Mutagenetix > Incidental Mutation

Incidental Mutation 'R4701:Lingo1'

356046

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

041949-MU

Accession Numbers

Genbank: NM_181074; MGI: 1915522

Essential gene?

Probably non essential (E-score: 0.132) question?

Stock #

R4701 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

56618475-56796468 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 56620258 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 349 (F349S)

Ref Sequence

ENSEMBL: ENSMUSP00000148179 (fasta)

Gene Model

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

AlphaFold

Q9D1T0

Predicted Effect

probably damaging
Transcript: ENSMUST00000053568
AA Change: F349S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000059050
Gene: ENSMUSG00000049556
AA Change: F349S

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 damaging
Transcript: ENSMUST00000114247
AA Change: F349S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000109885
Gene: ENSMUSG00000049556
AA Change: F349S

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 damaging
Transcript: ENSMUST00000114256
AA Change: F355S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000109894
Gene: ENSMUSG00000049556
AA Change: F355S

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 damaging
Transcript: ENSMUST00000210032
AA Change: F349S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Meta Mutation Damage Score

0.9415

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.6%

Validation Efficiency

96% (108/112)

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aarsd1	T	C	11: 101,411,160	I196V	probably benign	Het
Aass	T	A	6: 23,075,856	K761*	probably null	Het
Abca13	A	G	11: 9,292,306	T1390A	possibly damaging	Het
Abhd16a	T	C	17: 35,096,606		probably null	Het
Acad11	C	T	9: 104,095,565	Q486*	probably null	Het
Actl9	T	C	17: 33,433,935	L323P	probably benign	Het
Adam12	T	A	7: 133,916,462	I650F	possibly damaging	Het
Adgre4	A	T	17: 55,784,971	D77V	probably damaging	Het
Ankrd26	A	G	6: 118,506,485	F1586S	possibly damaging	Het
Anpep	T	C	7: 79,839,465	T320A	probably benign	Het
Arl15	T	A	13: 113,967,725	C133S	probably benign	Het
Ascc3	A	G	10: 50,720,664	N1230S	possibly damaging	Het
Atf4	T	A	15: 80,257,417	I336K	probably damaging	Het
Atp7b	A	T	8: 22,000,121	S1044T	probably benign	Het
Atp8b4	A	G	2: 126,414,293	F249L	probably damaging	Het
AU021092	G	T	16: 5,212,193	N319K	probably benign	Het
Bbs4	A	G	9: 59,323,519	V440A	probably benign	Het
Bpifb4	G	T	2: 153,950,385	G450C	probably damaging	Het
Cadm1	G	A	9: 47,818,822		probably benign	Het
Ccser2	G	A	14: 36,938,697	L500F	probably damaging	Het
Cd22	T	A	7: 30,876,153	I155F	probably damaging	Het
Cdkl4	A	T	17: 80,543,652	V207E	probably damaging	Het
Cfap65	T	C	1: 74,918,908	D947G	probably damaging	Het
Cntn6	T	C	6: 104,804,360	V397A	probably benign	Het
Cpox	T	A	16: 58,677,969	Y388*	probably null	Het
Dab1	C	T	4: 104,731,751	A524V	probably benign	Het
Dda1	T	A	8: 71,473,810	Y58N	probably damaging	Het
Dennd4a	C	T	9: 64,897,357	T1326I	possibly damaging	Het
Eps8l2	A	T	7: 141,357,260	I338F	probably damaging	Het
Fbxo42	A	G	4: 141,199,809	T467A	probably benign	Het
Flt4	T	C	11: 49,626,808	F319S	possibly damaging	Het
Fmn1	A	T	2: 113,584,071	Y895F	possibly damaging	Het
Gm6887	C	A	7: 42,465,093		noncoding transcript	Het
Grid2	A	G	6: 64,665,915	D887G	probably benign	Het
Grm6	C	T	11: 50,863,010	P714S	probably damaging	Het
Gsto2	A	G	19: 47,884,656	I157V	probably benign	Het
Il15ra	A	G	2: 11,718,345		probably null	Het
Impg1	A	G	9: 80,314,400	F713L	probably benign	Het
Jag1	T	A	2: 137,094,456	T373S	probably benign	Het
