Mutagenetix > Incidental Mutation

Incidental Mutation 'R7390:Lingo3'

573375

Institutional Source

Beutler Lab

Gene Symbol

Lingo3

Ensembl Gene

ENSMUSG00000051067

Gene Name

leucine rich repeat and Ig domain containing 3

Synonyms

LERN2

MMRRC Submission

045472-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.072) question?

Stock #

R7390 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

80668635-80679873 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 80670463 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 489 (T489I)

Ref Sequence

ENSEMBL: ENSMUSP00000054960 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000053986] [ENSMUST00000219924]

AlphaFold

Q6GQU6

Predicted Effect

probably damaging
Transcript: ENSMUST00000053986
AA Change: T489I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000054960
Gene: ENSMUSG00000051067
AA Change: T489I

Domain	Start	End	E-Value	Type
LRRNT	23	57	1.54e-5	SMART
LRR_TYP	76	99	1.38e-3	SMART
LRR_TYP	100	123	4.94e-5	SMART
LRR	124	147	3.86e0	SMART
LRR	148	171	4.98e-1	SMART
LRR	172	195	1.62e1	SMART
LRR	246	267	3.46e2	SMART
LRR	269	291	3.86e0	SMART
LRR	292	315	3.24e0	SMART
LRR	316	339	4.34e-1	SMART
LRRCT	351	404	7.18e-3	SMART
IGc2	419	486	3.12e-14	SMART
transmembrane domain	526	548	N/A	INTRINSIC
low complexity region	571	581	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000219924

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

97% (66/68)

