Mutagenetix > Incidental Mutation

Incidental Mutation 'R5583:Lgi4'

438570

Institutional Source

Beutler Lab

Gene Symbol

Lgi4

Ensembl Gene

ENSMUSG00000036560

Gene Name

leucine-rich repeat LGI family, member 4

Synonyms

clp

MMRRC Submission

043137-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5583 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30758767-30770360 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 30760562 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 39 (Y39C)

Ref Sequence

ENSEMBL: ENSMUSP00000145660 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039775] [ENSMUST00000164725] [ENSMUST00000169785]

AlphaFold

Q8K1S1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000039775
AA Change: Y101C

PolyPhen 2 Score 0.724 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000041579
Gene: ENSMUSG00000036560
AA Change: Y101C

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 benign
Transcript: ENSMUST00000164725

Predicted Effect

possibly damaging
Transcript: ENSMUST00000169785
AA Change: Y39C

PolyPhen 2 Score 0.924 (Sensitivity: 0.81; Specificity: 0.94)

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205392

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.4%
20x: 95.4%

Validation Efficiency

97% (60/62)

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A1bg	A	T	15: 60,793,083 (GRCm39)	L8Q	probably damaging	Het
Abca4	T	C	3: 121,942,550 (GRCm39)	V1681A	probably damaging	Het
Abce1	G	T	8: 80,416,922 (GRCm39)	A363E	probably benign	Het
Adgrl2	T	C	3: 148,564,800 (GRCm39)	Y256C	probably damaging	Het
Afm	T	C	5: 90,695,740 (GRCm39)	C416R	probably damaging	Het
Ahnak	T	A	19: 8,984,281 (GRCm39)	V1855D	probably damaging	Het
Alb	A	T	5: 90,616,452 (GRCm39)	H319L	probably benign	Het
Ankrd35	G	T	3: 96,592,219 (GRCm39)	R835L	probably damaging	Het
Atg2b	T	C	12: 105,615,414 (GRCm39)	D1014G	possibly damaging	Het
Cdk6	T	A	5: 3,394,436 (GRCm39)	Y24N	probably damaging	Het
Chd7	T	A	4: 8,752,473 (GRCm39)	N323K	probably damaging	Het
Cops9	A	T	1: 92,567,489 (GRCm39)		probably benign	Het
Crybg1	T	C	10: 43,879,506 (GRCm39)	T561A	probably benign	Het
Dcdc5	T	C	2: 106,195,778 (GRCm39)		noncoding transcript	Het
Dnah7b	G	T	1: 46,281,359 (GRCm39)	A2807S	probably benign	Het
Fam149b	A	G	14: 20,413,368 (GRCm39)	T196A	possibly damaging	Het
Fam217a	C	A	13: 35,094,280 (GRCm39)	C402F	probably damaging	Het
Fat2	A	T	11: 55,144,715 (GRCm39)	V4053E	probably benign	Het
Fcgbp	T	C	7: 27,791,004 (GRCm39)	V755A	probably damaging	Het
Fxr1	C	A	3: 34,123,125 (GRCm39)	S641R	probably benign	Het
Gata5	A	T	2: 179,976,047 (GRCm39)	M39K	probably benign	Het
Gon4l	T	A	3: 88,807,278 (GRCm39)	D1658E	probably damaging	Het
Gpr180	C	T	14: 118,400,110 (GRCm39)	T426M	probably damaging	Het
Gtf2h3	C	T	5: 124,722,360 (GRCm39)	T121I	probably benign	Het
Helq	T	C	5: 100,910,459 (GRCm39)	E1039G	probably damaging	Het
Hibch	T	A	1: 52,940,406 (GRCm39)	Y192N	probably damaging	Het
Hp1bp3	A	G	4: 137,949,426 (GRCm39)	I41M	probably damaging	Het
Itpripl2	G	T	7: 118,089,101 (GRCm39)	P486Q	probably benign	Het
Kcnj6	T	C	16: 94,634,060 (GRCm39)	D17G	probably benign	Het
Kprp	T	A	3: 92,731,643 (GRCm39)	Y469F	unknown	Het
Kremen2	T	C	17: 23,961,229 (GRCm39)	T373A	probably benign	Het
Lgr5	T	C	10: 115,314,409 (GRCm39)	D176G	probably benign	Het
Lrp1	T	C	10: 127,424,332 (GRCm39)	S785G	probably benign	Het
Ltbp1	A	T	17: 75,598,325 (GRCm39)	Q920L	probably benign	Het
Map2	A	G	1: 66,455,196 (GRCm39)	E1362G	probably damaging	Het
Nkx2-6	T	C	14: 69,409,272 (GRCm39)	S8P	probably damaging	Het
Or2h1b	T	C	17: 37,462,485 (GRCm39)	Q126R	probably benign	Het
Pde4dip	C	T	3: 97,654,892 (GRCm39)	R888Q	possibly damaging	Het
Per1	A	G	11: 68,994,271 (GRCm39)	H494R	probably damaging	Het
Pira2	A	G	7: 3,845,545 (GRCm39)	F280L	probably benign	Het
Plekhm3	C	T	1: 64,977,145 (GRCm39)	W108*	probably null	Het
Ptcd3	A	G	6: 71,879,920 (GRCm39)	S113P	probably damaging	Het
Scarf1	T	C	11: 75,404,842 (GRCm39)	L42P	possibly damaging	Het
Scart2	G	A	7: 139,876,739 (GRCm39)	C710Y	probably damaging	Het
Skint1	A	C	4: 111,876,253 (GRCm39)	Q58P	probably damaging	Het
Spata7	A	T	12: 98,635,590 (GRCm39)	N438I	probably damaging	Het
Spdya	C	A	17: 71,876,126 (GRCm39)	D164E	probably damaging	Het
Speer3	G	A	5: 13,844,782 (GRCm39)		probably null	Het
Ssc4d	A	T	5: 135,999,050 (GRCm39)	L51H	probably damaging	Het
Steap1	A	G	5: 5,790,579 (GRCm39)	I123T	possibly damaging	Het
Styx	T	A	14: 45,608,483 (GRCm39)	F147I	possibly damaging	Het
Suv39h2	T	A	2: 3,475,890 (GRCm39)		probably benign	Het
Tfb2m	A	G	1: 179,373,446 (GRCm39)	V84A	probably benign	Het
Tlcd1	T	G	11: 78,069,762 (GRCm39)	V25G	probably benign	Het
Tmem79	T	C	3: 88,239,870 (GRCm39)	Y280C	probably damaging	Het
Trim5	T	A	7: 103,926,042 (GRCm39)	N173I	probably damaging	Het
Ttc17	A	T	2: 94,208,027 (GRCm39)	D194E	probably damaging	Het
Zfp2	T	C	11: 50,790,984 (GRCm39)	E353G	possibly damaging	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
R5837:Lgi4	UTSW	7	30,770,208 (GRCm39)	unclassified	probably benign
R5917:Lgi4	UTSW	7	30,759,603 (GRCm39)	missense	possibly damaging	0.76
R6198:Lgi4	UTSW	7	30,768,547 (GRCm39)	splice site	probably null
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'- ATGGGGCTTTTCAGACACC -3'
(R):5'- AGATTTACTTCTGACCTGAGCTG -3'

Sequencing Primer
(F):5'- TTTCAGACACCTGTGAGGAC -3'
(R):5'- TGCCCACACTGCAGACTTC -3'

Posted On

2016-10-26