Mutagenetix > Incidental Mutation

Incidental Mutation 'R6198:Lgi4'

503040

Institutional Source

Beutler Lab

Gene Symbol

Lgi4

Ensembl Gene

ENSMUSG00000036560

Gene Name

leucine-rich repeat LGI family, member 4

Synonyms

clp

MMRRC Submission

044338-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6198 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

30758767-30770360 bp(+) (GRCm39)

Type of Mutation

splice site (1762 bp from exon)

DNA Base Change (assembly)

T to A at 30768547 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000128610 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039775] [ENSMUST00000072331] [ENSMUST00000167369] [ENSMUST00000171359]

AlphaFold

Q8K1S1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000039775
AA Change: F515L

PolyPhen 2 Score 0.781 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000041579
Gene: ENSMUSG00000036560
AA Change: F515L

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
low complexity region	49	59	N/A	INTRINSIC
LRR	75	98	7.17e1	SMART
LRR	99	122	2.76e1	SMART
LRR_TYP	123	146	2.43e-4	SMART
LRRCT	158	207	3.97e-5	SMART
Pfam:EPTP	214	251	1.1e-7	PFAM
Pfam:EPTP	396	438	2.7e-13	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000072331

Predicted Effect

probably null
Transcript: ENSMUST00000072331

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165265

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165465

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165862

Predicted Effect

probably benign
Transcript: ENSMUST00000167369

SMART Domains

Protein: ENSMUSP00000130245
Gene: ENSMUSG00000057092

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Pfam:ATP1G1_PLM_MAT8	25	71	5.5e-30	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169424

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169313

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000186929

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000186839

Predicted Effect

probably null
Transcript: ENSMUST00000171359

SMART Domains

Protein: ENSMUSP00000128610
Gene: ENSMUSG00000057092

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Pfam:ATP1G1_PLM_MAT8	23	72	4.9e-30	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170456

Predicted Effect

probably benign
Transcript: ENSMUST00000172001

SMART Domains

Protein: ENSMUSP00000125865
Gene: ENSMUSG00000036560

Domain	Start	End	E-Value	Type
LRRCT	9	58	3.97e-5	SMART

Coding Region Coverage

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

Validation Efficiency

99% (68/69)

