Mutagenetix > Incidental Mutation

Incidental Mutation 'R0201:Lgi1'

23688

Institutional Source

Beutler Lab

Gene Symbol

Lgi1

Ensembl Gene

ENSMUSG00000067242

Gene Name

leucine-rich repeat LGI family, member 1

Synonyms

MMRRC Submission

038458-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.808) question?

Stock #

R0201 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

38264536-38312214 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 38301293 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 269 (E269G)

Ref Sequence

ENSEMBL: ENSMUSP00000143128 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000087252] [ENSMUST00000196090] [ENSMUST00000197123] [ENSMUST00000198045] [ENSMUST00000198518] [ENSMUST00000199812]

AlphaFold

Q9JIA1

Predicted Effect

probably benign
Transcript: ENSMUST00000087252

SMART Domains

Protein: ENSMUSP00000084507
Gene: ENSMUSG00000067242

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
LRRNT	41	71	9.09e0	SMART
LRR	90	113	2.61e2	SMART
LRR_TYP	114	137	5.14e-3	SMART
LRR_TYP	138	161	2.27e-4	SMART
LRRCT	173	222	4.63e-6	SMART
Pfam:EPTP	225	266	3.8e-9	PFAM
Pfam:EPTP	271	312	6.5e-12	PFAM
Pfam:EPTP	317	363	7.2e-16	PFAM
Pfam:EPTP	366	414	1.4e-7	PFAM
Pfam:EPTP	419	461	1.6e-12	PFAM
Pfam:EPTP	464	505	7.7e-11	PFAM
Pfam:EPTP	510	550	3.4e-13	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130039

SMART Domains

Protein: ENSMUSP00000117936
Gene: ENSMUSG00000067242

Domain	Start	End	E-Value	Type
low complexity region	11	38	N/A	INTRINSIC
LRR	51	74	2.61e2	SMART
LRR_TYP	75	98	5.14e-3	SMART
LRR_TYP	99	122	2.27e-4	SMART
LRRCT	131	180	4.63e-6	SMART
Pfam:EPTP	182	218	3e-12	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000196090
AA Change: E221G

PolyPhen 2 Score 0.923 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: E221G

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
LRRNT	41	71	4.4e-2	SMART
LRR_TYP	90	113	3.3e-4	SMART
LRRCT	125	174	2.3e-8	SMART
Pfam:EPTP	177	218	3.1e-6	PFAM
Pfam:EPTP	223	264	5.3e-9	PFAM
Pfam:EPTP	269	315	5.8e-13	PFAM
Pfam:EPTP	318	366	1.1e-4	PFAM
Pfam:EPTP	371	413	1.3e-9	PFAM
Pfam:EPTP	416	457	6.2e-8	PFAM
Pfam:EPTP	462	502	2.7e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000197123

SMART Domains

Protein: ENSMUSP00000142953
Gene: ENSMUSG00000067242

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
LRRNT	41	71	4.3e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000198045
AA Change: E269G

PolyPhen 2 Score 0.082 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242
AA Change: E269G

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
LRRNT	41	71	4.3e-2	SMART
LRR	90	113	1.1e0	SMART
LRR_TYP	114	137	2.1e-5	SMART
LRR_TYP	138	161	9.2e-7	SMART
LRRCT	173	222	2.3e-8	SMART
Pfam:EPTP	224	267	2.8e-12	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000198518
AA Change: E269G

PolyPhen 2 Score 0.923 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: E269G

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
LRRNT	41	71	9.09e0	SMART
LRR	90	113	2.61e2	SMART
LRR_TYP	114	137	5.14e-3	SMART
LRR_TYP	138	161	2.27e-4	SMART
LRRCT	173	222	4.63e-6	SMART
Pfam:EPTP	224	267	8.3e-15	PFAM
Pfam:EPTP	270	313	9.4e-16	PFAM
Pfam:EPTP	316	364	3.3e-18	PFAM
Pfam:EPTP	365	415	5.2e-8	PFAM
Pfam:EPTP	418	462	1e-16	PFAM
Pfam:EPTP	463	506	1.9e-15	PFAM
Pfam:EPTP	509	550	2.8e-17	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000199812
AA Change: E245G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: E245G

