Mutagenetix > Incidental Mutation

Incidental Mutation 'R6180:Lgi1'

488046

Institutional Source

Beutler Lab

Gene Symbol

Lgi1

Ensembl Gene

ENSMUSG00000067242

Gene Name

leucine-rich repeat LGI family, member 1

Synonyms

MMRRC Submission

044322-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.740) question?

Stock #

R6180 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

38253135-38297387 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 38253404 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 25 (L25P)

Ref Sequence

ENSEMBL: ENSMUSP00000142953 (fasta)

Gene Model

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

AlphaFold

Q9JIA1

Predicted Effect

probably damaging
Transcript: ENSMUST00000087252
AA Change: L25P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000084507
Gene: ENSMUSG00000067242
AA Change: L25P

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

noncoding transcript
Transcript: ENSMUST00000134832

Predicted Effect

possibly damaging
Transcript: ENSMUST00000196090
AA Change: L25P

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: L25P

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 damaging
Transcript: ENSMUST00000197123
AA Change: L25P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000142953
Gene: ENSMUSG00000067242
AA Change: L25P

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000198045
AA Change: L25P

PolyPhen 2 Score 0.787 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242
AA Change: L25P

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: L25P

PolyPhen 2 Score 0.676 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: L25P

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

possibly damaging
Transcript: ENSMUST00000199812
AA Change: L25P

PolyPhen 2 Score 0.482 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: L25P

