Mutagenetix > Incidental Mutation

Incidental Mutation 'R8708:Limk2'

669383

Institutional Source

Beutler Lab

Gene Symbol

Limk2

Ensembl Gene

ENSMUSG00000020451

Gene Name

LIM domain kinase 2

Synonyms

whe, Limk2b, Limk2a, A930024P04Rik, LIM kinase 2

MMRRC Submission

068562-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.157) question?

Stock #

R8708 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

3294256-3359189 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 3300763 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 380 (M380T)

Ref Sequence

ENSEMBL: ENSMUSP00000099162 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101638] [ENSMUST00000101640] [ENSMUST00000101642] [ENSMUST00000110029]

AlphaFold

O54785

PDB Structure

Solution structure of the PDZ domain from mouse LIM domain kinase [SOLUTION NMR]

Predicted Effect

probably benign
Transcript: ENSMUST00000101638
AA Change: M380T

PolyPhen 2 Score 0.193 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000099162
Gene: ENSMUSG00000020451
AA Change: M380T

Domain	Start	End	E-Value	Type
LIM	11	63	2e-14	SMART
LIM	71	124	4.63e-10	SMART
PDZ	161	239	7.04e-10	SMART
low complexity region	241	255	N/A	INTRINSIC
low complexity region	280	306	N/A	INTRINSIC
low complexity region	310	322	N/A	INTRINSIC
Pfam:Pkinase	331	600	5.3e-48	PFAM
Pfam:Pkinase_Tyr	331	601	4.7e-50	PFAM
Pfam:Kdo	341	497	8.6e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000101640
AA Change: M365T

PolyPhen 2 Score 0.113 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000099163
Gene: ENSMUSG00000020451
AA Change: M365T

Domain	Start	End	E-Value	Type
LIM	7	42	4.91e-1	SMART
LIM	50	103	4.63e-10	SMART
PDZ	140	218	7.04e-10	SMART
low complexity region	220	234	N/A	INTRINSIC
low complexity region	259	285	N/A	INTRINSIC
low complexity region	289	301	N/A	INTRINSIC
Pfam:Pkinase	310	582	1.2e-45	PFAM
Pfam:Pkinase_Tyr	310	586	1.3e-51	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000101642
AA Change: M359T

PolyPhen 2 Score 0.092 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000099165
Gene: ENSMUSG00000020451
AA Change: M359T

Domain	Start	End	E-Value	Type
LIM	7	42	4.91e-1	SMART
LIM	50	103	4.63e-10	SMART
PDZ	140	218	7.04e-10	SMART
low complexity region	220	234	N/A	INTRINSIC
low complexity region	259	285	N/A	INTRINSIC
low complexity region	289	301	N/A	INTRINSIC
Pfam:Pkinase	310	579	4.9e-48	PFAM
Pfam:Pkinase_Tyr	310	580	4.3e-50	PFAM
Pfam:Kdo	320	476	8.2e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000110029
AA Change: M193T

PolyPhen 2 Score 0.193 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000105656
Gene: ENSMUSG00000020451
AA Change: M193T

Domain	Start	End	E-Value	Type
PDZ	1	52	4.55e-1	SMART
low complexity region	54	68	N/A	INTRINSIC
low complexity region	93	119	N/A	INTRINSIC
low complexity region	123	135	N/A	INTRINSIC
Pfam:Pkinase	144	411	2.7e-49	PFAM
Pfam:Pkinase_Tyr	144	414	1.7e-51	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

