Mutagenetix > Incidental Mutation

Incidental Mutation 'R7376:Lgi2'

572377

Institutional Source

Beutler Lab

Gene Symbol

Lgi2

Ensembl Gene

ENSMUSG00000039252

Gene Name

leucine-rich repeat LGI family, member 2

Synonyms

MMRRC Submission

045459-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.059) question?

Stock #

R7376 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

52690859-52723689 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 52695604 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 452 (R452C)

Ref Sequence

ENSEMBL: ENSMUSP00000040436 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039750] [ENSMUST00000199942]

AlphaFold

Q8K4Z0

Predicted Effect

probably damaging
Transcript: ENSMUST00000039750
AA Change: R452C

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000040436
Gene: ENSMUSG00000039252
AA Change: R452C

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Blast:LRRNT	32	62	9e-15	BLAST
LRR_TYP	81	104	7.26e-3	SMART
LRR_TYP	105	128	4.72e-2	SMART
LRRCT	140	189	4.49e-4	SMART
Pfam:EPTP	224	265	3.9e-12	PFAM
Pfam:EPTP	270	311	2e-13	PFAM
Pfam:EPTP	316	362	2.1e-16	PFAM
Pfam:EPTP	365	407	2.3e-9	PFAM
Pfam:EPTP	412	454	4.8e-12	PFAM
Pfam:EPTP	457	498	2.7e-14	PFAM
low complexity region	499	509	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000199942
AA Change: R444C

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000143707
Gene: ENSMUSG00000039252
AA Change: R444C

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Blast:LRRNT	32	62	7e-15	BLAST
LRR_TYP	81	104	7.26e-3	SMART
LRR_TYP	105	128	4.72e-2	SMART
LRR_TYP	129	152	5.99e-4	SMART
LRRCT	164	213	4.49e-4	SMART
Pfam:EPTP	216	257	5.6e-12	PFAM
Pfam:EPTP	262	303	2.8e-13	PFAM
Pfam:EPTP	308	354	3e-16	PFAM
Pfam:EPTP	357	399	3.3e-9	PFAM
Pfam:EPTP	404	446	6.8e-12	PFAM
Pfam:EPTP	449	490	3.8e-14	PFAM
low complexity region	491	501	N/A	INTRINSIC

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

Validation Efficiency

98% (60/61)

Allele List at MGI

Other mutations in this stock

Total: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	A	G	11: 9,241,118 (GRCm39)	I994V	probably benign	Het
Acan	T	G	7: 78,738,055 (GRCm39)		probably null	Het
Adamts12	G	A	15: 11,277,425 (GRCm39)	V680I	possibly damaging	Het
Adgrg7	T	C	16: 56,545,342 (GRCm39)	I712V	probably damaging	Het
Adgrl3	A	G	5: 81,942,597 (GRCm39)	H1477R	probably damaging	Het
Adgrv1	T	A	13: 81,666,245 (GRCm39)	D1937V	probably damaging	Het
Alms1	T	C	6: 85,599,088 (GRCm39)	S1305P	probably benign	Het
Banp	T	A	8: 122,701,236 (GRCm39)	M39K	probably damaging	Het
Bbs10	A	G	10: 111,135,111 (GRCm39)	T75A	probably benign	Het
BC028528	CTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTT	CTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTT	3: 95,795,448 (GRCm39)		probably benign	Het
Bltp3b	G	A	10: 89,645,518 (GRCm39)	G1197D	probably damaging	Het
Brinp2	C	T	1: 158,078,938 (GRCm39)	C295Y	probably damaging	Het
Card11	C	T	5: 140,883,993 (GRCm39)	V429I	probably benign	Het
Cdca3	G	A	6: 124,809,538 (GRCm39)	R184H	probably benign	Het
Cep104	A	G	4: 154,067,509 (GRCm39)		probably null	Het
Clspn	A	G	4: 126,484,430 (GRCm39)	K1196R	possibly damaging	Het
Cntnap5b	A	G	1: 99,894,994 (GRCm39)	T89A	possibly damaging	Het
Cpne9	A	T	6: 113,266,974 (GRCm39)	I136L	probably damaging	Het
Crat	T	A	2: 30,296,477 (GRCm39)	I330F	probably damaging	Het
Ctbp2	G	T	7: 132,615,697 (GRCm39)	Q413K	possibly damaging	Het
D630045J12Rik	T	C	6: 38,151,238 (GRCm39)	E1220G	probably damaging	Het
Dap	A	G	15: 31,235,985 (GRCm39)	D41G	probably damaging	Het
Dnah14	A	G	1: 181,590,967 (GRCm39)	I3287V	probably benign	Het
Dsp	A	G	13: 38,356,819 (GRCm39)	H233R	probably damaging	Het
Dst	T	C	1: 34,231,770 (GRCm39)	I3121T	probably benign	Het
Espnl	T	G	1: 91,250,036 (GRCm39)	L61R	probably damaging	Het
Evc2	T	C	5: 37,527,983 (GRCm39)	S331P	possibly damaging	Het
Gars1	A	G	6: 55,050,344 (GRCm39)	E535G	probably benign	Het
Hfm1	A	G	5: 107,043,084 (GRCm39)	I650T	possibly damaging	Het
Iyd	T	A	10: 3,495,690 (GRCm39)	I116N	probably damaging	Het
Kif16b	A	G	2: 142,553,792 (GRCm39)	L1002S	probably damaging	Het
Kifbp	C	T	10: 62,394,843 (GRCm39)	V600I	possibly damaging	Het
Lgi1	G	A	19: 38,272,468 (GRCm39)	G113D	probably damaging	Het
Man2b2	T	G	5: 36,970,722 (GRCm39)	N764T	probably damaging	Het
Mrps18b	A	G	17: 36,221,587 (GRCm39)	I246T	probably benign	Het
Muc5b	A	G	7: 141,426,287 (GRCm39)	T4795A	possibly damaging	Het
Mybl2	G	A	2: 162,924,513 (GRCm39)	G627D	possibly damaging	Het
Ndufb8	C	T	19: 44,543,794 (GRCm39)	R16K	probably benign	Het
Or5k17	A	T	16: 58,746,121 (GRCm39)	V271E	possibly damaging	Het
P4htm	C	T	9: 108,457,991 (GRCm39)	V335M	probably damaging	Het
Pbx3	A	G	2: 34,094,889 (GRCm39)	I249T	probably damaging	Het
Plod3	G	T	5: 137,019,335 (GRCm39)	V360L	probably benign	Het
Podxl2	C	T	6: 88,826,632 (GRCm39)	D161N	probably benign	Het
Polr1b	G	T	2: 128,960,993 (GRCm39)	V651L	probably benign	Het
Prr14	T	C	7: 127,075,749 (GRCm39)	S586P	probably benign	Het
Pum3	C	T	19: 27,371,728 (GRCm39)	G575D	probably benign	Het
Rnf157	C	A	11: 116,251,192 (GRCm39)	A111S	probably benign	Het
Robo3	A	G	9: 37,344,212 (GRCm39)	L29P	probably damaging	Het
Smarca5	T	C	8: 81,452,680 (GRCm39)	N342S	probably damaging	Het
Specc1	T	A	11: 62,009,078 (GRCm39)	I198K	probably benign	Het
Tmem177	A	T	1: 119,837,744 (GRCm39)	*312R	probably null	Het
Tom1l2	A	T	11: 60,152,026 (GRCm39)	M172K	probably benign	Het
Tsc22d4	T	C	5: 137,756,414 (GRCm39)	V3A	unknown	Het
Vmn1r128	G	T	7: 21,083,668 (GRCm39)	G124V	probably damaging	Het
Vmn1r15	T	C	6: 57,235,342 (GRCm39)	I70T	probably benign	Het
Vmn2r60	A	G	7: 41,844,631 (GRCm39)	T665A	probably damaging	Het
Vmn2r83	T	C	10: 79,314,790 (GRCm39)	F346S	probably benign	Het
Wdr7	T	A	18: 63,910,691 (GRCm39)	D694E	probably damaging	Het

