Mutagenetix > Incidental Mutation

Incidental Mutation 'R9156:Lgi1'

695406

Institutional Source

Beutler Lab

Gene Symbol

Lgi1

Ensembl Gene

ENSMUSG00000067242

Gene Name

leucine-rich repeat LGI family, member 1

Synonyms

MMRRC Submission

068974-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.740) question?

Stock #

R9156 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

38253135-38297387 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 38289746 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 271 (T271A)

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

probably benign
Transcript: ENSMUST00000196090
AA Change: T223A

PolyPhen 2 Score 0.076 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: T223A

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: T271A

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

SMART Domains

Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242
AA Change: T271A

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: T271A

PolyPhen 2 Score 0.076 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: T271A

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: T247A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: T247A

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

Meta Mutation Damage Score

0.0821

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.8%

Validation Efficiency

98% (61/62)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	T	G	6: 121,647,957 (GRCm39)	L1150V	probably damaging	Het
AB124611	A	G	9: 21,455,989 (GRCm39)	D194G	possibly damaging	Het
Adgrv1	A	G	13: 81,669,302 (GRCm39)	L2418P	probably benign	Het
Ap3m1	A	G	14: 21,090,152 (GRCm39)	S213P	probably damaging	Het
Apobec2	A	T	17: 48,739,531 (GRCm39)	L36H		Het
Arrb1	A	G	7: 99,237,280 (GRCm39)	D78G		Het
Astn1	A	G	1: 158,338,555 (GRCm39)	Q434R	probably damaging	Het
Cadps	C	G	14: 12,705,676 (GRCm38)	D240H	probably damaging	Het
Cfhr4	A	G	1: 139,660,085 (GRCm39)	I680T	probably damaging	Het
Cmya5	A	C	13: 93,233,878 (GRCm39)	D403E	unknown	Het
Crxos	A	C	7: 15,631,436 (GRCm39)	I45L	probably benign	Het
Dmxl1	C	G	18: 50,072,639 (GRCm39)	N2744K	probably damaging	Het
Dnah2	A	G	11: 69,313,687 (GRCm39)	I4204T		Het
Ei24	A	G	9: 36,697,327 (GRCm39)	S134P	probably damaging	Het
Eif2ak3	G	T	6: 70,860,614 (GRCm39)	V397F	probably damaging	Het
Eif4g2	T	C	7: 110,672,969 (GRCm39)	I134V		Het
Fam186a	A	G	15: 99,841,159 (GRCm39)	I1695T	possibly damaging	Het
Gcnt3	T	C	9: 69,941,939 (GRCm39)	M210V	probably damaging	Het
Gpatch8	A	G	11: 102,370,299 (GRCm39)	S1080P	probably benign	Het
Gtf3c1	A	G	7: 125,244,949 (GRCm39)	L1695P	possibly damaging	Het
Haus3	A	G	5: 34,324,994 (GRCm39)	F222L	probably damaging	Het
Kbtbd8	C	T	6: 95,099,825 (GRCm39)	Q445*	probably null	Het
Kcnc3	A	G	7: 44,240,592 (GRCm39)	N95D	probably damaging	Het
Krt40	C	T	11: 99,430,693 (GRCm39)		probably null	Het
Ltbp2	G	A	12: 84,837,864 (GRCm39)	P1192L	probably benign	Het
Map3k21	A	G	8: 126,665,463 (GRCm39)	T551A	possibly damaging	Het
Muc5ac	T	C	7: 141,363,529 (GRCm39)	I2280T	unknown	Het
Mug1	C	A	6: 121,851,390 (GRCm39)	D762E	probably damaging	Het
Myo1e	A	T	9: 70,266,605 (GRCm39)	N615I	probably damaging	Het
Or4k36	T	C	2: 111,145,827 (GRCm39)	M1T	probably null	Het
Or51f23	T	C	7: 102,453,339 (GRCm39)	L218P	probably damaging	Het
Pld5	T	C	1: 175,803,104 (GRCm39)	E387G	possibly damaging	Het
Pld5	A	G	1: 175,902,003 (GRCm39)	V195A	probably benign	Het
Rad54l	T	C	4: 115,980,349 (GRCm39)		probably benign	Het
Rnf123	A	T	9: 107,940,227 (GRCm39)		probably benign	Het
Rnf213	A	G	11: 119,331,574 (GRCm39)	E2262G		Het
Rp1	C	A	1: 4,234,161 (GRCm39)	V910L	unknown	Het
Rpp21	A	T	17: 36,568,407 (GRCm39)	C23S	probably benign	Het
Scn11a	T	C	9: 119,588,989 (GRCm39)	M1306V	possibly damaging	Het
Scn2b	C	T	9: 45,036,734 (GRCm39)	L81F	possibly damaging	Het
Sco2	T	C	15: 89,256,363 (GRCm39)	D97G	probably damaging	Het
Slc25a54	T	C	3: 109,001,548 (GRCm39)	V112A	probably benign	Het
Slc5a11	A	T	7: 122,864,492 (GRCm39)	K363*	probably null	Het
Smg1	G	T	7: 117,753,884 (GRCm39)	T2563K	unknown	Het
Snap47	A	T	11: 59,319,290 (GRCm39)	S283T	probably damaging	Het
Speer4a3	CTTT	C	5: 26,155,857 (GRCm39)		probably benign	Het
Stat1	G	T	1: 52,178,388 (GRCm39)	R274L	probably damaging	Het
Stoml1	A	G	9: 58,164,409 (GRCm39)	T166A		Het
Svs5	G	T	2: 164,079,509 (GRCm39)	Q133K	probably benign	Het
Tas2r107	T	A	6: 131,636,422 (GRCm39)	H209L	probably benign	Het
Tmco3	T	A	8: 13,360,228 (GRCm39)	V477D	possibly damaging	Het
Tmem131	A	T	1: 36,880,767 (GRCm39)	S168T	possibly damaging	Het
Tmem41a	T	C	16: 21,755,859 (GRCm39)	N149S	probably damaging	Het
Ttll4	T	C	1: 74,719,225 (GRCm39)	F359L	probably benign	Het
Ttn	T	A	2: 76,785,162 (GRCm39)	M784L	unknown	Het
Ubr1	A	G	2: 120,703,603 (GRCm39)		probably null	Het
Ubxn2b	C	T	4: 6,214,646 (GRCm39)	P227S	probably damaging	Het
Upb1	C	T	10: 75,265,961 (GRCm39)	L263F	probably benign	Het
Usp15	T	A	10: 122,949,553 (GRCm39)	T935S	probably benign	Het
Zscan4-ps3	G	A	7: 11,347,164 (GRCm39)	C400Y	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
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
R9484:Lgi1	UTSW	19	38,294,757 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CGGGTATTTGGGATCTAGCCAAG -3'
(R):5'- TTAGCAGGCAATCTCAAGTCAC -3'

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

Posted On

2022-01-20