Mutagenetix > Incidental Mutation

Incidental Mutation 'R9137:Lgi2'

694076

Institutional Source

Beutler Lab

Gene Symbol

Lgi2

Ensembl Gene

ENSMUSG00000039252

Gene Name

leucine-rich repeat LGI family, member 2

Synonyms

MMRRC Submission

068932-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.054) question?

Stock #

R9137 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

52690859-52723689 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 52695361 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Cysteine at position 533 (S533C)

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: S533C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000040436
Gene: ENSMUSG00000039252
AA Change: S533C

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: S525C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000143707
Gene: ENSMUSG00000039252
AA Change: S525C

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (55/55)

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930562C15Rik	A	G	16: 4,685,312 (GRCm39)	K299R	probably benign	Het
Abca12	T	G	1: 71,298,525 (GRCm39)	I2366L	possibly damaging	Het
Adgrv1	A	G	13: 81,688,133 (GRCm39)	V1749A	probably damaging	Het
Ano9	C	T	7: 140,684,028 (GRCm39)	V546M	probably damaging	Het
Atad5	A	T	11: 79,986,481 (GRCm39)	S523C	probably damaging	Het
Cacna1s	A	T	1: 135,996,744 (GRCm39)	D115V	possibly damaging	Het
Ccdc18	T	G	5: 108,296,856 (GRCm39)	C220G	probably damaging	Het
Cfap61	A	C	2: 146,042,685 (GRCm39)	K1153Q	probably benign	Het
Cmklr1	G	C	5: 113,752,043 (GRCm39)	H319Q	probably benign	Het
Cntnap5c	T	A	17: 58,601,203 (GRCm39)		probably benign	Het
Col11a1	A	G	3: 113,855,172 (GRCm39)	K144R	unknown	Het
Cr2	A	G	1: 194,850,640 (GRCm39)		probably null	Het
Cyp3a16	A	C	5: 145,406,413 (GRCm39)	V13G	unknown	Het
E330034G19Rik	A	G	14: 24,346,109 (GRCm39)	N72D	unknown	Het
Enah	A	G	1: 181,739,160 (GRCm39)		probably null	Het
Fezf1	T	A	6: 23,246,511 (GRCm39)		probably benign	Het
Gabrr2	T	A	4: 33,095,571 (GRCm39)	S487T	probably benign	Het
Gas2l2	G	A	11: 83,315,894 (GRCm39)	T275M	probably damaging	Het
Hectd4	A	G	5: 121,496,238 (GRCm39)	K3877E	possibly damaging	Het
Hhla1	G	T	15: 65,795,761 (GRCm39)	Q482K	probably damaging	Het
Hivep2	A	G	10: 14,004,712 (GRCm39)	T437A	probably benign	Het
Iars1	C	T	13: 49,855,350 (GRCm39)	T259M	probably benign	Het
Il18rap	C	T	1: 40,582,177 (GRCm39)	T366M	probably benign	Het
Itpk1	T	C	12: 102,540,291 (GRCm39)	E264G	probably benign	Het
Katnb1	G	A	8: 95,824,320 (GRCm39)	M501I	possibly damaging	Het
Kcna10	G	A	3: 107,102,497 (GRCm39)	G376E	probably damaging	Het
Kif23	A	T	9: 61,834,713 (GRCm39)	F397I	probably damaging	Het
Klf14	A	T	6: 30,934,855 (GRCm39)	C260S	probably damaging	Het
Marveld1	A	G	19: 42,136,440 (GRCm39)	D118G	probably benign	Het
Msln	C	T	17: 25,969,084 (GRCm39)	A434T	probably benign	Het
Neb	T	C	2: 52,150,502 (GRCm39)		probably benign	Het
Nes	G	T	3: 87,878,651 (GRCm39)	G48W	probably damaging	Het
Or5k3	T	A	16: 58,969,635 (GRCm39)	C141S	probably benign	Het
Osmr	T	A	15: 6,856,709 (GRCm39)	E479D	probably benign	Het
Otop3	A	G	11: 115,235,868 (GRCm39)	H500R	possibly damaging	Het
Peg10	CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG	CCACATCAGGATCCACATCAGGATGCACATCAG	6: 4,756,398 (GRCm39)		probably benign	Het
Phldb3	C	T	7: 24,310,723 (GRCm39)		probably benign	Het
Ppp4r3a	T	A	12: 101,021,794 (GRCm39)	I369F	possibly damaging	Het
Rarres1	T	A	3: 67,422,801 (GRCm39)		probably benign	Het
Scn4a	A	G	11: 106,214,736 (GRCm39)	V1287A	probably damaging	Het
Sertad2	A	T	11: 20,598,425 (GRCm39)	E207V	probably benign	Het
Sh3bp4	T	A	1: 89,072,647 (GRCm39)	C498*	probably null	Het
Smtn	T	G	11: 3,472,838 (GRCm39)	K278T	possibly damaging	Het
Sp140	T	C	1: 85,570,297 (GRCm39)	S405P	probably damaging	Het
Spata31e2	A	T	1: 26,724,715 (GRCm39)	I155N	probably benign	Het
Spem1	A	G	11: 69,712,433 (GRCm39)	V77A	probably benign	Het
St8sia2	T	G	7: 73,610,654 (GRCm39)	I210L	probably benign	Het
Stkld1	T	C	2: 26,840,572 (GRCm39)	I418T	probably benign	Het
Tpcn1	A	G	5: 120,695,990 (GRCm39)	F88L	probably damaging	Het
Trim66	C	T	7: 109,074,330 (GRCm39)	V644M	probably damaging	Het
Ttc41	T	C	10: 86,612,486 (GRCm39)	I1253T	probably benign	Het
Vmn2r86	T	C	10: 130,282,409 (GRCm39)	N736D	probably damaging	Het
Zfat	T	A	15: 68,051,794 (GRCm39)	T667S	probably benign	Het
Zfp874a	T	C	13: 67,590,841 (GRCm39)	E281G	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
R7376:Lgi2	UTSW	5	52,695,604 (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
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'- CCCCAGTGCATTGTGAATTTTAG -3'
(R):5'- TGCGTTGGAACAGTAAGCAG -3'

Sequencing Primer
(F):5'- GCATTGTGAATTTTAGTTTCAGAGC -3'
(R):5'- GGGGCTATGACCTTGCAAC -3'

Posted On

2022-01-20