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
LRRNT	41	71	4.4e-2	SMART
LRR_TYP	90	113	2.2e-5	SMART
LRR_TYP	114	137	9.4e-7	SMART
LRRCT	149	198	2.3e-8	SMART
Pfam:EPTP	201	242	3.2e-6	PFAM
Pfam:EPTP	247	288	5.6e-9	PFAM
Pfam:EPTP	293	339	6.1e-13	PFAM
Pfam:EPTP	342	390	1.2e-4	PFAM
Pfam:EPTP	395	437	1.4e-9	PFAM
Pfam:EPTP	440	481	6.6e-8	PFAM
Pfam:EPTP	486	526	2.9e-10	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200561

Meta Mutation Damage Score

0.1057

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 94.2%

Validation Efficiency

97% (91/94)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the secreted leucine-rich repeat (LRR) superfamily and shares homology with members of the SLIT protein family. The encoded protein may regulate the activity of voltage-gated potassium channels and may be involved in neuronal growth regulation and cell survival. This gene is rearranged as a result of translocations in glioblastoma cell lines, and it is frequently down-regulated or rearranged in malignant gliomas. Mutations in this gene result in autosomal dominant lateral temporal epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit growth retardation, seizures, and death by the third week of life. Mice heterozygous for this allele exhibit increased suseptibility to pentylenetetrazole-induced seizures. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamdec1	A	G	14: 68,581,957 (GRCm38)		probably null	Het
Adamts16	T	A	13: 70,779,644 (GRCm38)	Q492L	possibly damaging	Het
Aplnr	A	G	2: 85,137,177 (GRCm38)	D182G	probably damaging	Het
Arnt2	G	T	7: 84,361,659 (GRCm38)	S3*	probably null	Het
Asxl3	T	C	18: 22,523,154 (GRCm38)	V1407A	probably benign	Het
Atg13	A	T	2: 91,684,762 (GRCm38)		probably null	Het
Atm	A	T	9: 53,454,279 (GRCm38)		probably benign	Het
Birc6	T	G	17: 74,609,327 (GRCm38)	V1746G	possibly damaging	Het
Cbln1	G	T	8: 87,472,113 (GRCm38)	T43K	probably benign	Het
Cbx5	T	C	15: 103,199,700 (GRCm38)	T173A	probably damaging	Het
Cc2d2a	A	G	5: 43,737,512 (GRCm38)	Y1437C	probably damaging	Het
Ccdc78	C	A	17: 25,789,236 (GRCm38)		probably benign	Het
Cd2bp2	A	G	7: 127,193,828 (GRCm38)	Y341H	probably damaging	Het
Cdhr5	T	A	7: 141,276,378 (GRCm38)	D88V	probably damaging	Het
Ces1f	T	A	8: 93,267,329 (GRCm38)	T275S	probably null	Het
Clca4a	T	C	3: 144,960,717 (GRCm38)	N458S	probably benign	Het
Cog5	A	G	12: 31,839,841 (GRCm38)	K521R	probably damaging	Het
Csf2ra	T	A	19: 61,225,568 (GRCm38)	T305S	probably benign	Het
Csmd3	T	A	15: 47,619,729 (GRCm38)		probably benign	Het
Cts6	T	A	13: 61,201,499 (GRCm38)	R132*	probably null	Het
D5Ertd579e	G	T	5: 36,616,465 (GRCm38)	N195K	probably damaging	Het
Ddx1	A	G	12: 13,223,808 (GRCm38)	V606A	probably damaging	Het
Dip2b	G	A	15: 100,186,147 (GRCm38)	D884N	probably damaging	Het
Ehhadh	A	G	16: 21,773,493 (GRCm38)		probably null	Het
Enpp1	T	A	10: 24,653,917 (GRCm38)	T608S	probably benign	Het
Fancm	T	C	12: 65,101,632 (GRCm38)	Y674H	probably damaging	Het
Fat4	T	A	3: 38,891,596 (GRCm38)	V1546D	probably damaging	Het
Fsd1	G	A	17: 55,990,522 (GRCm38)	A158T	probably benign	Het
Fzd2	T	A	11: 102,606,122 (GRCm38)	M464K	probably damaging	Het
Gjc2	A	G	11: 59,177,590 (GRCm38)	F22S	possibly damaging	Het
Gm13101	T	C	4: 143,964,890 (GRCm38)	E421G	probably damaging	Het
Gria2	T	C	3: 80,707,838 (GRCm38)	Y445C	probably damaging	Het
