Mutagenetix > Incidental Mutation

Incidental Mutation 'R5879:Llgl1'

455728

Institutional Source

Beutler Lab

Gene Symbol

Llgl1

Ensembl Gene

ENSMUSG00000020536

Gene Name

LLGL1 scribble cell polarity complex component

Synonyms

Lgl1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5879 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

60590549-60605012 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 60603806 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Arginine at position 1016 (G1016R)

Ref Sequence

ENSEMBL: ENSMUSP00000104359 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002889] [ENSMUST00000052346] [ENSMUST00000108719]

AlphaFold

Q80Y17

Predicted Effect

probably benign
Transcript: ENSMUST00000002889

SMART Domains

Protein: ENSMUSP00000002889
Gene: ENSMUSG00000002812

Domain	Start	End	E-Value	Type
LRR	55	78	1.08e-1	SMART
LRR	103	126	4.08e0	SMART
LRR	127	149	2.27e1	SMART
LRR	150	173	1.25e-1	SMART
LRR	222	244	6.78e1	SMART
LRR	245	268	2.86e-1	SMART
LRR	269	291	3.78e-1	SMART
LRR	316	339	2.82e0	SMART
LRR	340	362	2.27e2	SMART
low complexity region	403	420	N/A	INTRINSIC
GEL	499	597	4.17e-25	SMART
GEL	617	709	1.72e-26	SMART
low complexity region	727	740	N/A	INTRINSIC
GEL	745	838	2.24e-25	SMART
GEL	905	1039	1.13e-3	SMART
GEL	1056	1152	7.28e-16	SMART
GEL	1167	1263	5.51e-25	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000052346
AA Change: G1016R

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000060749
Gene: ENSMUSG00000020536
AA Change: G1016R

Domain	Start	End	E-Value	Type
WD40	22	62	4.42e1	SMART
WD40	64	103	1.65e1	SMART
WD40	187	223	2.74e2	SMART
WD40	226	264	2.06e0	SMART
Pfam:LLGL	278	379	1.2e-43	PFAM
WD40	424	460	3.2e0	SMART
Blast:WD40	498	541	2e-13	BLAST
Blast:WD40	585	624	4e-9	BLAST
Pfam:Lgl_C	732	978	1.2e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108719
AA Change: G1016R

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000104359
Gene: ENSMUSG00000020536
AA Change: G1016R

Domain	Start	End	E-Value	Type
WD40	22	62	4.42e1	SMART
WD40	64	103	1.65e1	SMART
WD40	187	223	2.74e2	SMART
WD40	226	264	2.06e0	SMART
Pfam:LLGL	275	379	2e-48	PFAM
WD40	424	460	3.2e0	SMART
Blast:WD40	498	540	2e-13	BLAST
Blast:WD40	585	624	4e-9	BLAST
Pfam:Lgl_C	804	976	1.3e-8	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154141

