Mutagenetix > Incidental Mutation

Incidental Mutation 'R5917:Limk1'

461387

Institutional Source

Beutler Lab

Gene Symbol

Limk1

Ensembl Gene

ENSMUSG00000029674

Gene Name

LIM domain kinase 1

Synonyms

MMRRC Submission

044114-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5917 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

134684893-134717452 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 134686789 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 533 (F533L)

Ref Sequence

ENSEMBL: ENSMUSP00000015137 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000015137] [ENSMUST00000111233] [ENSMUST00000138590]

AlphaFold

P53668

Predicted Effect

probably damaging
Transcript: ENSMUST00000015137
AA Change: F533L

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

SMART Domains

Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674
AA Change: F533L

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

probably damaging
Transcript: ENSMUST00000111233
AA Change: F525L

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

SMART Domains

Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674
AA Change: F525L

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

probably benign
Transcript: ENSMUST00000134093

SMART Domains

Protein: ENSMUSP00000121718
Gene: ENSMUSG00000029674

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

probably benign
Transcript: ENSMUST00000138590

SMART Domains

Protein: ENSMUSP00000118268
Gene: ENSMUSG00000029674

Domain	Start	End	E-Value	Type
Pfam:Pkinase	3	59	3.6e-9	PFAM
Pfam:Pkinase_Tyr	3	80	2.6e-13	PFAM

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 95.0%

Validation Efficiency

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb5	T	A	12: 118,832,516 (GRCm39)	R1153*	probably null	Het
Amdhd1	T	C	10: 93,360,332 (GRCm39)	H409R	possibly damaging	Het
Anks1b	C	T	10: 90,412,803 (GRCm39)		probably benign	Het
Ascc2	T	C	11: 4,631,506 (GRCm39)	L649P	probably benign	Het
Chst15	A	G	7: 131,872,246 (GRCm39)	F12L	probably benign	Het
Clec4a4	A	T	6: 122,981,017 (GRCm39)	K83N	probably benign	Het
Comp	T	A	8: 70,829,011 (GRCm39)		probably null	Het
Cryz	T	A	3: 154,327,403 (GRCm39)	S144T	probably benign	Het
Ctss	A	G	3: 95,450,424 (GRCm39)	D125G	probably benign	Het
Dact1	G	T	12: 71,365,456 (GRCm39)	V746L	possibly damaging	Het
Dhx29	A	G	13: 113,099,377 (GRCm39)	H1134R	probably damaging	Het
Dlgap4	A	G	2: 156,546,460 (GRCm39)	D376G	probably damaging	Het
Dnah3	T	A	7: 119,615,749 (GRCm39)	H1660L	probably damaging	Het
Ep300	T	A	15: 81,512,808 (GRCm39)		probably benign	Het
Fbxo30	A	T	10: 11,165,262 (GRCm39)		probably null	Het
Fcrl2	T	A	3: 87,164,094 (GRCm39)	H345L	probably damaging	Het
Galnt11	C	A	5: 25,452,670 (GRCm39)		probably null	Het
Il31ra	A	G	13: 112,682,846 (GRCm39)	C87R	probably benign	Het
Itga4	A	T	2: 79,117,442 (GRCm39)	Q416L	probably damaging	Het
Kcnt2	A	T	1: 140,461,666 (GRCm39)	T806S	probably damaging	Het
Lama2	A	G	10: 27,066,693 (GRCm39)	S1063P	probably damaging	Het
Lama4	T	A	10: 38,924,028 (GRCm39)	S479T	probably benign	Het
Lgi4	C	T	7: 30,759,603 (GRCm39)	T53M	possibly damaging	Het
Loxl1	A	G	9: 58,220,006 (GRCm39)	L55P	probably damaging	Het
Map1a	A	G	2: 121,135,697 (GRCm39)	E1933G	probably damaging	Het
Matn2	T	A	15: 34,409,912 (GRCm39)	C447*	probably null	Het
Mmrn1	T	C	6: 60,950,134 (GRCm39)		probably null	Het
Or2a7	C	T	6: 43,151,646 (GRCm39)	S242F	probably damaging	Het
Or4a66	A	T	2: 88,531,049 (GRCm39)	I208N	possibly damaging	Het
Or4d1	A	T	11: 87,805,215 (GRCm39)	N172K	probably damaging	Het
Otor	A	G	2: 142,920,431 (GRCm39)	I4M	probably benign	Het
P2rx3	A	T	2: 84,865,591 (GRCm39)	V18E	probably damaging	Het
Pcdh7	T	C	5: 57,879,097 (GRCm39)	V884A	probably damaging	Het
Pcdhb4	T	A	18: 37,442,619 (GRCm39)	V643D	probably damaging	Het
Pelo	A	G	13: 115,225,930 (GRCm39)	S176P	possibly damaging	Het
Ppp2r3d	A	T	9: 101,089,183 (GRCm39)	V380E	probably benign	Het
Proc	T	A	18: 32,260,513 (GRCm39)	D204V	probably benign	Het
Prpsap2	C	T	11: 61,627,870 (GRCm39)	R202H	probably damaging	Het
Resf1	T	C	6: 149,236,179 (GRCm39)	F1500L	probably damaging	Het
Rtl1	T	G	12: 109,558,087 (GRCm39)	T1251P	possibly damaging	Het
Sema6a	T	G	18: 47,414,405 (GRCm39)	I482L	probably benign	Het
Smpdl3a	T	A	10: 57,681,654 (GRCm39)		probably null	Het
Strc	T	A	2: 121,209,790 (GRCm39)	M178L	probably benign	Het
Taok1	A	T	11: 77,451,144 (GRCm39)	M312K	probably damaging	Het
Tle2	T	C	10: 81,416,750 (GRCm39)		probably null	Het
Tle3	A	G	9: 61,316,190 (GRCm39)	D296G	probably benign	Het
Trank1	A	G	9: 111,191,485 (GRCm39)	D498G	probably benign	Het
Vars1	C	A	17: 35,231,491 (GRCm39)	L672M	probably damaging	Het
Vps13d	G	A	4: 144,826,580 (GRCm39)	T2866I	probably damaging	Het
Zfp423	C	A	8: 88,508,860 (GRCm39)	E370*	probably null	Het
Zfp521	T	A	18: 13,978,612 (GRCm39)	K600N	probably damaging	Het
Zfp788	A	G	7: 41,298,572 (GRCm39)	K351E	probably benign	Het
Zfp963	A	T	8: 70,195,510 (GRCm39)		probably null	Het
Zscan29	G	T	2: 120,994,518 (GRCm39)	T489N	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
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
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'- TATACCCCACTGATGCTGTGC -3'
(R):5'- AGATAGCACATGGGTCCCAC -3'

Sequencing Primer
(F):5'- ACTGATGCTGTGCTCTGC -3'
(R):5'- GAACCAGGAGTGTCTCATTTTATGC -3'

Posted On

2017-02-28