Mutagenetix > Incidental Mutation

Incidental Mutation 'R0046:Limk1'

43699

Institutional Source

Beutler Lab

Gene Symbol

Limk1

Ensembl Gene

ENSMUSG00000029674

Gene Name

LIM domain kinase 1

Synonyms

MMRRC Submission

038340-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0046 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

134684893-134717452 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 134701615 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 96 (Y96C)

Ref Sequence

ENSEMBL: ENSMUSP00000106864 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000015137] [ENSMUST00000111233]

AlphaFold

P53668

Predicted Effect

probably damaging
Transcript: ENSMUST00000015137
AA Change: Y104C

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674
AA Change: Y104C

Domain	Start	End	E-Value	Type
LIM	24	75	5.3e-19	SMART
LIM	83	137	1.73e-9	SMART
PDZ	176	258	1.51e-9	SMART
low complexity region	266	277	N/A	INTRINSIC
Pfam:Pkinase	339	604	1.7e-49	PFAM
Pfam:Pkinase_Tyr	339	604	1.5e-55	PFAM
Pfam:Kdo	345	509	2.5e-10	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000100641

SMART Domains

Protein: ENSMUSP00000098206
Gene: ENSMUSG00000072573

Domain	Start	End	E-Value	Type
low complexity region	27	42	N/A	INTRINSIC
low complexity region	48	67	N/A	INTRINSIC
low complexity region	147	158	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000111233
AA Change: Y96C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674
AA Change: Y96C

Domain	Start	End	E-Value	Type
LIM	23	67	2.19e-1	SMART
LIM	75	129	1.73e-9	SMART
PDZ	168	250	1.51e-9	SMART
low complexity region	258	269	N/A	INTRINSIC
Pfam:Pkinase_Tyr	331	596	1.5e-56	PFAM
Pfam:Pkinase	331	597	4.7e-50	PFAM
Pfam:Kdo	339	501	1.5e-9	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132027

Predicted Effect

unknown
Transcript: ENSMUST00000134093
AA Change: Y88C

SMART Domains

Protein: ENSMUSP00000121718
Gene: ENSMUSG00000029674
AA Change: Y88C

Domain	Start	End	E-Value	Type
LIM	16	60	2.19e-1	SMART
LIM	68	122	1.73e-9	SMART
PDZ	161	243	1.51e-9	SMART
low complexity region	251	262	N/A	INTRINSIC
Pfam:Pkinase	324	425	3.9e-16	PFAM
Pfam:Pkinase_Tyr	324	434	5.4e-14	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137897

Meta Mutation Damage Score

0.9583

Coding Region Coverage

1x: 99.6%
3x: 98.8%
10x: 96.7%
20x: 93.3%

Validation Efficiency

100% (83/83)