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.9%
20x: 93.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is similar to a tumor suppressor in Drosophila. The protein is part of a cytoskeletal network and is associated with nonmuscle myosin II heavy chain and a kinase that specifically phosphorylates this protein at serine residues. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice die neonatally exhibiting hydroencephaly. Neural progenitor cell physiology is abnormal, resulting in a loss of cell polarity and the development of neuroepithelial rosette-like structures throughout the brain. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aldh16a1	C	T	7: 44,796,930 (GRCm39)	W66*	probably null	Het
Arhgap39	T	C	15: 76,636,007 (GRCm39)	D76G	probably damaging	Het
Arhgef2	G	A	3: 88,550,924 (GRCm39)		probably null	Het
C1qtnf2	T	C	11: 43,376,835 (GRCm39)	M99T	probably damaging	Het
Cyren	A	G	6: 34,851,593 (GRCm39)	L87P	probably damaging	Het
Eml3	G	A	19: 8,912,379 (GRCm39)	C392Y	possibly damaging	Het
Ephb4	C	A	5: 137,358,678 (GRCm39)	P287Q	probably benign	Het
Fat4	G	T	3: 38,941,485 (GRCm39)	R126L	probably benign	Het
Flt3	T	C	5: 147,271,719 (GRCm39)	M858V	probably damaging	Het
Gprin3	A	C	6: 59,331,698 (GRCm39)	I203R	probably benign	Het
Insr	G	T	8: 3,248,173 (GRCm39)	Y457*	probably null	Het
Ipo13	G	A	4: 117,760,400 (GRCm39)	T649I	possibly damaging	Het
Krba1	A	G	6: 48,392,678 (GRCm39)	D818G	possibly damaging	Het
Loxl4	A	G	19: 42,596,066 (GRCm39)	V142A	probably benign	Het
Mthfd1	A	G	12: 76,340,992 (GRCm39)	I464V	probably benign	Het
Mycs	C	A	X: 5,380,131 (GRCm39)	K316N	probably damaging	Het
Ncor2	A	G	5: 125,103,839 (GRCm39)		probably benign	Het
Nlrc3	A	G	16: 3,781,909 (GRCm39)	F516S	probably damaging	Het
Oacyl	A	G	18: 65,882,743 (GRCm39)	S540G	probably damaging	Het
Olfml2a	A	T	2: 38,850,242 (GRCm39)	T653S	probably damaging	Het
Or8s16	C	T	15: 98,211,369 (GRCm39)	V21I	probably benign	Het
Pcnx2	A	T	8: 126,500,685 (GRCm39)	N1468K	probably damaging	Het
Plbd1	A	G	6: 136,611,503 (GRCm39)	I258T	probably damaging	Het
Ppargc1b	C	G	18: 61,442,164 (GRCm39)	D591H	probably damaging	Het
Pramel21	A	T	4: 143,344,161 (GRCm39)	Y487F	possibly damaging	Het
Prop1	C	T	11: 50,844,153 (GRCm39)	V27M	probably damaging	Het
Rfx4	T	G	10: 84,650,625 (GRCm39)		probably null	Het
Rgs11	C	T	17: 26,422,437 (GRCm39)		probably benign	Het
Slc6a5	T	A	7: 49,595,260 (GRCm39)	F541I	probably damaging	Het
Srgap3	A	T	6: 112,699,807 (GRCm39)	V1057E	possibly damaging	Het
Synpo2	A	T	3: 122,907,946 (GRCm39)	W457R	probably damaging	Het
Tet2	T	A	3: 133,193,721 (GRCm39)	N238Y	possibly damaging	Het
Tiam2	T	A	17: 3,487,540 (GRCm39)	M687K	probably damaging	Het
Ticrr	A	G	7: 79,346,438 (GRCm39)	E1866G	probably benign	Het
Tspan8	T	C	10: 115,669,156 (GRCm39)	S64P	possibly damaging	Het
Ugt2b37	C	T	5: 87,402,265 (GRCm39)	G122D	probably benign	Het
Uqcrc2	A	G	7: 120,237,111 (GRCm39)	E53G	probably damaging	Het
Vcan	T	C	13: 89,852,071 (GRCm39)	D963G	probably damaging	Het
Vmn2r24	T	A	6: 123,764,226 (GRCm39)	Y368N	possibly damaging	Het
Wdr5	A	G	2: 27,418,323 (GRCm39)	T208A	probably benign	Het
Zbtb18	A	G	1: 177,275,936 (GRCm39)	Y423C	probably damaging	Het
Zc3h6	A	G	2: 128,839,696 (GRCm39)		probably null	Het