Hsdl1	T	A	8: 119,566,256 (GRCm38)	I147F	possibly damaging	Het
Ifi44	T	C	3: 151,745,636 (GRCm38)	Y226C	probably damaging	Het
Il16	A	G	7: 83,722,308 (GRCm38)	C97R	probably damaging	Het
Impg1	A	T	9: 80,345,561 (GRCm38)	S369T	probably damaging	Het
Jmjd1c	A	G	10: 67,219,109 (GRCm38)	T390A	unknown	Het
Lrp6	G	T	6: 134,450,897 (GRCm38)	Y1577*	probably null	Het
Lrrc74a	G	T	12: 86,761,773 (GRCm38)		probably benign	Het
Man1c1	A	T	4: 134,640,398 (GRCm38)		probably null	Het
Map1lc3b	A	C	8: 121,590,550 (GRCm38)	Q9P	possibly damaging	Het
Mboat1	G	A	13: 30,202,375 (GRCm38)	R124H	probably benign	Het
Mcu	A	G	10: 59,456,677 (GRCm38)	L60P	probably damaging	Het
Mrs2	G	T	13: 25,018,534 (GRCm38)	Q75K	probably benign	Het
Muc2	CGTG	CGTGTG	7: 141,699,185 (GRCm38)		probably null	Het
Neb	G	A	2: 52,206,878 (GRCm38)		probably benign	Het
Nlrp2	C	T	7: 5,328,329 (GRCm38)	G356D	probably benign	Het
Notch3	A	G	17: 32,156,148 (GRCm38)		probably benign	Het
Npr2	A	C	4: 43,641,617 (GRCm38)	S474R	probably damaging	Het
Nupl1	A	G	14: 60,244,616 (GRCm38)	F100L	probably benign	Het
Osbpl6	A	C	2: 76,546,042 (GRCm38)	D87A	possibly damaging	Het
Pabpc2	A	T	18: 39,775,307 (GRCm38)	M542L	probably benign	Het
Papln	A	G	12: 83,783,027 (GRCm38)		probably benign	Het
Parpbp	T	C	10: 88,092,896 (GRCm38)	I561V	possibly damaging	Het
Pcdhb13	C	T	18: 37,442,581 (GRCm38)	A4V	probably benign	Het
Pelp1	T	C	11: 70,395,704 (GRCm38)	T533A	possibly damaging	Het
Poldip3	T	A	15: 83,135,296 (GRCm38)	M182L	probably benign	Het
Por	T	C	5: 135,731,178 (GRCm38)	S240P	possibly damaging	Het
Pramef20	A	T	4: 144,377,273 (GRCm38)		probably benign	Het
Prss22	A	T	17: 23,996,301 (GRCm38)	V167D	probably damaging	Het
Prss37	A	C	6: 40,516,349 (GRCm38)	L61R	probably damaging	Het
Psmd1	C	T	1: 86,118,616 (GRCm38)	T702M	probably benign	Het
Pxdn	G	T	12: 30,002,431 (GRCm38)	G869V	possibly damaging	Het
Rabgap1l	A	G	1: 160,453,745 (GRCm38)		probably benign	Het
Rapgef6	T	C	11: 54,619,941 (GRCm38)	V228A	probably damaging	Het
Rnf169	T	C	7: 99,926,003 (GRCm38)	R462G	possibly damaging	Het
Rnft2	A	G	5: 118,194,680 (GRCm38)		probably benign	Het
Sgo2b	T	C	8: 63,926,636 (GRCm38)	D1054G	probably benign	Het
Sh3bgr	T	C	16: 96,228,517 (GRCm38)		probably benign	Het
Slc12a4	A	G	8: 105,945,350 (GRCm38)	V910A	possibly damaging	Het
Slc6a12	A	T	6: 121,355,372 (GRCm38)	I222F	probably benign	Het
Spty2d1	G	A	7: 46,997,901 (GRCm38)	R427*	probably null	Het
Ssc5d	A	G	7: 4,944,663 (GRCm38)	T1339A	probably benign	Het
Sspo	A	C	6: 48,455,752 (GRCm38)	E854A	possibly damaging	Het
Stx7	A	G	10: 24,185,079 (GRCm38)		probably benign	Het
Styk1	A	T	6: 131,301,730 (GRCm38)		probably benign	Het
Tex33	T	A	15: 78,378,828 (GRCm38)	M209L	probably damaging	Het
Tmem163	T	G	1: 127,668,637 (GRCm38)		probably benign	Het
Tmppe	C	CT	9: 114,404,639 (GRCm38)		probably null	Het
Tmx2	A	G	2: 84,673,082 (GRCm38)	V229A	probably benign	Het
Top2b	T	C	14: 16,383,174 (GRCm38)	L54P	probably damaging	Het
Trim62	A	T	4: 128,902,550 (GRCm38)	Y280F	probably benign	Het
Tssk4	A	T	14: 55,651,559 (GRCm38)	K181*	probably null	Het
Tssk4	A	T	14: 55,651,560 (GRCm38)	K181M	probably damaging	Het
Ubn1	A	G	16: 5,064,614 (GRCm38)	D313G	probably damaging	Het
Ugt1a10	C	T	1: 88,215,123 (GRCm38)	P113L	probably damaging	Het
Ugt1a10	C	T	1: 88,218,249 (GRCm38)	P473L	probably damaging	Het