98% (99/101)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. LIM domains are highly conserved cysteine-rich structures containing 2 zinc fingers. Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. LIM kinase-1 and LIM kinase-2 belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. The protein encoded by this gene is phosphorylated and activated by ROCK, a downstream effector of Rho, and the encoded protein, in turn, phosphorylates cofilin, inhibiting its actin-depolymerizing activity. It is thought that this pathway contributes to Rho-induced reorganization of the actin cytoskeleton. At least three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Male homozygotes for targeted null mutations exhibit small testes but are fertile. Mutant kidneys have fewer glomeruli and dilated renal tubules, but function normally. Mice homozygous for a gene trap allele or spontaneous mutation have open eyelids at birth, corneal abnormalities and inflammation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 103 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adra1d	T	C	2: 131,403,400 (GRCm39)	K230R	probably damaging	Het
Ajm1	C	A	2: 25,467,814 (GRCm39)	R699L	possibly damaging	Het
Akp3	T	A	1: 87,054,091 (GRCm39)	Y236*	probably null	Het
Alg11	T	C	8: 22,555,129 (GRCm39)	F130S	probably damaging	Het
Ankfn1	A	T	11: 89,394,756 (GRCm39)	S276R	possibly damaging	Het
Ankhd1	T	A	18: 36,727,344 (GRCm39)	H486Q	probably damaging	Het
Ankrd23	T	C	1: 36,573,169 (GRCm39)	T68A	probably benign	Het
Arhgap23	A	G	11: 97,343,238 (GRCm39)	T507A	probably benign	Het
Arid1a	A	T	4: 133,409,145 (GRCm39)	D1787E	unknown	Het
Atad2b	T	A	12: 5,011,253 (GRCm39)	D504E	probably damaging	Het
Atg2b	T	A	12: 105,635,687 (GRCm39)		probably benign	Het
Bptf	C	A	11: 106,964,139 (GRCm39)	S1685I	probably damaging	Het
Bptf	T	A	11: 106,964,140 (GRCm39)	S1685C	probably damaging	Het
Cacna1c	A	T	6: 118,604,416 (GRCm39)	I1437N		Het
Capn1	T	C	19: 6,061,328 (GRCm39)	K197E	probably damaging	Het
Ccdc177	T	C	12: 80,805,891 (GRCm39)	T128A	probably benign	Het
Ccdc7b	G	T	8: 129,863,095 (GRCm39)	M9I	probably benign	Het
Celf1	T	A	2: 90,840,925 (GRCm39)		probably null	Het
Ckap5	T	A	2: 91,425,823 (GRCm39)	N1285K	probably benign	Het
Col24a1	C	T	3: 145,251,020 (GRCm39)	T1673I	probably damaging	Het
Dbp	A	G	7: 45,359,225 (GRCm39)	E300G	probably damaging	Het
Dchs2	C	A	3: 83,036,049 (GRCm39)	H265Q	probably benign	Het
Dicer1	A	T	12: 104,694,704 (GRCm39)	S198T	possibly damaging	Het
Dnase1l2	A	T	17: 24,661,266 (GRCm39)	F86L	probably benign	Het
Dnhd1	T	G	7: 105,343,487 (GRCm39)	Y1610*	probably null	Het
Dock5	A	G	14: 68,004,820 (GRCm39)	V1529A	probably benign	Het
Egfr	G	T	11: 16,817,300 (GRCm39)		probably benign	Het
Exph5	T	A	9: 53,287,096 (GRCm39)	H1392Q	probably benign	Het
Fam78b	A	G	1: 166,906,332 (GRCm39)	K164E	possibly damaging	Het
Fignl2	C	A	15: 100,950,734 (GRCm39)	R516L	unknown	Het
Fndc7	C	T	3: 108,774,528 (GRCm39)	E577K	probably benign	Het
Fryl	T	C	5: 73,289,905 (GRCm39)	E107G	probably benign	Het
Gbp10	A	T	5: 105,368,831 (GRCm39)	M336K	probably damaging	Het
Gm11444	A	T	11: 85,737,723 (GRCm39)	C156S		Het
Golga3	C	A	5: 110,350,721 (GRCm39)	A752E	probably benign	Het
Gper1	G	T	5: 139,411,690 (GRCm39)	V12L	probably benign	Het
Hmbox1	G	T	14: 65,061,089 (GRCm39)	A394E	probably damaging	Het
Ighv1-71	T	A	12: 115,705,955 (GRCm39)	I77L	probably benign	Het
Ing4	A	T	6: 125,024,895 (GRCm39)	N214Y	probably damaging	Het
Ints8	A	G	4: 11,208,824 (GRCm39)		probably null	Het
Itpa	T	A	2: 130,517,639 (GRCm39)	V129E	probably damaging	Het
Itpripl1	T	A	2: 126,983,262 (GRCm39)	M287L	probably benign	Het