Other mutations in Llgl1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01137:Llgl1	APN	11	60,600,825 (GRCm39)	missense	probably benign	0.38
IGL01400:Llgl1	APN	11	60,597,316 (GRCm39)	missense	probably damaging	1.00
IGL03066:Llgl1	APN	11	60,596,860 (GRCm39)	missense	possibly damaging	0.75
IGL03174:Llgl1	APN	11	60,597,036 (GRCm39)	missense	probably benign	0.15
IGL03306:Llgl1	APN	11	60,602,180 (GRCm39)	missense	possibly damaging	0.92
R0284:Llgl1	UTSW	11	60,602,967 (GRCm39)	missense	probably damaging	0.98
R1137:Llgl1	UTSW	11	60,595,559 (GRCm39)	missense	probably benign	0.01
R1432:Llgl1	UTSW	11	60,599,380 (GRCm39)	missense	probably damaging	1.00
R1769:Llgl1	UTSW	11	60,597,873 (GRCm39)	missense	probably damaging	1.00
R1786:Llgl1	UTSW	11	60,598,066 (GRCm39)	missense	probably benign	0.19
R1835:Llgl1	UTSW	11	60,595,556 (GRCm39)	missense	probably benign	0.00
R1943:Llgl1	UTSW	11	60,596,842 (GRCm39)	missense	probably benign
R2197:Llgl1	UTSW	11	60,600,865 (GRCm39)	missense	possibly damaging	0.62
R2510:Llgl1	UTSW	11	60,600,862 (GRCm39)	missense	probably damaging	1.00
R2568:Llgl1	UTSW	11	60,599,638 (GRCm39)	missense	probably damaging	1.00
R3690:Llgl1	UTSW	11	60,597,828 (GRCm39)	missense	probably damaging	1.00
R3853:Llgl1	UTSW	11	60,598,075 (GRCm39)	missense	probably damaging	1.00
R4079:Llgl1	UTSW	11	60,601,110 (GRCm39)	splice site	probably null
R4259:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4348:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4349:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4352:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4353:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4396:Llgl1	UTSW	11	60,596,834 (GRCm39)	missense	probably benign
R4584:Llgl1	UTSW	11	60,602,908 (GRCm39)	missense	probably damaging	0.99
R4594:Llgl1	UTSW	11	60,597,147 (GRCm39)	missense	probably benign	0.15
R4628:Llgl1	UTSW	11	60,600,811 (GRCm39)	missense	probably damaging	1.00
R4651:Llgl1	UTSW	11	60,599,477 (GRCm39)	missense	possibly damaging	0.80
R4653:Llgl1	UTSW	11	60,599,477 (GRCm39)	missense	possibly damaging	0.80
R4731:Llgl1	UTSW	11	60,597,051 (GRCm39)	nonsense	probably null
R4869:Llgl1	UTSW	11	60,598,036 (GRCm39)	nonsense	probably null
R4898:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4899:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4939:Llgl1	UTSW	11	60,600,805 (GRCm39)	critical splice acceptor site	probably null
R4941:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4942:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R4958:Llgl1	UTSW	11	60,602,261 (GRCm39)	missense	probably benign	0.02
R4995:Llgl1	UTSW	11	60,600,550 (GRCm39)	missense	probably benign	0.00
R4997:Llgl1	UTSW	11	60,600,394 (GRCm39)	missense	probably benign
R5177:Llgl1	UTSW	11	60,602,833 (GRCm39)	missense	possibly damaging	0.94
R5257:Llgl1	UTSW	11	60,602,389 (GRCm39)	splice site	probably null
R5258:Llgl1	UTSW	11	60,602,389 (GRCm39)	splice site	probably null
R5401:Llgl1	UTSW	11	60,597,297 (GRCm39)	missense	probably benign
R5406:Llgl1	UTSW	11	60,604,010 (GRCm39)	missense	probably damaging	0.99
R5432:Llgl1	UTSW	11	60,598,449 (GRCm39)	missense	probably benign
R5587:Llgl1	UTSW	11	60,601,168 (GRCm39)	missense	probably benign	0.00
R5732:Llgl1	UTSW	11	60,600,286 (GRCm39)	missense	probably benign	0.00
R5758:Llgl1	UTSW	11	60,599,393 (GRCm39)	missense	probably damaging	1.00
R6268:Llgl1	UTSW	11	60,602,989 (GRCm39)	missense	probably benign	0.13
R6286:Llgl1	UTSW	11	60,600,358 (GRCm39)	missense	probably damaging	1.00
R6455:Llgl1	UTSW	11	60,600,486 (GRCm39)	missense	probably damaging	0.98
R6805:Llgl1	UTSW	11	60,593,691 (GRCm39)	missense	probably benign	0.25
R6929:Llgl1	UTSW	11	60,601,179 (GRCm39)	nonsense	probably null
R7274:Llgl1	UTSW	11	60,596,812 (GRCm39)	missense	possibly damaging	0.89
R7889:Llgl1	UTSW	11	60,598,138 (GRCm39)	missense	probably damaging	1.00
R7986:Llgl1	UTSW	11	60,602,221 (GRCm39)	missense	probably benign	0.16
R8141:Llgl1	UTSW	11	60,601,142 (GRCm39)	missense	probably benign	0.02
R8176:Llgl1	UTSW	11	60,597,387 (GRCm39)	missense	probably benign	0.27
R8223:Llgl1	UTSW	11	60,593,648 (GRCm39)	missense	possibly damaging	0.86
R8332:Llgl1	UTSW	11	60,601,210 (GRCm39)	missense	possibly damaging	0.90
R8350:Llgl1	UTSW	11	60,602,947 (GRCm39)	missense	probably damaging	1.00
R8500:Llgl1	UTSW	11	60,595,809 (GRCm39)	critical splice donor site	probably null
R8979:Llgl1	UTSW	11	60,601,129 (GRCm39)	missense	probably benign	0.25
R9155:Llgl1	UTSW	11	60,597,934 (GRCm39)	missense	probably benign	0.00
R9163:Llgl1	UTSW	11	60,600,402 (GRCm39)	missense	probably benign	0.02
R9225:Llgl1	UTSW	11	60,600,889 (GRCm39)	missense	probably damaging	1.00
R9234:Llgl1	UTSW	11	60,600,956 (GRCm39)	critical splice donor site	probably null
Z1186:Llgl1	UTSW	11	60,603,923 (GRCm39)	frame shift	probably null
Z1187:Llgl1	UTSW	11	60,603,923 (GRCm39)	frame shift	probably null
Z1188:Llgl1	UTSW	11	60,603,923 (GRCm39)	frame shift	probably null
Z1189:Llgl1	UTSW	11	60,603,923 (GRCm39)	frame shift	probably null
Z1190:Llgl1	UTSW	11	60,603,923 (GRCm39)	frame shift	probably null
Z1191:Llgl1	UTSW	11	60,603,923 (GRCm39)	frame shift	probably null
Z1192:Llgl1	UTSW	11	60,603,923 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- CGTAAGCTCAGGTTCCACTG -3'
(R):5'- CATTTAATCAGAAGGGTGTAGGC -3'

Sequencing Primer
(F):5'- TCAGGTTCCACTGAGCCAG -3'
(R):5'- TGTAGGCCCGACAAGCATC -3'

Posted On

2017-02-10