Mutagenetix > Incidental Mutation

Incidental Mutation 'R4814:Lgi1'

369682

Institutional Source

Beutler Lab

Gene Symbol

Lgi1

Ensembl Gene

ENSMUSG00000067242

Gene Name

leucine-rich repeat LGI family, member 1

Synonyms

MMRRC Submission

042432-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.772) question?

Stock #

R4814 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

38253135-38297387 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to T at 38289326 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000143502 (fasta)

Gene Model

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

probably null
Transcript: ENSMUST00000196090

SMART Domains

Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242

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 null
Transcript: ENSMUST00000196090

SMART Domains

Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242

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 null
Transcript: ENSMUST00000198045

SMART Domains

Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242

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

probably null
Transcript: ENSMUST00000198045

SMART Domains

Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242

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

probably null
Transcript: ENSMUST00000198518

SMART Domains

Protein: ENSMUSP00000143128
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	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 null
Transcript: ENSMUST00000199812

SMART Domains

Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242

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

probably null
Transcript: ENSMUST00000199812

SMART Domains

Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242

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

0.9486

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.7%
20x: 93.7%

Validation Efficiency

100% (79/79)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abi3bp	T	G	16: 56,471,116 (GRCm39)	V587G	probably benign	Het
Abtb2	A	G	2: 103,547,632 (GRCm39)	D1002G	probably benign	Het
Acap2	A	G	16: 30,926,944 (GRCm39)	S524P	probably benign	Het
Acsm1	A	T	7: 119,254,687 (GRCm39)	I385L	probably benign	Het
Adra1a	C	G	14: 66,875,481 (GRCm39)	A152G	probably benign	Het
Agbl4	A	T	4: 111,513,565 (GRCm39)	Y437F	possibly damaging	Het
Amt	A	G	9: 108,176,979 (GRCm39)	T196A	probably benign	Het
Apobr	G	A	7: 126,185,859 (GRCm39)	V457M	probably benign	Het
Birc6	A	G	17: 74,956,667 (GRCm39)	K3563E	probably damaging	Het
Cdadc1	AGACGGA	AGA	14: 59,806,440 (GRCm39)		probably null	Het
Chrna9	T	C	5: 66,134,492 (GRCm39)	W448R	probably damaging	Het
Cyp4a31	A	T	4: 115,427,466 (GRCm39)	D224V	probably damaging	Het
Ddx10	C	A	9: 53,115,405 (GRCm39)	R643L	possibly damaging	Het
Dip2c	A	G	13: 9,586,896 (GRCm39)	H200R	probably benign	Het
Dnah8	A	T	17: 30,986,898 (GRCm39)	R3182S	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Egfr	T	C	11: 16,819,354 (GRCm39)	C295R	probably damaging	Het
Garem1	A	T	18: 21,281,173 (GRCm39)	N394K	probably damaging	Het
Gcat	T	C	15: 78,915,322 (GRCm39)		probably null	Het
Gckr	C	T	5: 31,455,644 (GRCm39)	Q66*	probably null	Het
Gm26996	A	T	6: 130,556,317 (GRCm39)		noncoding transcript	Het
Gm9386	C	A	17: 81,246,141 (GRCm39)		noncoding transcript	Het
Gpr6	A	T	10: 40,947,258 (GRCm39)	M108K	possibly damaging	Het
H2-Q10	A	C	17: 35,784,481 (GRCm39)		probably benign	Het
Hpf1	A	G	8: 61,346,841 (GRCm39)	D52G	probably damaging	Het
Jak2	A	G	19: 29,279,377 (GRCm39)	R989G	probably damaging	Het
Kat7	A	G	11: 95,193,949 (GRCm39)		probably benign	Het
Kcnn3	G	T	3: 89,570,031 (GRCm39)	V615F	probably damaging	Het
Lrrtm4	A	T	6: 80,000,117 (GRCm39)	T510S	possibly damaging	Het
Map7d1	A	G	4: 126,128,114 (GRCm39)		probably null	Het
Mapt	T	C	11: 104,189,786 (GRCm39)	V252A	probably benign	Het
Mbd4	A	T	6: 115,826,260 (GRCm39)	S223T	possibly damaging	Het
Meig1	T	A	2: 3,412,959 (GRCm39)	I21L	probably benign	Het
Mia3	A	G	1: 183,113,684 (GRCm39)	Y447H	probably damaging	Het
Mrpl46	A	C	7: 78,430,343 (GRCm39)	N142K	probably benign	Het
Myo18a	C	A	11: 77,750,062 (GRCm39)		probably benign	Het
Nup188	A	G	2: 30,216,523 (GRCm39)	T776A	possibly damaging	Het
Oas1h	C	A	5: 121,000,728 (GRCm39)	H113N	probably damaging	Het
Or6c202	T	A	10: 128,996,245 (GRCm39)	T203S	possibly damaging	Het
Or7g18	A	G	9: 18,787,213 (GRCm39)	I197V	probably benign	Het
Or7g27	C	T	9: 19,250,476 (GRCm39)	T240M	probably damaging	Het
Or9i1b	A	T	19: 13,896,817 (GRCm39)	L144F	possibly damaging	Het
Orc3	T	A	4: 34,572,450 (GRCm39)		probably benign	Het
Osbpl3	T	A	6: 50,329,980 (GRCm39)	L65F	probably damaging	Het
Papola	C	A	12: 105,765,912 (GRCm39)	P4Q	probably damaging	Het
Pepd	A	G	7: 34,645,022 (GRCm39)	N151S	probably damaging	Het
Plekhm2	A	G	4: 141,355,150 (GRCm39)	L959P	probably benign	Het
Prpf40a	A	T	2: 53,080,032 (GRCm39)	H82Q	probably damaging	Het
Robo1	C	T	16: 72,768,923 (GRCm39)	T496M	probably benign	Het
Samd9l	T	G	6: 3,372,863 (GRCm39)	Q1466P	probably damaging	Het
Serpina1a	T	C	12: 103,821,022 (GRCm39)	T342A	probably benign	Het
Serpina3i	A	G	12: 104,231,470 (GRCm39)	T36A	probably benign	Het
Serpinb5	G	T	1: 106,800,069 (GRCm39)	L86F	probably damaging	Het
Slc35g1	A	G	19: 38,391,275 (GRCm39)	S186G	possibly damaging	Het
Slco6d1	T	A	1: 98,350,899 (GRCm39)	D126E	probably benign	Het
Smchd1	A	G	17: 71,718,763 (GRCm39)		probably null	Het
Smpdl3a	C	A	10: 57,687,337 (GRCm39)	T355K	probably damaging	Het
Sntg2	A	G	12: 30,423,267 (GRCm39)		probably benign	Het
Sox14	T	A	9: 99,757,284 (GRCm39)	M152L	probably benign	Het
Spats2l	G	T	1: 57,977,085 (GRCm39)	A308S	possibly damaging	Het
Tcf12	T	C	9: 71,777,323 (GRCm39)		probably benign	Het
Tcf7l2	T	A	19: 55,912,504 (GRCm39)	C478*	probably null	Het
Tekt5	A	G	16: 10,200,771 (GRCm39)	L250P	probably damaging	Het
Tmem132d	T	G	5: 128,061,328 (GRCm39)	I425L	probably benign	Het
Tmem174	T	A	13: 98,773,456 (GRCm39)	I125F	probably damaging	Het
Trafd1	T	G	5: 121,512,079 (GRCm39)	I404L	probably benign	Het
Trpm5	G	A	7: 142,636,373 (GRCm39)	P500S	possibly damaging	Het
Trpm6	T	A	19: 18,839,576 (GRCm39)	N1616K	probably benign	Het
Vmn1r4	A	G	6: 56,933,715 (GRCm39)	D73G	possibly damaging	Het
Vmn2r85	T	A	10: 130,254,567 (GRCm39)	I706F	probably benign	Het
Zc3h14	C	G	12: 98,719,107 (GRCm39)	D157E	probably damaging	Het
Zfp982	A	G	4: 147,597,090 (GRCm39)	Q149R	possibly damaging	Het

