Mutagenetix > Incidental Mutation

Incidental Mutation 'R9484:Lgi1'

716490

Institutional Source

Beutler Lab

Gene Symbol

Lgi1

Ensembl Gene

ENSMUSG00000067242

Gene Name

leucine-rich repeat LGI family, member 1

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.808) question?

Stock #

R9484 (G1)

Quality Score

96.0077

Status

Not validated

Chromosome

Chromosomal Location

38264536-38312214 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 38306309 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 510 (K510E)

Ref Sequence

ENSEMBL: ENSMUSP00000143128 (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 benign
Transcript: ENSMUST00000196090
AA Change: K462E

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: K462E

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 benign
Transcript: ENSMUST00000198518
AA Change: K510E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: K510E

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: K486E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: K486E

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: 99.9%
3x: 99.8%
10x: 99.2%
20x: 97.1%

Validation Efficiency

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acads	A	T	5: 115,112,786 (GRCm38)	C151S	probably damaging	Het
Actr8	T	C	14: 29,986,344 (GRCm38)	I193T	probably benign	Het
Btbd2	T	C	10: 80,644,269 (GRCm38)	N419S	probably benign	Het
Cacna2d1	T	A	5: 16,356,833 (GRCm38)	W821R	probably damaging	Het
Cadps2	T	C	6: 23,626,647 (GRCm38)	Y214C	probably benign	Het
Calu	T	A	6: 29,366,163 (GRCm38)	L180Q	probably damaging	Het
Corin	C	T	5: 72,339,937 (GRCm38)	V615I	probably damaging	Het
Cyp8b1	A	T	9: 121,915,917 (GRCm38)	D116E	probably benign	Het
D630036H23Rik	C	A	12: 36,381,712 (GRCm38)	A96S	unknown	Het
Ddx24	A	T	12: 103,411,296 (GRCm38)	Y717N	probably damaging	Het
Dmap1	G	T	4: 117,676,111 (GRCm38)	Q249K	probably benign	Het
Dnah10	T	A	5: 124,823,444 (GRCm38)	W3922R	probably damaging	Het
Dnah14	T	C	1: 181,690,208 (GRCm38)	F2036L	probably benign	Het
Dnah14	T	C	1: 181,797,746 (GRCm38)	I4064T	probably benign	Het
Dock9	A	C	14: 121,581,432 (GRCm38)	V1546G	probably damaging	Het
Eif3a	A	T	19: 60,766,568 (GRCm38)	S1059T	unknown	Het
Ep300	A	G	15: 81,636,825 (GRCm38)	E1262G	unknown	Het
Evl	T	A	12: 108,686,457 (GRCm38)	I387N	probably damaging	Het
Fat2	A	C	11: 55,309,926 (GRCm38)	V774G	probably damaging	Het
Fez1	T	A	9: 36,843,797 (GRCm38)	Y31N	probably benign	Het
Fkbp10	A	G	11: 100,423,134 (GRCm38)	I435V	probably damaging	Het
Flnb	A	G	14: 7,929,004 (GRCm38)	D1911G	probably benign	Het
Fnbp1	T	C	2: 31,083,026 (GRCm38)	Y154C	probably benign	Het
Fndc10	T	C	4: 155,695,039 (GRCm38)	I180T	possibly damaging	Het
Frmd4a	G	A	2: 4,604,215 (GRCm38)	V965I	possibly damaging	Het
Gabrr2	A	G	4: 33,071,352 (GRCm38)	H64R	possibly damaging	Het
Glis3	T	C	19: 28,531,003 (GRCm38)	D527G	probably damaging	Het
Gm2022	A	T	12: 87,895,479 (GRCm38)	Q37L	possibly damaging	Het
H2-Ob	T	A	17: 34,241,015 (GRCm38)	F33L	probably damaging	Het
Hbb-bh1	C	T	7: 103,843,032 (GRCm38)	E27K	probably benign	Het
Ifnb1	T	A	4: 88,522,678 (GRCm38)	T33S	probably benign	Het
Igkv4-80	T	A	6: 69,016,782 (GRCm38)	T42S	probably damaging	Het
Irs2	C	T	8: 11,007,334 (GRCm38)	G366D	probably damaging	Het
Kcnk2	CAAA	CAA	1: 189,256,694 (GRCm38)		probably null	Het
Krtap5-3	T	A	7: 142,202,331 (GRCm38)	C302S	unknown	Het