Kcnh3	T	A	15: 99,241,945	L904Q	probably benign	Het
Kctd19	C	A	8: 105,390,429	G356V	possibly damaging	Het
Kdm5b	T	A	1: 134,606,012		probably benign	Het
Kif1a	T	C	1: 93,078,835	I37V	probably damaging	Het
Lama5	G	A	2: 180,191,696	R1508C	probably damaging	Het
Lamb1	T	A	12: 31,266,848	C65*	probably null	Het
Loxl4	G	A	19: 42,607,613	H147Y	probably benign	Het
Lrrn4cl	T	A	19: 8,852,055	N132K	probably damaging	Het
Med17	A	T	9: 15,270,360	H31Q	probably damaging	Het
Med23	A	T	10: 24,893,648	L476F	probably damaging	Het
Mgst1	A	T	6: 138,150,838	D66V	probably damaging	Het
Mroh2a	T	C	1: 88,234,612		probably null	Het
Mroh2a	A	C	1: 88,241,618	I672L	probably benign	Het
Muc4	A	T	16: 32,755,846		probably benign	Het
Myo18a	C	T	11: 77,817,665	T30M	probably damaging	Het
Ncapg2	G	T	12: 116,440,618	R903L	probably benign	Het
Nme1	A	G	11: 93,965,908	I9T	probably damaging	Het
Nmt2	T	A	2: 3,322,641	I357N	probably benign	Het
Nphp4	T	C	4: 152,496,659	F100S	probably damaging	Het
Oca2	C	A	7: 56,255,002	T72K	probably benign	Het
Olfr1411	C	A	1: 92,597,438	D306E	probably benign	Het
Olfr625-ps1	G	A	7: 103,683,062	V105M	probably damaging	Het
Olfr676	A	T	7: 105,035,591	D131V	probably damaging	Het
Olfr677	A	T	7: 105,056,879	D211V	probably damaging	Het
Olfr871	T	C	9: 20,212,625	I92T	probably damaging	Het
Plce1	A	T	19: 38,725,007	T1240S	probably benign	Het
Plch1	A	T	3: 63,699,496		probably null	Het
Plxna4	T	C	6: 32,516,688	D331G	probably damaging	Het
Ppp1r3a	T	C	6: 14,718,993	T641A	probably benign	Het
Rab32	A	G	10: 10,550,854	L116P	probably benign	Het
Recql4	C	T	15: 76,708,585	C302Y	probably damaging	Het
Rorc	G	C	3: 94,391,710	E391Q	probably null	Het
Saa4	A	T	7: 46,731,627	F24I	possibly damaging	Het
Sall1	T	A	8: 89,031,160	K772M	probably damaging	Het
Sdk1	T	G	5: 142,185,231	L1950V	probably damaging	Het
Sil1	T	C	18: 35,266,896	E352G	probably benign	Het
Slc26a3	C	T	12: 31,447,774	P59L	probably damaging	Het
Smco2	T	C	6: 146,861,942		probably benign	Het
Sppl3	A	G	5: 115,103,313		probably null	Het
St6gal2	T	A	17: 55,496,344	V360D	probably damaging	Het
Stard9	G	A	2: 120,705,713	R345Q	possibly damaging	Het
Susd4	T	A	1: 182,892,061	Y414N	probably damaging	Het
Tenm4	T	C	7: 96,895,349	Y2191H	probably damaging	Het
Tln2	A	G	9: 67,346,527	V754A	probably benign	Het
Tmem132c	T	A	5: 127,564,496		probably benign	Het
Tnn	A	T	1: 160,147,768	S30T	possibly damaging	Het
Trpd52l3	G	T	19: 30,004,495	V217F	probably damaging	Het
Trpm1	G	T	7: 64,243,500	L1033F	probably damaging	Het
Tulp2	A	G	7: 45,517,924	E182G	probably damaging	Het
Ubr4	A	G	4: 139,471,336	K4490R	possibly damaging	Het
Usp17la	A	T	7: 104,860,649	R154*	probably null	Het
Vmn2r17	T	G	5: 109,427,983	M240R	probably damaging	Het
Vmn2r22	T	A	6: 123,650,469	N56I	probably benign	Het
Wdr66	A	G	5: 123,322,613	K1213E	probably benign	Het
Zdhhc21	A	T	4: 82,820,334	I206N	possibly damaging	Het
Zfp148	T	A	16: 33,456,908	D122E	probably benign	Het
Zfp804a	A	T	2: 82,256,582	S252C	probably damaging	Het
Zgrf1	C	T	3: 127,598,704	T1291I	probably benign	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
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
R6254:Lingo1	UTSW	9	56620087	missense	possibly damaging	0.55
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
R9794:Lingo1	UTSW	9	56621308	missense	probably benign
X0023:Lingo1	UTSW	9	56620028	nonsense	probably null
Z1177:Lingo1	UTSW	9	56620942	missense	possibly damaging	0.87

Predicted Primers

PCR Primer
(F):5'- TGTGGCCCTCATCTACAAAC -3'
(R):5'- CCAATCGGTACAATCGAGGG -3'

Sequencing Primer
(F):5'- TGAAGTAGTTGGGTAGGAGTACATC -3'
(R):5'- TACAATCGAGGGCTCCATGCTG -3'

Posted On

2015-10-21