Mutagenetix > Incidental Mutation

Incidental Mutation 'R6479:Limk1'

516973

Institutional Source

Beutler Lab

Gene Symbol

Limk1

Ensembl Gene

ENSMUSG00000029674

Gene Name

LIM domain kinase 1

Synonyms

MMRRC Submission

044611-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6479 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

134684893-134717452 bp(-) (GRCm39)

Type of Mutation

utr 3 prime

DNA Base Change (assembly)

G to A at 134690373 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

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

AlphaFold

P53668

Predicted Effect

probably benign
Transcript: ENSMUST00000015137

SMART Domains

Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674

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 benign
Transcript: ENSMUST00000111233

SMART Domains

Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674

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

noncoding transcript
Transcript: ENSMUST00000137897

Predicted Effect

unknown
Transcript: ENSMUST00000138590
AA Change: T61I

SMART Domains

Protein: ENSMUSP00000118268
Gene: ENSMUSG00000029674
AA Change: T61I

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

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.7%
20x: 92.0%

Validation Efficiency

95% (55/58)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	A	C	8: 25,119,681 (GRCm39)	S533A	probably benign	Het
Akap6	T	G	12: 53,187,952 (GRCm39)	S1789A	probably damaging	Het
Alox15	A	G	11: 70,236,011 (GRCm39)	S519P	probably damaging	Het
Anapc2	A	G	2: 25,175,407 (GRCm39)	K816E	probably benign	Het
Atp6v1a	T	C	16: 43,919,121 (GRCm39)	D488G	probably benign	Het
Banp	A	G	8: 122,718,176 (GRCm39)		probably null	Het
Camsap1	A	G	2: 25,825,874 (GRCm39)	C1367R	possibly damaging	Het
Casz1	C	A	4: 149,021,535 (GRCm39)	H539Q	probably damaging	Het
Ccl5	A	G	11: 83,421,212 (GRCm39)	Y26H	probably benign	Het
Cops3	A	T	11: 59,723,898 (GRCm39)	S86R	probably benign	Het
Cts7	A	G	13: 61,503,455 (GRCm39)	S170P	probably benign	Het
Cxcl15	A	T	5: 90,943,104 (GRCm39)	E35D	possibly damaging	Het
Dennd1b	C	T	1: 138,969,698 (GRCm39)		probably benign	Het
Dicer1	T	C	12: 104,662,982 (GRCm39)	D1533G	probably damaging	Het
Dnah8	G	A	17: 30,967,542 (GRCm39)	D2585N	probably benign	Het
Dock4	A	G	12: 40,878,954 (GRCm39)	E1531G	probably damaging	Het
Erap1	A	G	13: 74,811,612 (GRCm39)		probably null	Het
Fsip2	A	G	2: 82,820,430 (GRCm39)	T5388A	possibly damaging	Het
Gab1	C	A	8: 81,515,226 (GRCm39)	R364L	possibly damaging	Het
Gm10309	A	T	17: 86,812,007 (GRCm39)	M1K	probably null	Het
Gm4884	A	T	7: 40,690,211 (GRCm39)	N36Y	probably damaging	Het
Hmcn1	G	A	1: 150,553,053 (GRCm39)	R2546*	probably null	Het
Hmcn2	A	G	2: 31,315,480 (GRCm39)	D3743G	probably damaging	Het
Hsd3b9	T	A	3: 98,354,157 (GRCm39)	E114V	possibly damaging	Het
Irak2	A	T	6: 113,663,902 (GRCm39)	N423Y	probably damaging	Het
Jarid2	G	A	13: 45,001,765 (GRCm39)	G26D	probably benign	Het
Kif13b	A	G	14: 64,988,974 (GRCm39)	K785R	probably benign	Het
Lamc3	A	T	2: 31,777,413 (GRCm39)	I20F	probably benign	Het
Lrp4	C	T	2: 91,317,429 (GRCm39)	T851I	probably damaging	Het
Med13	G	A	11: 86,248,353 (GRCm39)		probably benign	Het
Megf10	T	C	18: 57,379,642 (GRCm39)	F273L	possibly damaging	Het
Meltf	T	A	16: 31,700,700 (GRCm39)	D73E	probably damaging	Het
Mroh7	A	G	4: 106,560,385 (GRCm39)	F640L	possibly damaging	Het
Mtor	T	C	4: 148,635,457 (GRCm39)	S2448P	probably benign	Het
Myo3a	T	C	2: 22,467,877 (GRCm39)	V377A	probably benign	Het
Myo5b	T	C	18: 74,750,086 (GRCm39)	V183A	probably damaging	Het
Nedd4l	G	A	18: 65,342,752 (GRCm39)	R755H	probably damaging	Het
Nrde2	T	C	12: 100,110,207 (GRCm39)	T275A	probably benign	Het
Or52n4	A	G	7: 104,294,333 (GRCm39)	I80T	probably benign	Het
Osgepl1	T	C	1: 53,360,702 (GRCm39)	V381A	probably benign	Het
Pcdha1	C	T	18: 37,064,509 (GRCm39)	T391I	probably benign	Het
Pdp1	T	C	4: 11,961,327 (GRCm39)	N328S	probably damaging	Het
Pepd	A	G	7: 34,740,147 (GRCm39)	E340G	probably benign	Het
Plch1	T	C	3: 63,651,931 (GRCm39)	T387A	probably benign	Het
Plxnb1	C	A	9: 108,940,733 (GRCm39)	T1536K	possibly damaging	Het
Rbp7	T	C	4: 149,534,347 (GRCm39)	T130A	probably benign	Het
Rhot2	A	T	17: 26,060,054 (GRCm39)	V309E	probably benign	Het
Slc37a1	A	G	17: 31,557,964 (GRCm39)	I421M	possibly damaging	Het
Slit2	T	A	5: 48,389,331 (GRCm39)	L585H	probably damaging	Het
Spint4	C	A	2: 164,542,764 (GRCm39)	A119D	probably benign	Het
Strip2	G	T	6: 29,944,496 (GRCm39)		probably null	Het
Stxbp4	T	C	11: 90,510,013 (GRCm39)	Y59C	probably damaging	Het
Syne1	G	A	10: 5,181,679 (GRCm39)	Q4219*	probably null	Het
Syne1	A	T	10: 5,406,826 (GRCm39)	I37N	probably damaging	Het
Syne4	G	T	7: 30,016,340 (GRCm39)	G179*	probably null	Het
Tead1	T	C	7: 112,460,672 (GRCm39)	V192A	probably benign	Het
Trim37	G	T	11: 87,107,313 (GRCm39)	E317*	probably null	Het
Wdfy3	A	C	5: 102,061,045 (GRCm39)	Y1390D	probably damaging	Het
Wdr81	A	G	11: 75,342,931 (GRCm39)	F779L	possibly damaging	Het
Zfp1002	C	T	2: 150,096,511 (GRCm39)	G306D	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
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
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'- TATGGGAGCAGGACTCTAGG -3'
(R):5'- TTTCAGGGCTTCCACTAGAGG -3'

Sequencing Primer
(F):5'- AGCAGGACTCTAGGCACTTG -3'
(R):5'- GCTTCCACTAGAGGTCAGGTG -3'

Posted On

2018-05-21