Lgi2	T	A	5: 52,538,594 (GRCm38)	D341V	probably benign	Het
Lin7c	T	C	2: 109,894,468 (GRCm38)	I14T	probably benign	Het
Lrrc19	A	T	4: 94,643,336 (GRCm38)	M13K	probably benign	Het
Lrrc69	T	C	4: 14,666,012 (GRCm38)	I315M	probably benign	Het
Myo5c	A	T	9: 75,297,488 (GRCm38)	D1541V	probably damaging	Het
Mypn	T	G	10: 63,167,240 (GRCm38)	M373L	probably benign	Het
Nckipsd	C	A	9: 108,812,638 (GRCm38)	H333N	probably damaging	Het
Nrg2	A	T	18: 36,024,348 (GRCm38)	L428Q	probably null	Het
Olfr1367	C	A	13: 21,347,417 (GRCm38)	T163K	probably damaging	Het
Olfr235	T	C	19: 12,268,371 (GRCm38)	I47T	possibly damaging	Het
Olfr53	T	C	7: 140,651,991 (GRCm38)	L4S	probably benign	Het
Otogl	C	T	10: 107,901,295 (GRCm38)	G86D	probably damaging	Het
Otogl	T	A	10: 107,822,033 (GRCm38)		probably null	Het
Papln	A	T	12: 83,791,844 (GRCm38)	Q1249L	probably benign	Het
Plxna2	G	T	1: 194,644,894 (GRCm38)	G379C	probably damaging	Het
Pofut2	T	C	10: 77,259,426 (GRCm38)	I35T	probably benign	Het
Pros1	A	G	16: 62,924,524 (GRCm38)	T501A	possibly damaging	Het
Rapgef1	T	C	2: 29,735,809 (GRCm38)	S1042P	possibly damaging	Het
Rps6kb1	C	T	11: 86,517,617 (GRCm38)	E185K	probably damaging	Het
Slc13a2	A	T	11: 78,403,407 (GRCm38)	L216Q	probably damaging	Het
Slc22a14	T	C	9: 119,180,549 (GRCm38)	Y160C	probably damaging	Het
Slc22a4	T	A	11: 53,988,947 (GRCm38)	I429F	possibly damaging	Het
Slc26a3	A	G	12: 31,461,786 (GRCm38)	K457E	probably damaging	Het
Slc47a2	T	C	11: 61,336,234 (GRCm38)	I169M	possibly damaging	Het
Slco1a1	C	T	6: 141,908,946 (GRCm38)	V660I	probably benign	Het
Smyd1	A	G	6: 71,225,466 (GRCm38)	Y252H	probably damaging	Het
Soga3	G	A	10: 29,196,973 (GRCm38)	D754N	probably damaging	Het
Spp2	A	T	1: 88,406,973 (GRCm38)		probably benign	Het
Stra8	T	A	6: 34,934,186 (GRCm38)	W250R	probably damaging	Het
Syne1	A	C	10: 5,220,359 (GRCm38)	L5183R	probably damaging	Het
Tdrd9	T	C	12: 112,046,250 (GRCm38)	S1203P	probably damaging	Het
Th	C	A	7: 142,899,883 (GRCm38)	E27*	probably null	Het
Thada	C	A	17: 84,429,191 (GRCm38)	L887F	probably damaging	Het
Timm23	T	C	14: 32,180,629 (GRCm38)	T186A	probably benign	Het
Tmem132b	A	T	5: 125,783,356 (GRCm38)	E555V	probably damaging	Het
Tnik	A	T	3: 28,594,944 (GRCm38)	Q457L	unknown	Het
Uba7	C	A	9: 107,983,838 (GRCm38)	H942Q	probably benign	Het
Upf2	T	C	2: 5,961,267 (GRCm38)	S233P	unknown	Het
Urm1	T	A	2: 29,842,748 (GRCm38)	N72K	probably damaging	Het
Usp10	T	C	8: 119,948,765 (GRCm38)	S508P	possibly damaging	Het
Usp37	G	A	1: 74,459,922 (GRCm38)	P632S	probably damaging	Het
Wdr77	T	A	3: 105,965,088 (GRCm38)	N209K	probably benign	Het
Zbtb24	C	T	10: 41,451,433 (GRCm38)	T105M	probably benign	Het
Zfp341	T	A	2: 154,643,843 (GRCm38)	I671N	probably damaging	Het
Zfp414	A	G	17: 33,630,010 (GRCm38)	T73A	probably benign	Het
Zfp574	A	T	7: 25,081,979 (GRCm38)	I809F	possibly damaging	Het
Zfp62	T	C	11: 49,217,281 (GRCm38)	I733T	probably damaging	Het
Zfp719	A	G	7: 43,590,157 (GRCm38)	I390V	possibly 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
R0201:Lgi1	UTSW	19	38,301,293 (GRCm38)	missense	possibly damaging	0.92
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

Predicted Primers

PCR Primer
(F):5'- TGACCAGATTCATTGGCGACTC -3'
(R):5'- CATGCATTGAGTTCATCCAGGTC -3'

Sequencing Primer
(F):5'- GACCAGATTCATTGGCGACTCTAAAG -3'
(R):5'- CGCACTGTAGAAAGTTTCCG -3'

Posted On

2022-07-18