Other mutations in Lgi1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02882:Lgi1	APN	19	38,284,005 (GRCm38)	missense	probably benign	0.24
IGL03112:Lgi1	APN	19	38,284,030 (GRCm38)	missense	possibly damaging	0.84
R1573:Lgi1	UTSW	19	38,284,181 (GRCm38)	missense	probably benign	0.30
R1795:Lgi1	UTSW	19	38,306,183 (GRCm38)	missense	probably benign
R2010:Lgi1	UTSW	19	38,301,235 (GRCm38)	missense	probably damaging	1.00
R3732:Lgi1	UTSW	19	38,306,246 (GRCm38)	missense	probably damaging	1.00
R3732:Lgi1	UTSW	19	38,306,246 (GRCm38)	missense	probably damaging	1.00
R3733:Lgi1	UTSW	19	38,306,246 (GRCm38)	missense	probably damaging	1.00
R4643:Lgi1	UTSW	19	38,300,710 (GRCm38)	missense	probably damaging	1.00
R4678:Lgi1	UTSW	19	38,301,289 (GRCm38)	missense	probably damaging	1.00
R4814:Lgi1	UTSW	19	38,300,878 (GRCm38)	critical splice donor site	probably null
R4857:Lgi1	UTSW	19	38,306,250 (GRCm38)	missense	probably damaging	1.00
R5598:Lgi1	UTSW	19	38,306,181 (GRCm38)	missense	possibly damaging	0.94
R6180:Lgi1	UTSW	19	38,264,956 (GRCm38)	missense	probably damaging	1.00
R6196:Lgi1	UTSW	19	38,305,809 (GRCm38)	missense	probably benign	0.23
R6847:Lgi1	UTSW	19	38,301,290 (GRCm38)	missense	probably damaging	1.00
R7178:Lgi1	UTSW	19	38,306,285 (GRCm38)	missense	probably damaging	1.00
R7376:Lgi1	UTSW	19	38,284,020 (GRCm38)	missense	probably damaging	1.00
R7448:Lgi1	UTSW	19	38,301,265 (GRCm38)	missense	probably damaging	1.00
R8790:Lgi1	UTSW	19	38,300,848 (GRCm38)	missense	possibly damaging	0.58
R8899:Lgi1	UTSW	19	38,306,090 (GRCm38)	missense	probably damaging	1.00
R9089:Lgi1	UTSW	19	38,305,647 (GRCm38)	missense	possibly damaging	0.56
R9156:Lgi1	UTSW	19	38,301,298 (GRCm38)	missense	probably benign	0.08
R9484:Lgi1	UTSW	19	38,306,309 (GRCm38)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CTGTGAAGGCCCACCGGAATATAAG -3'
(R):5'- GGGGTTAACACAACTAAGACCAGTCAG -3'

Sequencing Primer
(F):5'- TATTTGGGATCTAGCCAAGAAGTGC -3'
(R):5'- CCCTTGGGCAAAGCAGTTTA -3'

Posted On

2013-04-16