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930486L24Rik	A	T	13: 60,992,152 (GRCm39)	D291E	probably benign	Het
Abca9	C	T	11: 110,036,487 (GRCm39)	V541I	probably benign	Het
Adamts15	A	T	9: 30,822,404 (GRCm39)		probably null	Het
Adgrg7	A	G	16: 56,553,207 (GRCm39)	I630T	probably damaging	Het
Ahnak	A	G	19: 8,980,569 (GRCm39)	I618V	probably benign	Het
Amotl2	T	A	9: 102,608,889 (GRCm39)	V801E	probably damaging	Het
Ankrd17	T	C	5: 90,430,779 (GRCm39)	T1002A	probably benign	Het
Bmp7	C	T	2: 172,711,998 (GRCm39)	D409N	probably damaging	Het
Bpifb2	A	G	2: 153,731,726 (GRCm39)	N293S	possibly damaging	Het
Ccdc162	A	G	10: 41,510,044 (GRCm39)	C854R	probably benign	Het
Ccdc171	A	G	4: 83,736,304 (GRCm39)	E1225G	probably damaging	Het
Cep350	T	C	1: 155,741,833 (GRCm39)	E2146G	possibly damaging	Het
Ces1a	A	C	8: 93,771,469 (GRCm39)		probably null	Het
Cfap45	T	G	1: 172,368,925 (GRCm39)	D444E	probably benign	Het
Cfap61	T	C	2: 145,843,802 (GRCm39)	V296A	probably benign	Het
Cgnl1	C	T	9: 71,552,931 (GRCm39)	R1011H	probably benign	Het
Cops4	C	T	5: 100,691,741 (GRCm39)	R347C	probably damaging	Het
D16Ertd472e	G	T	16: 78,344,576 (GRCm39)	D177E	probably benign	Het
Dcdc2a	T	C	13: 25,291,600 (GRCm39)	V195A	possibly damaging	Het
Dipk2a	A	G	9: 94,419,436 (GRCm39)	S165P	probably damaging	Het
Dpagt1	G	A	9: 44,243,319 (GRCm39)	V285I	probably benign	Het
Dspp	G	T	5: 104,323,552 (GRCm39)	A232S	probably damaging	Het
Efcab3	T	C	11: 104,615,411 (GRCm39)	I726T	possibly damaging	Het
Ephx2	G	A	14: 66,347,904 (GRCm39)			Het
Fat1	T	C	8: 45,405,511 (GRCm39)	V754A	possibly damaging	Het
Fstl3	G	A	10: 79,615,865 (GRCm39)	C117Y	probably damaging	Het
Gldc	A	T	19: 30,077,314 (GRCm39)	S953T	possibly damaging	Het
Gm1123	T	C	9: 98,893,033 (GRCm39)	N315S	probably benign	Het
Golga2	A	G	2: 32,178,202 (GRCm39)	E37G		Het
Gpr139	T	A	7: 118,743,835 (GRCm39)	Q250L	probably benign	Het
Grik3	C	T	4: 125,543,532 (GRCm39)	R283C	probably damaging	Het
Haao	A	C	17: 84,154,081 (GRCm39)	V22G	probably damaging	Het
Hspg2	T	A	4: 137,266,490 (GRCm39)	F1884I	probably damaging	Het
Hyal3	G	A	9: 107,462,166 (GRCm39)	G67S	probably damaging	Het
Kbtbd3	T	A	9: 4,330,424 (GRCm39)	I266K	probably benign	Het
Klhl26	A	C	8: 70,905,499 (GRCm39)	L137R	probably damaging	Het
Krt15	A	T	11: 100,026,386 (GRCm39)	V100E	possibly damaging	Het
Lars1	A	G	18: 42,343,083 (GRCm39)		probably null	Het
Lats1	C	T	10: 7,577,859 (GRCm39)	Q328*	probably null	Het
Lmtk2	T	C	5: 144,066,261 (GRCm39)	V65A	possibly damaging	Het
Lysmd1	T	C	3: 95,045,795 (GRCm39)	S211P	probably damaging	Het
Med15	C	T	16: 17,540,626 (GRCm39)	S21N	unknown	Het
Nav1	T	C	1: 135,512,656 (GRCm39)	T135A	probably benign	Het
Nt5c1a	G	C	4: 123,102,272 (GRCm39)	R66T	probably benign	Het
Pclo	T	C	5: 14,732,024 (GRCm39)	Y3509H	unknown	Het
Pkp4	G	A	2: 59,140,484 (GRCm39)	G397R	possibly damaging	Het
Ppp1r21	G	A	17: 88,856,958 (GRCm39)	A138T	probably benign	Het
Pum3	A	T	19: 27,401,642 (GRCm39)	V136D	probably benign	Het
Rab11fip3	A	T	17: 26,287,126 (GRCm39)	D342E	possibly damaging	Het
Rcvrn	T	A	11: 67,590,883 (GRCm39)	W156R	probably damaging	Het
Rspry1	C	T	8: 95,349,813 (GRCm39)	T67I	probably benign	Het
Serpina1d	T	C	12: 103,734,037 (GRCm39)	D89G	possibly damaging	Het
Sgsm3	T	A	15: 80,893,021 (GRCm39)	V366E	possibly damaging	Het
Shank3	T	G	15: 89,433,515 (GRCm39)	L1420R	probably benign	Het
Sirpb1b	A	T	3: 15,608,100 (GRCm39)	L215*	probably null	Het
Slc16a13	C	T	11: 70,109,797 (GRCm39)	V235I	probably benign	Het
Slc16a14	T	C	1: 84,907,187 (GRCm39)	D29G	probably benign	Het
Speer1a	T	C	5: 11,394,879 (GRCm39)	V122A	probably benign	Het
Spns2	T	A	11: 72,347,704 (GRCm39)	T329S	possibly damaging	Het
Sufu	G	A	19: 46,439,108 (GRCm39)		probably null	Het
Tll2	A	G	19: 41,108,608 (GRCm39)		probably null	Het
Trim10	G	A	17: 37,180,773 (GRCm39)	M1I	probably null	Het
Trim42	A	C	9: 97,241,182 (GRCm39)	N683K	probably damaging	Het
Trmt5	A	G	12: 73,328,394 (GRCm39)	S270P	probably damaging	Het
Vmn1r59	C	A	7: 5,456,986 (GRCm39)	R258L	possibly damaging	Het
Vmn2r32	A	G	7: 7,482,851 (GRCm39)	L41S	probably benign	Het
Vmn2r93	A	T	17: 18,525,329 (GRCm39)	E329V	probably damaging	Het
Ywhae	G	T	11: 75,655,487 (GRCm39)	E253*	probably null	Het