Klc3	T	C	7: 19,129,784 (GRCm39)	I362V	probably damaging	Het
Ky	T	A	9: 102,402,590 (GRCm39)		probably benign	Het
Lasp1	A	G	11: 97,697,709 (GRCm39)	N43S	possibly damaging	Het
Lrp2	T	A	2: 69,289,957 (GRCm39)	E3627D	probably damaging	Het
Lrrc25	T	C	8: 71,070,459 (GRCm39)	L80P	probably damaging	Het
Mcoln3	A	T	3: 145,846,276 (GRCm39)	K529*	probably null	Het
Mdn1	A	C	4: 32,725,854 (GRCm39)	D2591A	probably damaging	Het
Med12l	A	G	3: 59,159,751 (GRCm39)	I1267V	probably benign	Het
Mei4	C	A	9: 81,809,595 (GRCm39)	S226*	probably null	Het
Mios	G	A	6: 8,234,255 (GRCm39)	V809M	probably benign	Het
Mmp17	G	A	5: 129,672,486 (GRCm39)	R146Q	possibly damaging	Het
Mob3a	G	A	10: 80,527,218 (GRCm39)	Q36*	probably null	Het
Myo3a	T	A	2: 22,296,607 (GRCm39)		probably benign	Het
Naca	A	T	10: 127,883,943 (GRCm39)	I2125F	probably damaging	Het
Ndst3	A	C	3: 123,322,564 (GRCm39)	S840A	probably benign	Het
Nlrp4c	T	C	7: 6,068,603 (GRCm39)	M168T	probably damaging	Het
Nt5c3	A	G	6: 56,874,758 (GRCm39)		probably null	Het
Or1af1	T	A	2: 37,109,956 (GRCm39)	S152T	probably damaging	Het
Or4a72	C	A	2: 89,405,623 (GRCm39)	G149V	probably damaging	Het
Or5b124	T	C	19: 13,611,401 (GRCm39)	S309P	probably benign	Het
Or6c5	T	A	10: 129,074,678 (GRCm39)	I220N	possibly damaging	Het
Pcgf3	A	G	5: 108,634,063 (GRCm39)	D107G	probably benign	Het
Pde2a	A	G	7: 101,159,588 (GRCm39)	D816G	probably damaging	Het
Phf10	T	A	17: 15,176,261 (GRCm39)	T131S	possibly damaging	Het
Phf11	A	T	14: 59,482,262 (GRCm39)	C164S	probably damaging	Het
Phrf1	A	G	7: 140,812,446 (GRCm39)	D70G	unknown	Het
Piezo2	A	G	18: 63,226,086 (GRCm39)	L850S	probably damaging	Het
Plcg1	T	A	2: 160,596,473 (GRCm39)		probably benign	Het
Plekhh2	A	T	17: 84,882,421 (GRCm39)	I676L	probably benign	Het
Ppp1r9a	T	G	6: 5,115,196 (GRCm39)	V804G	probably damaging	Het
Ppt2	T	C	17: 34,844,613 (GRCm39)	H180R	possibly damaging	Het
Prdm15	T	C	16: 97,618,066 (GRCm39)	H398R	unknown	Het
Rab26	A	T	17: 24,748,772 (GRCm39)	M208K	probably damaging	Het
Rab31	A	C	17: 65,974,859 (GRCm39)		probably benign	Het
Radil	A	G	5: 142,471,204 (GRCm39)	V1024A	probably damaging	Het
Rorb	A	G	19: 18,960,780 (GRCm39)	I65T	probably damaging	Het
Sall1	A	T	8: 89,759,483 (GRCm39)	V207E	probably damaging	Het
Sart3	A	T	5: 113,882,728 (GRCm39)	M864K	possibly damaging	Het
Sdcbp2	T	A	2: 151,431,457 (GRCm39)	S277T	probably benign	Het
Septin5	A	G	16: 18,443,622 (GRCm39)	V100A	probably benign	Het
Sipa1	C	T	19: 5,710,980 (GRCm39)	R10Q	probably damaging	Het
Ski	A	T	4: 155,245,119 (GRCm39)	S376T	probably damaging	Het
Slc15a4	A	T	5: 127,673,715 (GRCm39)	D566E	probably benign	Het
Srgap2	G	A	1: 131,273,544 (GRCm39)	Q372*	probably null	Het
Stard9	A	G	2: 120,534,059 (GRCm39)	T3439A	probably damaging	Het
Tln1	T	C	4: 43,534,769 (GRCm39)		probably benign	Het
Tmco3	A	G	8: 13,345,998 (GRCm39)	M279V	probably benign	Het
Tmem39b	T	C	4: 129,570,191 (GRCm39)		probably benign	Het
Trio	T	A	15: 27,732,632 (GRCm39)	N3083I	probably damaging	Het
Ube3b	G	A	5: 114,531,151 (GRCm39)	R215Q	probably benign	Het
Ubr1	T	C	2: 120,696,964 (GRCm39)	N1646S	probably benign	Het
Uqcrc1	T	G	9: 108,776,108 (GRCm39)	F270C	probably damaging	Het
Vmn2r108	T	A	17: 20,682,687 (GRCm39)	N839I	probably damaging	Het
Vmn2r75	A	T	7: 85,812,476 (GRCm39)	S514R	probably damaging	Het
Wdfy4	C	G	14: 32,689,489 (GRCm39)	V3016L		Het
Wdr11	A	G	7: 129,200,780 (GRCm39)	N77S	probably benign	Het
Wdr17	C	A	8: 55,093,127 (GRCm39)		probably benign	Het
Wrn	T	A	8: 33,782,671 (GRCm39)	N753I	probably damaging	Het
Zan	A	G	5: 137,461,539 (GRCm39)		probably null	Het
Zfat	T	A	15: 67,956,278 (GRCm39)	T1203S	possibly damaging	Het
Zfhx2	A	C	14: 55,312,509 (GRCm39)	S62A	probably benign	Het