Other mutations in Lgi2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00861:Lgi2	APN	5	52,695,463 (GRCm39)	missense	probably benign
IGL01310:Lgi2	APN	5	52,711,807 (GRCm39)	missense	probably benign	0.44
IGL02086:Lgi2	APN	5	52,723,299 (GRCm39)	missense	probably damaging	0.96
IGL03091:Lgi2	APN	5	52,721,307 (GRCm39)	critical splice donor site	probably null
IGL03367:Lgi2	APN	5	52,719,502 (GRCm39)	missense	probably damaging	1.00
IGL03388:Lgi2	APN	5	52,695,819 (GRCm39)	missense	probably damaging	1.00
R0388:Lgi2	UTSW	5	52,711,891 (GRCm39)	missense	probably damaging	0.99
R0602:Lgi2	UTSW	5	52,711,765 (GRCm39)	missense	probably damaging	0.98
R0633:Lgi2	UTSW	5	52,711,802 (GRCm39)	missense	probably damaging	0.97
R1616:Lgi2	UTSW	5	52,703,980 (GRCm39)	missense	probably benign	0.00
R1916:Lgi2	UTSW	5	52,703,974 (GRCm39)	missense	probably benign
R2072:Lgi2	UTSW	5	52,695,847 (GRCm39)	missense	probably damaging	1.00
R2512:Lgi2	UTSW	5	52,695,307 (GRCm39)	makesense	probably null
R4614:Lgi2	UTSW	5	52,695,775 (GRCm39)	missense	probably damaging	0.99
R4855:Lgi2	UTSW	5	52,695,849 (GRCm39)	missense	probably damaging	1.00
R5092:Lgi2	UTSW	5	52,695,429 (GRCm39)	missense	probably damaging	1.00
R5181:Lgi2	UTSW	5	52,711,792 (GRCm39)	missense	probably damaging	1.00
R5311:Lgi2	UTSW	5	52,711,827 (GRCm39)	missense	probably damaging	0.99
R6074:Lgi2	UTSW	5	52,703,984 (GRCm39)	missense	probably benign
R7089:Lgi2	UTSW	5	52,695,832 (GRCm39)	missense	probably damaging	0.99
R7396:Lgi2	UTSW	5	52,695,753 (GRCm39)	missense	probably damaging	1.00
R7733:Lgi2	UTSW	5	52,695,873 (GRCm39)	missense	probably benign	0.03
R8007:Lgi2	UTSW	5	52,723,375 (GRCm39)	missense	probably benign	0.01
R8073:Lgi2	UTSW	5	52,704,013 (GRCm39)	missense	probably benign
R9137:Lgi2	UTSW	5	52,695,361 (GRCm39)	missense	probably damaging	1.00
R9484:Lgi2	UTSW	5	52,695,936 (GRCm39)	missense	probably benign	0.36
R9505:Lgi2	UTSW	5	52,711,775 (GRCm39)	missense	probably benign	0.00
R9723:Lgi2	UTSW	5	52,695,843 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CGCCTGCACATAGATTTCTTTAAAC -3'
(R):5'- GCGGAGTTTGTTGACATCGAC -3'

Sequencing Primer
(F):5'- GCCAGGTAGTGGTTATCT -3'
(R):5'- GACGGGAAGTCTCACCTCATC -3'

Posted On

2019-09-13