Other mutations in Lingo3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01141:Lingo3	APN	10	80,671,147 (GRCm39)	missense	probably damaging	1.00
IGL02120:Lingo3	APN	10	80,671,693 (GRCm39)	missense	probably damaging	1.00
IGL02755:Lingo3	APN	10	80,671,843 (GRCm39)	missense	possibly damaging	0.49
IGL02938:Lingo3	APN	10	80,670,988 (GRCm39)	missense	probably benign	0.00
IGL02945:Lingo3	APN	10	80,670,532 (GRCm39)	missense	probably damaging	1.00
IGL03167:Lingo3	APN	10	80,671,178 (GRCm39)	missense	probably damaging	1.00
R0639:Lingo3	UTSW	10	80,671,618 (GRCm39)	missense	probably benign	0.11
R0645:Lingo3	UTSW	10	80,671,169 (GRCm39)	missense	probably benign	0.00
R0673:Lingo3	UTSW	10	80,671,618 (GRCm39)	missense	probably benign	0.11
R1250:Lingo3	UTSW	10	80,670,605 (GRCm39)	missense	probably benign	0.05
R1521:Lingo3	UTSW	10	80,671,555 (GRCm39)	missense	probably benign
R1794:Lingo3	UTSW	10	80,671,432 (GRCm39)	missense	probably benign	0.19
R4665:Lingo3	UTSW	10	80,671,372 (GRCm39)	missense	probably damaging	1.00
R5587:Lingo3	UTSW	10	80,671,364 (GRCm39)	missense	probably damaging	0.98
R6458:Lingo3	UTSW	10	80,671,150 (GRCm39)	missense	probably damaging	1.00
R7082:Lingo3	UTSW	10	80,671,625 (GRCm39)	missense	probably benign
R7231:Lingo3	UTSW	10	80,670,938 (GRCm39)	missense	possibly damaging	0.86
R7314:Lingo3	UTSW	10	80,670,707 (GRCm39)	missense	possibly damaging	0.92
R7450:Lingo3	UTSW	10	80,670,671 (GRCm39)	nonsense	probably null
R7650:Lingo3	UTSW	10	80,671,597 (GRCm39)	missense	probably damaging	1.00
R7894:Lingo3	UTSW	10	80,670,610 (GRCm39)	nonsense	probably null
R7920:Lingo3	UTSW	10	80,670,382 (GRCm39)	missense	probably benign	0.09
R8070:Lingo3	UTSW	10	80,671,955 (GRCm39)	start gained	probably benign
R8095:Lingo3	UTSW	10	80,671,255 (GRCm39)	missense	probably benign	0.01
R8171:Lingo3	UTSW	10	80,670,595 (GRCm39)	missense	probably benign
R8178:Lingo3	UTSW	10	80,670,464 (GRCm39)	missense	possibly damaging	0.80
R8425:Lingo3	UTSW	10	80,670,816 (GRCm39)	missense	probably benign	0.04
R9053:Lingo3	UTSW	10	80,670,821 (GRCm39)	missense	probably benign	0.00
R9059:Lingo3	UTSW	10	80,670,523 (GRCm39)	missense	probably benign	0.12
R9706:Lingo3	UTSW	10	80,670,288 (GRCm39)	missense	probably damaging	0.99
R9794:Lingo3	UTSW	10	80,670,707 (GRCm39)	missense	possibly damaging	0.92
Z1176:Lingo3	UTSW	10	80,670,689 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- TCCACAGAGAAGTTATTCTTGTGC -3'
(R):5'- AGTACTTCGTGTGCCGCAAG -3'

Sequencing Primer
(F):5'- ACAGAGAAGTTATTCTTGTGCTGTCC -3'
(R):5'- ACGACGTGCGCTTTCTG -3'

Posted On

2019-09-13