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: ENSMUST00000199665

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.5%

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam39	A	G	8: 41,279,610 (GRCm39)	N667S	probably benign	Het
Ap4e1	T	A	2: 126,908,508 (GRCm39)	C1085*	probably null	Het
BC035044	A	T	6: 128,861,997 (GRCm39)		probably benign	Het
Bltp2	A	G	11: 78,164,084 (GRCm39)	M1142V	possibly damaging	Het
Capn11	T	C	17: 45,941,692 (GRCm39)	D693G	probably damaging	Het
Cavin4	A	T	4: 48,663,917 (GRCm39)	H99L	possibly damaging	Het
Ccdc86	T	C	19: 10,925,945 (GRCm39)	K218R	possibly damaging	Het
Ccno	T	C	13: 113,126,379 (GRCm39)	S283P	probably damaging	Het
Ccser2	A	T	14: 36,662,276 (GRCm39)	S303T	probably benign	Het
Cd53	T	A	3: 106,674,680 (GRCm39)	N129I	probably damaging	Het
Cd63	G	A	10: 128,747,933 (GRCm39)		probably null	Het
Cyp2j6	G	C	4: 96,424,323 (GRCm39)	L145V	probably damaging	Het
Daam2	A	G	17: 49,776,694 (GRCm39)	M797T	probably damaging	Het
Dennd2b	A	C	7: 109,156,095 (GRCm39)	D218E	probably benign	Het
Dmgdh	G	A	13: 93,888,794 (GRCm39)	V811I	possibly damaging	Het
Dpysl4	A	T	7: 138,670,250 (GRCm39)	T123S	probably damaging	Het
Erap1	A	G	13: 74,814,345 (GRCm39)	E428G	possibly damaging	Het
Fam124b	T	A	1: 80,177,902 (GRCm39)	T366S	possibly damaging	Het
Fbxw22	T	C	9: 109,215,747 (GRCm39)	D167G	probably damaging	Het
Flrt2	C	T	12: 95,746,012 (GRCm39)	Q117*	probably null	Het
Ftsj3	A	T	11: 106,144,166 (GRCm39)		probably null	Het
Ggn	A	G	7: 28,872,474 (GRCm39)	Y618C	probably damaging	Het
Glis1	T	A	4: 107,484,710 (GRCm39)	S402T	probably benign	Het
Gm4781	T	A	10: 100,232,349 (GRCm39)		noncoding transcript	Het
Gm7168	T	A	17: 14,168,858 (GRCm39)	I75K	probably damaging	Het
Gm7298	C	T	6: 121,737,782 (GRCm39)	H348Y	probably benign	Het
Gria1	G	T	11: 57,133,618 (GRCm39)	R499L	probably damaging	Het
Gtf2ird2	C	T	5: 134,245,389 (GRCm39)	T549M	probably damaging	Het
H2-M10.6	T	A	17: 37,125,178 (GRCm39)	V323E	probably damaging	Het
Hoxb3	G	A	11: 96,236,929 (GRCm39)	V336I	probably benign	Het
Il12b	G	A	11: 44,303,453 (GRCm39)	A327T	probably benign	Het
Inpp4a	C	A	1: 37,419,183 (GRCm39)	P588T	probably benign	Het
Kctd12	C	A	14: 103,219,027 (GRCm39)	D284Y	probably damaging	Het
Kif28	C	A	1: 179,525,337 (GRCm39)		probably null	Het
Krt1c	T	C	15: 101,723,479 (GRCm39)	N332S	probably benign	Het
Lama2	G	A	10: 26,857,495 (GRCm39)	T3118I	probably benign	Het
Lhx3	T	A	2: 26,091,503 (GRCm39)	M269L	probably benign	Het
Lmtk2	A	T	5: 144,112,160 (GRCm39)	E960V	probably damaging	Het
Loxl4	A	T	19: 42,596,791 (GRCm39)	D60E	probably damaging	Het
Lrp2	T	A	2: 69,333,868 (GRCm39)	N1458Y	possibly damaging	Het
Ltn1	A	T	16: 87,224,677 (GRCm39)	S16T	probably damaging	Het
Mllt6	G	A	11: 97,569,362 (GRCm39)	A875T	possibly damaging	Het
Mrgprb4	A	T	7: 47,848,574 (GRCm39)	I118N	probably damaging	Het
Mrps7	A	G	11: 115,495,707 (GRCm39)	T82A	possibly damaging	Het
Mug2	A	G	6: 122,056,565 (GRCm39)	E1170G	probably benign	Het
Nav2	A	G	7: 49,107,915 (GRCm39)	H647R	probably benign	Het
Nbeal2	T	C	9: 110,454,215 (GRCm39)	Y2710C	probably damaging	Het
Ndc1	A	T	4: 107,268,395 (GRCm39)	I644L	possibly damaging	Het
Or4c108	T	G	2: 88,804,226 (GRCm39)	N3T	probably damaging	Het
Or8g33	A	T	9: 39,338,008 (GRCm39)	Y120N	probably damaging	Het
Padi4	A	G	4: 140,483,784 (GRCm39)	M352T	possibly damaging	Het
Pals1	C	T	12: 78,864,084 (GRCm39)	H216Y	probably benign	Het
Pcdhgc3	C	A	18: 37,939,990 (GRCm39)	D130E	probably damaging	Het
Pde6a	A	T	18: 61,417,163 (GRCm39)		probably null	Het
Pdpn	C	T	4: 143,025,792 (GRCm39)	G12R	probably damaging	Het
Pot1a	A	T	6: 25,771,620 (GRCm39)	D200E	probably benign	Het
Ppa1	A	T	10: 61,503,431 (GRCm39)	D236V	probably benign	Het
Ptprn2	T	A	12: 116,822,739 (GRCm39)	S273T	probably benign	Het
Rasgrf2	T	C	13: 92,165,609 (GRCm39)	E297G	probably damaging	Het
Rgl1	T	C	1: 152,394,923 (GRCm39)	N750S	probably damaging	Het
Rinl	A	G	7: 28,496,365 (GRCm39)	N449D	probably benign	Het
Samd8	T	A	14: 21,825,093 (GRCm39)	H79Q	probably benign	Het
Scn11a	T	C	9: 119,583,933 (GRCm39)	I1561V	probably benign	Het
Slc39a12	T	C	2: 14,400,938 (GRCm39)	L105P	probably benign	Het
Slc7a12	A	T	3: 14,546,200 (GRCm39)		probably null	Het
Slco1a4	A	G	6: 141,763,546 (GRCm39)	I390T	possibly damaging	Het
Snta1	T	C	2: 154,219,102 (GRCm39)	N411S	probably benign	Het
Srgap2	T	C	1: 131,277,279 (GRCm39)	T323A	probably benign	Het
Ssh2	G	T	11: 77,344,291 (GRCm39)	V759L	probably benign	Het
Swap70	G	T	7: 109,869,188 (GRCm39)	R327L	probably damaging	Het
Tbc1d4	C	A	14: 101,696,206 (GRCm39)	C914F	probably benign	Het
Tbx3	A	G	5: 119,812,132 (GRCm39)	D144G	probably damaging	Het
Tgfbr2	T	C	9: 115,939,212 (GRCm39)	K205R	possibly damaging	Het
Tmem94	A	T	11: 115,681,857 (GRCm39)		probably null	Het
Usf3	T	A	16: 44,041,468 (GRCm39)	F1983I	probably damaging	Het
Ush2a	T	A	1: 188,132,068 (GRCm39)	C763*	probably null	Het
Vmn1r115	A	C	7: 20,578,640 (GRCm39)	L91V	probably damaging	Het
Vmn1r201	A	T	13: 22,659,499 (GRCm39)	I238F	possibly damaging	Het
Vmn1r28	T	A	6: 58,242,476 (GRCm39)	S106R	probably damaging	Het
Vmn1r82	T	C	7: 12,039,012 (GRCm39)	V95A	probably damaging	Het
Vrk3	A	T	7: 44,419,035 (GRCm39)	N371I	possibly damaging	Het
Wnt8b	C	A	19: 44,500,082 (GRCm39)	A223E	probably benign	Het
Xirp2	T	C	2: 67,335,921 (GRCm39)		probably null	Het
Xpo7	T	C	14: 70,920,243 (GRCm39)	N642S	probably benign	Het
Ythdc1	G	A	5: 86,975,953 (GRCm39)	R520H	possibly damaging	Het
Zfp367	T	C	13: 64,283,204 (GRCm39)	E316G	probably damaging	Het
Zfp488	T	A	14: 33,692,751 (GRCm39)	R137S	possibly damaging	Het
Zfp532	G	T	18: 65,789,542 (GRCm39)	V994L	probably benign	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
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'- AAGGGTGGACTCCTATGTGAC -3'
(R):5'- ATCTGTCTCACGAGCTCCATG -3'

Sequencing Primer
(F):5'- GTGACCTGTTCTTAGAGCAAGAC -3'
(R):5'- GAGCTCCATGCCCCTCTCAG -3'

Posted On

2017-10-10