Other mutations in Limk2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01105:Limk2	APN	11	3,305,475 (GRCm39)	splice site	probably benign
IGL01592:Limk2	APN	11	3,309,052 (GRCm39)	missense	probably benign	0.00
IGL01716:Limk2	APN	11	3,308,990 (GRCm39)	splice site	probably null
IGL01911:Limk2	APN	11	3,305,340 (GRCm39)	missense	probably benign
R0900:Limk2	UTSW	11	3,300,731 (GRCm39)	missense	probably damaging	1.00
R1587:Limk2	UTSW	11	3,303,455 (GRCm39)	missense	possibly damaging	0.82
R1632:Limk2	UTSW	11	3,296,250 (GRCm39)	missense	probably damaging	1.00
R1695:Limk2	UTSW	11	3,303,275 (GRCm39)	critical splice donor site	probably null
R1712:Limk2	UTSW	11	3,308,104 (GRCm39)	splice site	probably null
R1792:Limk2	UTSW	11	3,308,236 (GRCm39)	missense	probably benign
R1982:Limk2	UTSW	11	3,305,461 (GRCm39)	missense	probably benign	0.00
R3009:Limk2	UTSW	11	3,309,046 (GRCm39)	missense	probably benign	0.01
R4565:Limk2	UTSW	11	3,298,634 (GRCm39)	missense	probably damaging	0.98
R4703:Limk2	UTSW	11	3,297,586 (GRCm39)	nonsense	probably null
R4978:Limk2	UTSW	11	3,359,069 (GRCm39)	utr 5 prime	probably benign
R5160:Limk2	UTSW	11	3,300,772 (GRCm39)	missense	probably damaging	1.00
R5460:Limk2	UTSW	11	3,302,332 (GRCm39)	missense	probably benign	0.30
R6497:Limk2	UTSW	11	3,310,492 (GRCm39)	missense	probably benign	0.00
R6543:Limk2	UTSW	11	3,300,682 (GRCm39)	missense	probably damaging	1.00
R6666:Limk2	UTSW	11	3,310,493 (GRCm39)	missense	probably damaging	1.00
R7054:Limk2	UTSW	11	3,305,448 (GRCm39)	missense	possibly damaging	0.95
R7330:Limk2	UTSW	11	3,296,311 (GRCm39)	missense	probably benign	0.39
R7681:Limk2	UTSW	11	3,303,354 (GRCm39)	missense	probably damaging	0.96
R7722:Limk2	UTSW	11	3,306,092 (GRCm39)	splice site	probably null
R7745:Limk2	UTSW	11	3,305,896 (GRCm39)	missense	probably damaging	0.99
R8120:Limk2	UTSW	11	3,298,589 (GRCm39)	splice site	probably null
R8193:Limk2	UTSW	11	3,297,691 (GRCm39)	missense	possibly damaging	0.79
R8379:Limk2	UTSW	11	3,321,162 (GRCm39)	start gained	probably benign
R8557:Limk2	UTSW	11	3,296,379 (GRCm39)	missense	possibly damaging	0.89
R9617:Limk2	UTSW	11	3,297,715 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- AGTAATGAGCACAGGTGTCC -3'
(R):5'- TTGCTCCTTAGGTAGCTGCAG -3'

Sequencing Primer
(F):5'- TAATGAGCACAGGTGTCCCTCTG -3'
(R):5'- CATTGGGGCAACTGCAGTG -3'

Posted On

2021-04-30