Mutagenetix > Incidental Mutation

Incidental Mutation 'R4752:Limk1'

357666

Institutional Source

Beutler Lab

Gene Symbol

Limk1

Ensembl Gene

ENSMUSG00000029674

Gene Name

LIM domain kinase 1

Synonyms

MMRRC Submission

042032-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4752 (G1)

Quality Score

125

Status

Validated

Chromosome

Chromosomal Location

134684893-134717452 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 134699295 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 154 (T154I)

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: T162I

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674
AA Change: T162I

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: T154I

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674
AA Change: T154I

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: T146I

SMART Domains

Protein: ENSMUSP00000121718
Gene: ENSMUSG00000029674
AA Change: T146I

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

0.3300

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.8%

Validation Efficiency

99% (68/69)

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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	C	A	3: 137,775,751 (GRCm39)	Q1647K	possibly damaging	Het
Abcf3	A	G	16: 20,369,326 (GRCm39)	E236G	probably damaging	Het
Adamts17	A	G	7: 66,654,218 (GRCm39)	T483A	probably damaging	Het
Ankrd26	G	T	6: 118,517,426 (GRCm39)	P465Q	probably null	Het
Babam2	C	T	5: 31,859,391 (GRCm39)		probably benign	Het
Bpifb1	T	A	2: 154,058,200 (GRCm39)		probably benign	Het
Ccnb1ip1	T	A	14: 51,031,122 (GRCm39)	T64S	possibly damaging	Het
Cdhr3	A	G	12: 33,136,102 (GRCm39)	V46A	probably damaging	Het
Cep170	A	T	1: 176,584,254 (GRCm39)	D708E	probably benign	Het
Cpsf6	A	T	10: 117,197,273 (GRCm39)		probably benign	Het
Cryzl2	C	T	1: 157,286,219 (GRCm39)		probably null	Het
Dgka	A	T	10: 128,572,528 (GRCm39)	F42I	probably benign	Het
Dip2a	A	T	10: 76,112,491 (GRCm39)	V1059E	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Dock4	T	A	12: 40,496,364 (GRCm39)	I3K	probably benign	Het
Dsc2	A	T	18: 20,171,279 (GRCm39)	N573K	probably damaging	Het
Eif2b4	G	A	5: 31,348,575 (GRCm39)	R213*	probably null	Het
Eif3b	A	G	5: 140,426,856 (GRCm39)	D704G	probably benign	Het
Epn2	T	C	11: 61,437,197 (GRCm39)	E125G	probably damaging	Het
F830016B08Rik	A	G	18: 60,434,153 (GRCm39)	N412S	probably benign	Het
Fbln2	A	G	6: 91,233,225 (GRCm39)	M570V	probably benign	Het
Gm16686	A	T	4: 88,673,725 (GRCm39)		probably benign	Het
Hook2	C	T	8: 85,729,349 (GRCm39)	Q632*	probably null	Het
Ipcef1	A	T	10: 6,929,573 (GRCm39)	W56R	probably damaging	Het
Krt78	T	C	15: 101,856,637 (GRCm39)	I418M	probably benign	Het
Lyl1	A	T	8: 85,430,910 (GRCm39)	T271S	probably benign	Het
Megf6	A	G	4: 154,336,895 (GRCm39)	I333V	probably damaging	Het
Meioc	A	G	11: 102,565,259 (GRCm39)	T236A	probably benign	Het
Nbas	A	G	12: 13,532,538 (GRCm39)	T1749A	possibly damaging	Het
Nfib	T	A	4: 82,215,016 (GRCm39)	Q529L	probably damaging	Het
Nfkb2	G	T	19: 46,296,006 (GRCm39)	E170D	probably benign	Het
Nisch	A	T	14: 30,914,545 (GRCm39)	F42L	probably damaging	Het
Nomo1	T	A	7: 45,706,626 (GRCm39)	Y547N	probably damaging	Het
Or10g3	C	T	14: 52,609,764 (GRCm39)	V249I	probably damaging	Het
Or13a24	T	C	7: 140,154,515 (GRCm39)	S150P	possibly damaging	Het
Or5l14	A	G	2: 87,792,693 (GRCm39)	L181P	probably damaging	Het
Or8g51	T	C	9: 38,609,266 (GRCm39)	Y136C	probably damaging	Het
Pcdh18	T	A	3: 49,709,563 (GRCm39)	N117I	probably damaging	Het
Prkn	T	C	17: 12,223,010 (GRCm39)	S387P	probably benign	Het
Prl3c1	A	T	13: 27,387,508 (GRCm39)	K164N	probably benign	Het
Prr23a3	T	A	9: 98,747,700 (GRCm39)	L218Q	probably damaging	Het
Prss43	A	G	9: 110,656,836 (GRCm39)	H114R	possibly damaging	Het
Ptcd3	A	T	6: 71,878,296 (GRCm39)	M142K	probably damaging	Het
Shisa7	G	A	7: 4,837,249 (GRCm39)	T89I	possibly damaging	Het
Slco1a1	C	T	6: 141,892,340 (GRCm39)	A9T	possibly damaging	Het
Srcap	C	T	7: 127,158,172 (GRCm39)		probably benign	Het
Tdg-ps	G	A	15: 82,400,572 (GRCm39)		noncoding transcript	Het
Tgm4	A	G	9: 122,880,451 (GRCm39)	D284G	probably damaging	Het
Tmc1	T	A	19: 20,804,013 (GRCm39)	I355F	probably benign	Het
Tmem121b	A	T	6: 120,469,995 (GRCm39)	F241I	possibly damaging	Het
Tmem200c	T	A	17: 69,149,235 (GRCm39)	V606E	probably benign	Het
Ttc39c	A	G	18: 12,861,782 (GRCm39)	K370R	probably benign	Het
Vmn2r87	G	A	10: 130,314,336 (GRCm39)	Q417*	probably null	Het
Vps45	T	C	3: 95,955,699 (GRCm39)	Y97C	possibly damaging	Het
Zfp407	A	G	18: 84,581,039 (GRCm39)	S25P	probably benign	Het
Zfp566	A	G	7: 29,777,306 (GRCm39)	S292P	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
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'- CTGCTTCTAGTATGTGGATACTCTG -3'
(R):5'- TTTGAGACAACTGGGCCTG -3'

Sequencing Primer
(F):5'- CCACACAGGTTGTTTGCATCAGG -3'
(R):5'- AGACAACTGGGCCTGCCTTG -3'

Posted On

2015-11-11