MGI Phenotype

FUNCTION: This gene encodes a member of the LIM kinase family of proteins. This protein is a serine/threonine kinase that regulates actin polymerization via phosphorylation and inactivation of the actin binding factor cofilin. This protein also stimulates axon growth and may play a role in brain development. Homozygous knockout mice for this gene exhibit reduced bone mass, abnormal neuronal morphology and altered synaptic function. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
PHENOTYPE: Mice homozygous for disruptions in this gene display an abnormal actin cytoskeleton in neurons of the central nervous system and structural abnormalities of the dendritic spines. Long term potentiation is altered and behavioral anomalies are seen. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actl7a	A	T	4: 56,743,877 (GRCm39)	K135*	probably null	Het
Adamts16	A	G	13: 70,911,579 (GRCm39)	S871P	probably benign	Het
Adcy10	A	T	1: 165,367,403 (GRCm39)	I558F	probably damaging	Het
Adsl	T	G	15: 80,846,989 (GRCm39)		probably null	Het
Aldob	T	C	4: 49,543,842 (GRCm39)	I47V	possibly damaging	Het
Alkbh8	A	G	9: 3,343,247 (GRCm39)	E46G	probably damaging	Het
Ankrd33b	G	A	15: 31,367,483 (GRCm39)	P19L	probably damaging	Het
Apoa5	T	C	9: 46,181,296 (GRCm39)	L124S	probably damaging	Het
Atp1a4	A	T	1: 172,067,664 (GRCm39)	L533Q	probably benign	Het
Atp7b	T	C	8: 22,550,011 (GRCm39)	T9A	probably benign	Het
Auh	G	A	13: 53,083,421 (GRCm39)		probably benign	Het
B3gnt3	T	C	8: 72,145,567 (GRCm39)	Y267C	probably damaging	Het
Card11	T	C	5: 140,894,279 (GRCm39)	T117A	possibly damaging	Het
Ccdc39	A	G	3: 33,898,301 (GRCm39)	F15L	possibly damaging	Het
Chtf18	C	T	17: 25,942,434 (GRCm39)	R468Q	probably benign	Het
Cntnap5c	T	G	17: 58,666,295 (GRCm39)	D1108E	probably benign	Het
Col14a1	G	A	15: 55,272,359 (GRCm39)		probably benign	Het
Col6a6	C	T	9: 105,626,047 (GRCm39)		probably benign	Het
Col9a3	G	A	2: 180,251,280 (GRCm39)	A317T	possibly damaging	Het
Cpt1c	A	T	7: 44,609,256 (GRCm39)		probably benign	Het
Cpt2	A	G	4: 107,761,559 (GRCm39)		probably null	Het
Crebrf	T	A	17: 26,982,308 (GRCm39)	L565M	probably damaging	Het
Cyp2d41-ps	T	A	15: 82,666,236 (GRCm39)		noncoding transcript	Het
Dhx9	C	T	1: 153,348,453 (GRCm39)	V291M	probably benign	Het
Dmxl1	T	A	18: 50,011,149 (GRCm39)	V1102E	probably benign	Het
Dnah7a	A	T	1: 53,496,033 (GRCm39)		probably null	Het
Dock4	G	A	12: 40,787,359 (GRCm39)		probably benign	Het
Dpp3	G	T	19: 4,964,671 (GRCm39)	N545K	probably damaging	Het
Elmo2	T	A	2: 165,140,646 (GRCm39)	N275I	probably damaging	Het
Farp1	A	G	14: 121,492,925 (GRCm39)	K509R	probably benign	Het
Fat3	T	C	9: 15,877,275 (GRCm39)	Y3446C	possibly damaging	Het
Fgd2	T	A	17: 29,593,964 (GRCm39)		probably benign	Het
Flg	T	A	3: 93,185,028 (GRCm39)		probably benign	Het
Gas2l2	A	T	11: 83,312,736 (GRCm39)	W859R	probably damaging	Het
Gatm	T	C	2: 122,431,225 (GRCm39)	D254G	probably damaging	Het
Gjd4	T	A	18: 9,280,998 (GRCm39)	I27F	probably damaging	Het
Gsdmc2	C	A	15: 63,699,604 (GRCm39)		probably benign	Het
Haus5	C	T	7: 30,353,605 (GRCm39)	V591I	probably benign	Het
Kcnab3	G	A	11: 69,221,053 (GRCm39)		probably null	Het
Khdrbs2	A	G	1: 32,658,283 (GRCm39)	D281G	possibly damaging	Het
Krt86	A	T	15: 101,375,283 (GRCm39)	M393L	probably benign	Het
Lrp2bp	T	A	8: 46,466,192 (GRCm39)	Y100*	probably null	Het
Mamstr	T	G	7: 45,291,194 (GRCm39)		probably benign	Het
Man1a	A	G	10: 53,795,283 (GRCm39)	Y657H	probably damaging	Het
Marf1	G	A	16: 13,929,591 (GRCm39)	P1672S	possibly damaging	Het
Mboat7	T	C	7: 3,686,817 (GRCm39)	Y341C	probably damaging	Het
Nhsl1	A	T	10: 18,401,417 (GRCm39)	N881I	probably damaging	Het
Nox3	T	C	17: 3,733,236 (GRCm39)	Y225C	probably benign	Het
Nrp1	C	T	8: 129,227,089 (GRCm39)		probably benign	Het
Or11g26	T	A	14: 50,753,596 (GRCm39)	*312K	probably null	Het
Or4c109	C	T	2: 88,817,693 (GRCm39)	M284I	probably benign	Het
Or4c35	C	T	2: 89,808,851 (GRCm39)	T243I	probably damaging	Het
Or5b105	G	A	19: 13,080,642 (GRCm39)	R3C	possibly damaging	Het
Or8k33	A	G	2: 86,383,976 (GRCm39)	F164S	probably damaging	Het
Pcdhb13	A	T	18: 37,577,310 (GRCm39)	M563L	probably benign	Het
Pclo	C	T	5: 14,590,493 (GRCm39)	T931M	unknown	Het
Peli2	C	T	14: 48,358,659 (GRCm39)	P16S	possibly damaging	Het
Pfas	G	T	11: 68,881,293 (GRCm39)	R1025S	probably benign	Het
Pik3c2a	A	T	7: 115,953,307 (GRCm39)	I1196N	probably damaging	Het
Pmfbp1	A	T	8: 110,262,617 (GRCm39)		probably benign	Het
Prg4	T	C	1: 150,331,837 (GRCm39)	T279A	possibly damaging	Het
Psma1	A	T	7: 113,866,440 (GRCm39)		probably benign	Het
Rab11fip1	A	G	8: 27,643,149 (GRCm39)	L550P	probably damaging	Het
Rgs12	T	A	5: 35,122,664 (GRCm39)	I149N	probably damaging	Het
Rmnd5a	T	C	6: 71,376,215 (GRCm39)	H195R	probably damaging	Het
Rnf17	T	C	14: 56,708,830 (GRCm39)	L750P	probably damaging	Het
Rtcb	T	C	10: 85,793,520 (GRCm39)	N18D	probably benign	Het
Seh1l	T	C	18: 67,925,086 (GRCm39)		probably null	Het
Sis	T	G	3: 72,839,427 (GRCm39)	N813T	probably benign	Het
Sptbn2	T	C	19: 4,795,405 (GRCm39)		probably benign	Het
Stag3	C	T	5: 138,281,285 (GRCm39)		probably benign	Het
Taar2	G	A	10: 23,817,393 (GRCm39)	R311H	probably benign	Het
Taok3	C	T	5: 117,410,294 (GRCm39)	Q829*	probably null	Het
Tnfrsf21	C	T	17: 43,349,104 (GRCm39)	H239Y	probably benign	Het
Tsbp1	T	C	17: 34,679,095 (GRCm39)		probably null	Het
Ttn	A	G	2: 76,781,886 (GRCm39)		probably benign	Het
Unc79	A	G	12: 103,091,940 (GRCm39)	E1756G	probably damaging	Het
Usp35	A	T	7: 96,962,804 (GRCm39)		probably null	Het
Vmn2r111	A	G	17: 22,766,990 (GRCm39)	F836L	probably benign	Het
Vmn2r77	A	G	7: 86,451,146 (GRCm39)	D344G	possibly damaging	Het
Zbtb40	A	G	4: 136,714,589 (GRCm39)	C1067R	probably damaging	Het