MGI Phenotype

PHENOTYPE: Homozygous mutant animals have an abnormal posture where the forelimbs are flexed and rotated inwards. The peripheral nervous system is delayed in myelination. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	A	T	3: 124,210,499 (GRCm39)		probably null	Het
2610318N02Rik	A	G	16: 16,936,233 (GRCm39)	S164P	probably damaging	Het
Acsbg3	A	G	17: 57,189,679 (GRCm39)	S265G	probably damaging	Het
Acyp2	C	T	11: 30,456,354 (GRCm39)	E98K	possibly damaging	Het
Adam19	A	C	11: 46,012,329 (GRCm39)	N275T	probably damaging	Het
Adgrg7	T	A	16: 56,597,556 (GRCm39)	T84S	possibly damaging	Het
Asl	C	T	5: 130,047,757 (GRCm39)	V70I	probably benign	Het
Atp2c1	A	G	9: 105,398,271 (GRCm39)	S26P	probably benign	Het
Bcas3	A	T	11: 85,400,261 (GRCm39)	D410V	probably damaging	Het
Cc2d1b	C	T	4: 108,490,422 (GRCm39)	R825W	probably damaging	Het
Ccdc15	A	C	9: 37,225,581 (GRCm39)		probably null	Het
Cfh	A	G	1: 140,033,178 (GRCm39)	S789P	probably damaging	Het
Cltc	T	C	11: 86,611,188 (GRCm39)	N561S	probably benign	Het
Cnst	A	G	1: 179,420,430 (GRCm39)	Q187R	probably damaging	Het
Csmd3	T	C	15: 48,177,273 (GRCm39)	T422A	probably benign	Het
Cyp2c55	A	T	19: 38,995,565 (GRCm39)	R26*	probably null	Het
Dgkb	A	T	12: 38,223,822 (GRCm39)	M414L	probably benign	Het
Dgkd	A	G	1: 87,851,930 (GRCm39)	D444G	probably damaging	Het
Dipk1b	A	G	2: 26,525,710 (GRCm39)	K215E	probably damaging	Het
Dnmt3c	T	C	2: 153,561,929 (GRCm39)	V544A	noncoding transcript	Het
Dus3l	A	T	17: 57,074,858 (GRCm39)	T327S	possibly damaging	Het
Elf2	A	T	3: 51,184,670 (GRCm39)	L5Q	probably damaging	Het
Fxyd6	A	G	9: 45,301,968 (GRCm39)	Y30C	probably damaging	Het
Gcc2	A	T	10: 58,128,412 (GRCm39)	T1375S	probably benign	Het
Git2	A	T	5: 114,883,556 (GRCm39)	Y393*	probably null	Het
Gm14403	AAACCCTA	AA	2: 177,201,448 (GRCm39)		probably benign	Het
Golgb1	T	C	16: 36,713,757 (GRCm39)	L246P	probably damaging	Het
Grp	G	T	18: 66,013,057 (GRCm39)	Q74H	possibly damaging	Het
Ifi203	A	T	1: 173,751,648 (GRCm39)	M391K	probably damaging	Het
Itih2	A	G	2: 10,103,352 (GRCm39)	Y712H	probably benign	Het
Kdm5a	T	A	6: 120,415,958 (GRCm39)	V1626E	probably benign	Het
Klhl40	A	G	9: 121,607,833 (GRCm39)	Y331C	probably damaging	Het
Kprp	T	A	3: 92,731,994 (GRCm39)	Y352F	probably damaging	Het
Lama2	G	T	10: 27,064,018 (GRCm39)	H1286Q	probably damaging	Het
Lrrc47	A	T	4: 154,100,129 (GRCm39)	N235I	probably damaging	Het
Lrrc74b	T	A	16: 17,366,650 (GRCm39)	I308F	probably damaging	Het
Map7d1	T	A	4: 126,135,636 (GRCm39)	K135M	probably damaging	Het
Marchf5	A	G	19: 37,188,140 (GRCm39)	R36G	probably damaging	Het
Mtx3	C	A	13: 92,989,359 (GRCm39)	P299Q	probably benign	Het
Muc21	T	A	17: 35,931,808 (GRCm39)		probably benign	Het
Ncapd2	C	A	6: 125,156,286 (GRCm39)	E500*	probably null	Het
Nckap5l	T	C	15: 99,323,869 (GRCm39)	K878R	probably damaging	Het
Nphs1	T	C	7: 30,167,340 (GRCm39)	I756T	probably damaging	Het
Olfm4	T	G	14: 80,237,813 (GRCm39)	S17A	probably benign	Het
Or1j15	A	G	2: 36,458,963 (GRCm39)	M118V	probably damaging	Het
Or4b1	A	T	2: 89,979,782 (GRCm39)	D189E	probably damaging	Het
Pak1ip1	G	T	13: 41,154,886 (GRCm39)	Q27H	probably benign	Het
Piezo2	A	T	18: 63,290,281 (GRCm39)	C159*	probably null	Het
Pkn2	G	T	3: 142,516,165 (GRCm39)	T538K	probably benign	Het
Ppp3cc	A	T	14: 70,485,060 (GRCm39)	M198K	probably benign	Het
Rrm1	T	G	7: 102,095,936 (GRCm39)		probably null	Het
Setd3	T	C	12: 108,131,427 (GRCm39)	K7E	possibly damaging	Het
Shc1	A	G	3: 89,329,414 (GRCm39)	K86R	probably benign	Het
Slc16a7	T	C	10: 125,064,084 (GRCm39)	T418A	probably benign	Het
Spocd1	C	T	4: 129,849,208 (GRCm39)	P676S	probably damaging	Het
Spp1	A	G	5: 104,587,374 (GRCm39)		probably null	Het
Syne1	A	G	10: 5,252,269 (GRCm39)	Y2462H	probably damaging	Het
Tiam2	T	C	17: 3,464,396 (GRCm39)	S42P	probably benign	Het
Tmem63b	C	T	17: 45,972,442 (GRCm39)	V722I	probably benign	Het
Ubqln1	A	G	13: 58,344,404 (GRCm39)	S130P	probably benign	Het
Usp34	G	T	11: 23,434,127 (GRCm39)	L3215F	probably damaging	Het
Uvssa	A	G	5: 33,566,854 (GRCm39)	Y517C	probably damaging	Het
Vps13d	A	T	4: 144,875,560 (GRCm39)	F1649Y	probably benign	Het
Zfp236	A	G	18: 82,675,278 (GRCm39)	S405P	probably damaging	Het
Zfp9	T	C	6: 118,454,282 (GRCm39)	M1V	probably null	Het
Zfp946	A	T	17: 22,673,896 (GRCm39)	S217C	probably damaging	Het
Zfp970	T	A	2: 177,167,253 (GRCm39)	C276S	probably damaging	Het
Zswim5	T	A	4: 116,735,204 (GRCm39)	F183Y	probably benign	Het

