Mutagenetix > Incidental Mutation

Incidental Mutation 'R8899:Lgi1'

679876

Institutional Source

Beutler Lab

Gene Symbol

Lgi1

Ensembl Gene

ENSMUSG00000067242

Gene Name

leucine-rich repeat LGI family, member 1

Synonyms

MMRRC Submission

068756-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.740) question?

Stock #

R8899 (G1)

Quality Score

194.009

Status

Not validated

Chromosome

Chromosomal Location

38253135-38297387 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 38294538 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Tyrosine at position 413 (H413Y)

Ref Sequence

ENSEMBL: ENSMUSP00000143502 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000087252] [ENSMUST00000196090] [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

probably damaging
Transcript: ENSMUST00000196090
AA Change: H389Y

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

SMART Domains

Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: H389Y

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: 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 damaging
Transcript: ENSMUST00000198518
AA Change: H437Y

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

SMART Domains

Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: H437Y

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 damaging
Transcript: ENSMUST00000199812
AA Change: H413Y

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

SMART Domains

Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: H413Y

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.4%

Validation Efficiency

100% (70/70)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Agxt2	A	T	15: 10,378,900 (GRCm39)	N167I	probably damaging	Het
Arel1	A	G	12: 84,981,017 (GRCm39)	I330T	probably benign	Het
Ate1	T	C	7: 129,996,389 (GRCm39)	K484E	possibly damaging	Het
Atl2	T	C	17: 80,183,469 (GRCm39)	D42G	probably benign	Het
Bltp1	T	C	3: 37,042,429 (GRCm39)	I2805T	probably damaging	Het
Cd209e	C	T	8: 3,901,212 (GRCm39)	W147*	probably null	Het
Cdc40	G	A	10: 40,717,809 (GRCm39)	Q365*	probably null	Het
Cenpe	A	G	3: 134,945,644 (GRCm39)	T1053A	probably benign	Het
Colgalt1	T	C	8: 72,076,306 (GRCm39)	S586P	probably damaging	Het
Crem	A	G	18: 3,295,370 (GRCm39)	I91T	probably damaging	Het
Csrnp3	G	A	2: 65,852,987 (GRCm39)	V460I	possibly damaging	Het
Cul1	T	A	6: 47,474,246 (GRCm39)	I136N	possibly damaging	Het
Ddx19b	A	T	8: 111,737,929 (GRCm39)	I273N	probably damaging	Het
Fap	A	G	2: 62,348,817 (GRCm39)	I505T	probably damaging	Het
Fbxo44	A	T	4: 148,238,078 (GRCm39)	Y216*	probably null	Het
Fbxw10	T	A	11: 62,748,567 (GRCm39)	M398K	probably damaging	Het
Fut10	T	C	8: 31,726,514 (GRCm39)	V423A	possibly damaging	Het
Fyco1	A	C	9: 123,655,646 (GRCm39)	D1037E	probably benign	Het
Gabrg2	G	A	11: 41,867,377 (GRCm39)	R81*	probably null	Het
Gcn1	T	C	5: 115,717,220 (GRCm39)	V204A	probably benign	Het
Gnl1	T	C	17: 36,299,608 (GRCm39)	L593P	probably damaging	Het
Grm4	T	C	17: 27,653,754 (GRCm39)	Q732R	probably damaging	Het
Icam5	T	C	9: 20,948,415 (GRCm39)	V741A	possibly damaging	Het
Iqub	C	T	6: 24,505,768 (GRCm39)	E47K	probably benign	Het