Other mutations in Limk1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01355:Limk1	APN	5	134,686,754 (GRCm39)	unclassified	probably benign
IGL02029:Limk1	APN	5	134,686,808 (GRCm39)	nonsense	probably null
IGL02211:Limk1	APN	5	134,686,491 (GRCm39)	missense	probably damaging	1.00
IGL03000:Limk1	APN	5	134,699,355 (GRCm39)	missense	probably damaging	0.99
extremist	UTSW	5	134,699,295 (GRCm39)	missense	probably damaging	1.00
R0046:Limk1	UTSW	5	134,701,615 (GRCm39)	missense	probably damaging	1.00
R0058:Limk1	UTSW	5	134,688,725 (GRCm39)	missense	probably damaging	1.00
R0058:Limk1	UTSW	5	134,688,725 (GRCm39)	missense	probably damaging	1.00
R0071:Limk1	UTSW	5	134,690,245 (GRCm39)	missense	probably benign	0.01
R0180:Limk1	UTSW	5	134,698,115 (GRCm39)	missense	probably damaging	0.97
R1456:Limk1	UTSW	5	134,686,364 (GRCm39)	missense	probably benign	0.09
R2225:Limk1	UTSW	5	134,690,410 (GRCm39)	splice site	probably null
R2379:Limk1	UTSW	5	134,708,335 (GRCm39)	unclassified	probably benign
R2899:Limk1	UTSW	5	134,717,154 (GRCm39)	splice site	probably null
R3423:Limk1	UTSW	5	134,701,523 (GRCm39)	critical splice donor site	probably null
R4235:Limk1	UTSW	5	134,699,332 (GRCm39)	missense	probably benign	0.00
R4516:Limk1	UTSW	5	134,705,640 (GRCm39)	intron	probably benign
R4566:Limk1	UTSW	5	134,715,537 (GRCm39)	missense	probably benign	0.12
R4752:Limk1	UTSW	5	134,699,295 (GRCm39)	missense	probably damaging	1.00
R5682:Limk1	UTSW	5	134,694,059 (GRCm39)	critical splice donor site	probably null
R5917:Limk1	UTSW	5	134,686,789 (GRCm39)	missense	probably damaging	1.00
R6163:Limk1	UTSW	5	134,686,809 (GRCm39)	missense	probably damaging	1.00
R6479:Limk1	UTSW	5	134,690,373 (GRCm39)	utr 3 prime	probably benign
R6952:Limk1	UTSW	5	134,699,332 (GRCm39)	missense	possibly damaging	0.76
R7009:Limk1	UTSW	5	134,701,553 (GRCm39)	missense	probably benign
R7147:Limk1	UTSW	5	134,686,195 (GRCm39)	missense	probably benign	0.14
R7453:Limk1	UTSW	5	134,698,091 (GRCm39)	missense	probably damaging	1.00
R7471:Limk1	UTSW	5	134,686,825 (GRCm39)	splice site	probably null
R9427:Limk1	UTSW	5	134,686,358 (GRCm39)	missense	probably benign	0.07
R9449:Limk1	UTSW	5	134,701,864 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- AGCAATGGTACTTGCCCTCTCCTG -3'
(R):5'- GGACAGCTCTTCTGCAAGAAGGAC -3'

Sequencing Primer
(F):5'- GCTCACTATAGAGTATGGAACTCAC -3'
(R):5'- CTCTTCTGCAAGAAGGACTACTGG -3'

Posted On

2013-05-29