Other mutations in Lgi4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01288:Lgi4	APN	7	30,768,468 (GRCm39)	missense	probably benign	0.01
IGL01624:Lgi4	APN	7	30,767,113 (GRCm39)	missense	probably damaging	1.00
IGL02251:Lgi4	APN	7	30,766,688 (GRCm39)	splice site	probably null
IGL02755:Lgi4	APN	7	30,762,530 (GRCm39)	missense	probably damaging	1.00
IGL03153:Lgi4	APN	7	30,759,983 (GRCm39)	missense	probably damaging	1.00
IGL03392:Lgi4	APN	7	30,762,605 (GRCm39)	splice site	probably null
R0060:Lgi4	UTSW	7	30,762,996 (GRCm39)	missense	probably damaging	0.97
R0575:Lgi4	UTSW	7	30,759,518 (GRCm39)	missense	probably benign	0.12
R2139:Lgi4	UTSW	7	30,762,548 (GRCm39)	missense	probably damaging	1.00
R2276:Lgi4	UTSW	7	30,760,037 (GRCm39)	missense	probably damaging	1.00
R2277:Lgi4	UTSW	7	30,760,037 (GRCm39)	missense	probably damaging	1.00
R2278:Lgi4	UTSW	7	30,760,037 (GRCm39)	missense	probably damaging	1.00
R2939:Lgi4	UTSW	7	30,767,253 (GRCm39)	nonsense	probably null
R3039:Lgi4	UTSW	7	30,759,492 (GRCm39)	missense	probably benign
R3922:Lgi4	UTSW	7	30,766,873 (GRCm39)	missense	probably benign
R4650:Lgi4	UTSW	7	30,768,554 (GRCm39)	missense	probably benign	0.38
R5184:Lgi4	UTSW	7	30,770,182 (GRCm39)	unclassified	probably benign
R5583:Lgi4	UTSW	7	30,760,562 (GRCm39)	missense	possibly damaging	0.92
R5837:Lgi4	UTSW	7	30,770,208 (GRCm39)	unclassified	probably benign
R5917:Lgi4	UTSW	7	30,759,603 (GRCm39)	missense	possibly damaging	0.76
R6454:Lgi4	UTSW	7	30,759,557 (GRCm39)	missense	probably benign
R6845:Lgi4	UTSW	7	30,760,510 (GRCm39)	missense	probably damaging	0.99
R6897:Lgi4	UTSW	7	30,768,315 (GRCm39)	missense	probably benign	0.00
R7232:Lgi4	UTSW	7	30,766,776 (GRCm39)	missense	possibly damaging	0.67
R7354:Lgi4	UTSW	7	30,760,047 (GRCm39)	missense	probably damaging	1.00
R8224:Lgi4	UTSW	7	30,763,017 (GRCm39)	missense	probably damaging	1.00
R8257:Lgi4	UTSW	7	30,766,766 (GRCm39)	critical splice acceptor site	probably null
R8320:Lgi4	UTSW	7	30,768,366 (GRCm39)	missense	probably benign	0.14
R8440:Lgi4	UTSW	7	30,760,049 (GRCm39)	critical splice donor site	probably null
R8469:Lgi4	UTSW	7	30,767,065 (GRCm39)	missense	probably damaging	1.00
R9066:Lgi4	UTSW	7	30,759,446 (GRCm39)	start codon destroyed	probably benign
R9763:Lgi4	UTSW	7	30,760,020 (GRCm39)	missense	probably damaging	1.00
Z1186:Lgi4	UTSW	7	30,768,596 (GRCm39)	missense	probably benign	0.09

Predicted Primers

PCR Primer
(F):5'- GGCTCCATGTTCCGACTGTTAC -3'
(R):5'- TATCACACAGGACTGGCTGTG -3'

Sequencing Primer
(F):5'- ATGTTCCGACTGTTACAGCAAC -3'
(R):5'- GGTTACCCAGATATCCCAGA -3'

Posted On

2018-02-27