser1	T	C	2: 104,790,090	S126G	probably benign	Het
Rab3ip	A	T	10: 116,915,867	C332S	probably damaging	Het
Raly	C	A	2: 154,857,366	T30K	probably damaging	Het
Rbp2	G	T	9: 98,490,647	S13I	probably benign	Het
Rps6ka1	C	T	4: 133,867,224	M159I	possibly damaging	Het
Rufy3	C	T	5: 88,584,309	T57I	probably benign	Het
Samd4	A	G	14: 47,016,631	D184G	probably damaging	Het
Slc35f3	T	C	8: 126,321,094	C58R	possibly damaging	Het
Smarca4	T	C	9: 21,699,877	I1467T	probably damaging	Het
Spag17	T	G	3: 100,065,585	I1371S	probably benign	Het
Sptan1	T	C	2: 30,007,549	L1228P	possibly damaging	Het
Stk31	C	T	6: 49,421,697	A344V	probably benign	Het
Supt16	A	G	14: 52,170,834	W885R	probably damaging	Het
Tdrd9	T	A	12: 112,025,900		probably null	Het
Tmod1	A	G	4: 46,078,469		probably null	Het
Tnfsf13	A	C	11: 69,684,483		probably null	Het
Trim75	C	A	8: 64,983,442	E119*	probably null	Het
Wdr6	T	C	9: 108,574,911	Y591C	probably damaging	Het
Wdr86	C	T	5: 24,718,283	R137H	probably benign	Het
Ythdf1	T	A	2: 180,911,150	Y424F	probably damaging	Het
Zfp984	G	T	4: 147,756,186	S69R	possibly damaging	Het
Zyg11a	A	G	4: 108,181,794	F743L	probably damaging	Het

Other mutations in Lingo1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01648:Lingo1	APN	9	56619827	missense	probably damaging	1.00
IGL02335:Lingo1	APN	9	56620081	missense	probably damaging	1.00
IGL03093:Lingo1	APN	9	56619464	missense	possibly damaging	0.90
3-1:Lingo1	UTSW	9	56620420	missense	probably benign	0.02
R1840:Lingo1	UTSW	9	56620558	missense	probably benign	0.38
R1932:Lingo1	UTSW	9	56619650	missense	possibly damaging	0.89
R2475:Lingo1	UTSW	9	56619626	missense	probably benign	0.03
R3439:Lingo1	UTSW	9	56620733	missense	probably benign	0.23
R3870:Lingo1	UTSW	9	56619725	missense	probably benign	0.00
R4241:Lingo1	UTSW	9	56620102	missense	probably damaging	1.00
R4701:Lingo1	UTSW	9	56620258	missense	probably damaging	1.00
R4757:Lingo1	UTSW	9	56619925	missense	probably benign	0.14
R5451:Lingo1	UTSW	9	56620427	missense	probably damaging	1.00
R6190:Lingo1	UTSW	9	56619650	missense	possibly damaging	0.89
R6836:Lingo1	UTSW	9	56619772	missense	probably damaging	0.99
R6849:Lingo1	UTSW	9	56619616	missense	probably damaging	1.00
R6935:Lingo1	UTSW	9	56619865	missense	probably damaging	1.00
R7051:Lingo1	UTSW	9	56620183	missense	probably benign	0.35
R7116:Lingo1	UTSW	9	56620627	missense	probably benign	0.17
R7196:Lingo1	UTSW	9	56620619	missense	probably damaging	1.00
R7470:Lingo1	UTSW	9	56620624	missense	probably damaging	1.00
R7471:Lingo1	UTSW	9	56620883	nonsense	probably null
R7804:Lingo1	UTSW	9	56619514	missense	probably benign	0.00
R8179:Lingo1	UTSW	9	56619850	missense	probably damaging	1.00
R8534:Lingo1	UTSW	9	56621069	missense	probably benign	0.00
R8684:Lingo1	UTSW	9	56620822	missense	probably damaging	0.98
R9430:Lingo1	UTSW	9	56620228	missense	probably benign	0.09
X0023:Lingo1	UTSW	9	56620028	nonsense	probably null
Z1177:Lingo1	UTSW	9	56620942	missense	possibly damaging	0.87

Predicted Primers

PCR Primer
(F):5'- ATCAGGGAAGACTGTGAGCC -3'
(R):5'- CGTGTGCTCAATGTCTCTGG -3'

Sequencing Primer
(F):5'- AGACTGTGAGCCGCCCATTG -3'
(R):5'- TGGAGGAGTCAGCCTTCCATTC -3'

Posted On

2018-02-28