Kcnk3	A	G	5: 30,779,580 (GRCm39)	K210R	probably benign	Het
Kdm2b	T	A	5: 123,125,851 (GRCm39)	R12*	probably null	Het
Kifbp	T	C	10: 62,399,282 (GRCm39)		probably benign	Het
Kndc1	C	T	7: 139,507,708 (GRCm39)	S1222F	possibly damaging	Het
Lhx8	A	G	3: 154,033,653 (GRCm39)	Y51H	probably damaging	Het
Lim2	T	C	7: 43,083,055 (GRCm39)	I80T	probably benign	Het
Macf1	A	G	4: 123,368,852 (GRCm39)	F405L	probably benign	Het
Mefv	G	A	16: 3,528,764 (GRCm39)	T559I	probably damaging	Het
Nin	A	G	12: 70,077,710 (GRCm39)	W1739R	probably damaging	Het
Or10h1	A	T	17: 33,418,718 (GRCm39)	K232M	probably damaging	Het
Or11j4	T	C	14: 50,630,269 (GRCm39)	F19L	probably damaging	Het
Or5t16	A	G	2: 86,818,710 (GRCm39)	I270T	probably benign	Het
Or8b3b	C	T	9: 38,584,147 (GRCm39)	V198I	probably damaging	Het
Otop3	T	C	11: 115,231,886 (GRCm39)		probably null	Het
Pate9	A	T	9: 36,446,254 (GRCm39)	C53S	probably damaging	Het
Pip5kl1	A	G	2: 32,469,082 (GRCm39)	I247V	probably benign	Het
Polr2d	T	A	18: 31,922,226 (GRCm39)	M1K	probably null	Het
Prss53	T	C	7: 127,488,193 (GRCm39)	T141A	possibly damaging	Het
Rdh12	A	G	12: 79,268,802 (GRCm39)	N293S	probably benign	Het
Rnf146	G	A	10: 29,223,754 (GRCm39)	T44I	probably benign	Het
Rsbn1l	A	T	5: 21,101,865 (GRCm39)	C588S	probably damaging	Het
Septin8	G	A	11: 53,426,862 (GRCm39)	V208I	probably damaging	Het
Sgo2a	T	G	1: 58,058,822 (GRCm39)	S1134A	possibly damaging	Het
Sh3bp4	C	T	1: 89,073,297 (GRCm39)	T715I	probably benign	Het
Snrnp200	A	G	2: 127,078,517 (GRCm39)	T1758A	probably damaging	Het
Snx6	A	T	12: 54,812,423 (GRCm39)	D70E	probably benign	Het
Spag9	T	C	11: 93,983,695 (GRCm39)	S341P	probably damaging	Het
Sparcl1	T	C	5: 104,240,590 (GRCm39)	D278G	probably benign	Het
Spmap2l	T	A	5: 77,185,200 (GRCm39)		probably null	Het
Srbd1	T	A	17: 86,292,885 (GRCm39)	S895C		Het
Stxbp5l	ATTTT	ATTTTT	16: 37,036,414 (GRCm39)		probably null	Het
Tas2r136	T	C	6: 132,754,323 (GRCm39)	D268G	probably benign	Het
Tas2r143	T	A	6: 42,377,888 (GRCm39)	Y239*	probably null	Het
Tbc1d17	C	T	7: 44,492,328 (GRCm39)	G419D	probably damaging	Het
Tff2	C	T	17: 31,362,113 (GRCm39)	W68*	probably null	Het
Thop1	T	C	10: 80,916,440 (GRCm39)	C483R	probably damaging	Het
Tmem245	A	C	4: 56,903,916 (GRCm39)		probably null	Het
Tmem67	A	G	4: 12,055,038 (GRCm39)	F655S	probably damaging	Het
Trim36	T	G	18: 46,302,264 (GRCm39)	S583R	possibly damaging	Het
Ucp1	T	C	8: 84,017,216 (GRCm39)	V2A	probably benign	Het
Ugt1a6a	T	A	1: 88,066,803 (GRCm39)	M203K	probably damaging	Het
Usp1	A	G	4: 98,819,347 (GRCm39)	K270E	probably damaging	Het
Vps13c	T	C	9: 67,841,783 (GRCm39)	F1935S	probably damaging	Het
Zfp521	C	A	18: 13,979,137 (GRCm39)	L425F	probably damaging	Het
Zfp799	G	T	17: 33,039,348 (GRCm39)	P306Q	probably damaging	Het
Zfp831	A	T	2: 174,485,978 (GRCm39)	R218W	probably 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
R4814:Lgi1	UTSW	19	38,289,326 (GRCm39)	critical splice donor site	probably null
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
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'- GGAAACGGATTCTACTCCCACC -3'
(R):5'- GAGTAAAGGAGTAATCGCTTCCG -3'

Sequencing Primer
(F):5'- ACCAATCCTTACATGCCTGG -3'
(R):5'- CGCTTCCGAGAATTGCATATTG -3'

Posted On

2021-08-31