Other mutations in Lgi1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02882:Lgi1	APN	19	38,272,453 (GRCm39)	missense	probably benign	0.24
IGL03112:Lgi1	APN	19	38,272,478 (GRCm39)	missense	possibly damaging	0.84
R0201:Lgi1	UTSW	19	38,289,741 (GRCm39)	missense	possibly damaging	0.92
R1573:Lgi1	UTSW	19	38,272,629 (GRCm39)	missense	probably benign	0.30
R1795:Lgi1	UTSW	19	38,294,631 (GRCm39)	missense	probably benign
R2010:Lgi1	UTSW	19	38,289,683 (GRCm39)	missense	probably damaging	1.00
R3732:Lgi1	UTSW	19	38,294,694 (GRCm39)	missense	probably damaging	1.00
R3732:Lgi1	UTSW	19	38,294,694 (GRCm39)	missense	probably damaging	1.00
R3733:Lgi1	UTSW	19	38,294,694 (GRCm39)	missense	probably damaging	1.00
R4643:Lgi1	UTSW	19	38,289,158 (GRCm39)	missense	probably damaging	1.00
R4678:Lgi1	UTSW	19	38,289,737 (GRCm39)	missense	probably damaging	1.00
R4857:Lgi1	UTSW	19	38,294,698 (GRCm39)	missense	probably damaging	1.00
R5598:Lgi1	UTSW	19	38,294,629 (GRCm39)	missense	possibly damaging	0.94
R6180:Lgi1	UTSW	19	38,253,404 (GRCm39)	missense	probably damaging	1.00
R6196:Lgi1	UTSW	19	38,294,257 (GRCm39)	missense	probably benign	0.23
R6847:Lgi1	UTSW	19	38,289,738 (GRCm39)	missense	probably damaging	1.00
R7178:Lgi1	UTSW	19	38,294,733 (GRCm39)	missense	probably damaging	1.00
R7376:Lgi1	UTSW	19	38,272,468 (GRCm39)	missense	probably damaging	1.00
R7448:Lgi1	UTSW	19	38,289,713 (GRCm39)	missense	probably damaging	1.00
R8790:Lgi1	UTSW	19	38,289,296 (GRCm39)	missense	possibly damaging	0.58
R8899:Lgi1	UTSW	19	38,294,538 (GRCm39)	missense	probably damaging	1.00
R9089:Lgi1	UTSW	19	38,294,095 (GRCm39)	missense	possibly damaging	0.56
R9156:Lgi1	UTSW	19	38,289,746 (GRCm39)	missense	probably benign	0.08
R9484:Lgi1	UTSW	19	38,294,757 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CTGTTTCAGGGACCTAAGAGG -3'
(R):5'- GGCTAGATCCCAAATACCCG -3'

Sequencing Primer
(F):5'- CCTAAGAGGGAACGCATTTAATTGTG -3'
(R):5'- GGCTAGATCCCAAATACCCGTACATC -3'

Posted On

2016-02-04