Mutagenetix > Incidental Mutation

Incidental Mutation 'R9234:Lims2'

701018

Institutional Source

Beutler Lab

Gene Symbol

Lims2

Ensembl Gene

ENSMUSG00000024395

Gene Name

LIM and senescent cell antigen like domains 2

Synonyms

PINCH2

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9234 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

32055346-32091673 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 32090943 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 309 (Y309F)

Ref Sequence

ENSEMBL: ENSMUSP00000025254 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025254] [ENSMUST00000134663] [ENSMUST00000223753] [ENSMUST00000224328] [ENSMUST00000224383] [ENSMUST00000225404]

AlphaFold

Q91XD2

Predicted Effect

probably benign
Transcript: ENSMUST00000025254
AA Change: Y309F

PolyPhen 2 Score 0.119 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000025254
Gene: ENSMUSG00000024395
AA Change: Y309F

Domain	Start	End	E-Value	Type
LIM	14	67	1.15e-14	SMART
LIM	75	126	2.74e-12	SMART
LIM	139	189	3.87e-12	SMART
LIM	197	248	4.31e-19	SMART
LIM	256	308	2.67e-15	SMART
low complexity region	314	330	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000134663

SMART Domains

Protein: ENSMUSP00000118046
Gene: ENSMUSG00000024388

Domain	Start	End	E-Value	Type
MYSc	59	761	N/A	SMART
IQ	762	784	1.07e-1	SMART
IQ	785	807	7.01e-6	SMART
IQ	831	853	4.93e-1	SMART
IQ	854	876	1.63e-1	SMART
MyTH4	989	1189	1.14e-71	SMART
B41	1190	1409	3.66e-16	SMART
SH3	1501	1563	3.25e-7	SMART
MyTH4	1641	1790	7.66e-55	SMART
B41	1792	2009	8.19e-28	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000223753

Predicted Effect

probably benign
Transcript: ENSMUST00000224328

Predicted Effect

probably benign
Transcript: ENSMUST00000224383

Predicted Effect

probably benign
Transcript: ENSMUST00000225404

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
PHENOTYPE: Homozygous null mice are viable and fertile with no gross abnormalities. Mice homozygous for a different targeted allele exhibit decreased fractional shortening and increased area affected following myocardial infarct. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6430550D23Rik	A	G	2: 155,845,798 (GRCm39)	Y20H	probably benign	Het
Arid5b	A	G	10: 67,964,628 (GRCm39)	F348L	possibly damaging	Het
Bms1	C	A	6: 118,375,044 (GRCm39)	A777S	probably damaging	Het
C2cd3	A	G	7: 100,049,012 (GRCm39)	Y61C		Het
Caprin2	A	T	6: 148,744,337 (GRCm39)	Y1029*	probably null	Het
Casp1	A	T	9: 5,303,128 (GRCm39)	D194V	probably benign	Het
Crkl	A	G	16: 17,286,822 (GRCm39)	E126G	probably damaging	Het
Crp	A	T	1: 172,526,413 (GRCm39)	D166V	probably damaging	Het
Dnah10	A	C	5: 124,818,989 (GRCm39)	D425A	possibly damaging	Het
Dnah11	A	T	12: 117,951,095 (GRCm39)	L3071Q	probably damaging	Het
Dnah9	T	A	11: 65,924,751 (GRCm39)	I2168F	possibly damaging	Het
Elp3	T	A	14: 65,788,920 (GRCm39)	I388F	probably damaging	Het
Espn	C	A	4: 152,217,380 (GRCm39)		probably null	Het
Fbrsl1	G	T	5: 110,511,250 (GRCm39)	F504L	probably benign	Het
Fzd9	A	C	5: 135,279,540 (GRCm39)	M115R	probably damaging	Het
Git2	A	T	5: 114,899,682 (GRCm39)	Y224N	possibly damaging	Het
Gm9195	A	T	14: 72,695,786 (GRCm39)	Y1415*	probably null	Het
Gnpat	T	A	8: 125,610,179 (GRCm39)	L454Q	probably damaging	Het
Grm5	C	T	7: 87,723,440 (GRCm39)	P577S	probably damaging	Het
Hfm1	T	C	5: 107,041,334 (GRCm39)	N683S	probably benign	Het
Hps4	G	A	5: 112,525,905 (GRCm39)	S642N	possibly damaging	Het
Leng8	C	A	7: 4,145,247 (GRCm39)	P216T	probably damaging	Het
Letm2	C	A	8: 26,084,102 (GRCm39)	R43L	probably benign	Het
Llgl1	T	C	11: 60,600,956 (GRCm39)		probably null	Het
Ltn1	A	T	16: 87,194,089 (GRCm39)	D1417E	probably damaging	Het
Map4k4	T	A	1: 40,029,261 (GRCm39)	N345K	unknown	Het
Mapre2	T	C	18: 23,937,236 (GRCm39)	I26T	probably benign	Het
Nfe2	A	G	15: 103,159,636 (GRCm39)		probably benign	Het
Nlgn3	T	C	X: 100,352,390 (GRCm39)	V179A	probably damaging	Het
Ntrk1	A	G	3: 87,695,622 (GRCm39)		probably null	Het
Or51b6b	T	A	7: 103,309,950 (GRCm39)	Y169F	possibly damaging	Het
Or52e18	A	G	7: 104,609,651 (GRCm39)	F96S	probably damaging	Het
Or5h19	T	C	16: 58,856,789 (GRCm39)	N104D	probably benign	Het
Otud7b	G	T	3: 96,047,771 (GRCm39)	Q43H	probably damaging	Het
Pcdhb5	T	C	18: 37,453,695 (GRCm39)	V25A	probably benign	Het
Pcolce2	A	G	9: 95,560,439 (GRCm39)	T163A	probably benign	Het
Pdgfra	T	A	5: 75,324,262 (GRCm39)	V39E	possibly damaging	Het
Pdgfrb	T	A	18: 61,194,300 (GRCm39)	W26R	probably null	Het
Pigp	T	A	16: 94,165,522 (GRCm39)	*206Y	probably null	Het
Pip5kl1	G	T	2: 32,468,211 (GRCm39)	G126C	probably benign	Het
Plekhg2	G	T	7: 28,064,215 (GRCm39)	T442K	probably benign	Het
Prmt5	A	T	14: 54,748,674 (GRCm39)	S375T	possibly damaging	Het
Rnf213	T	A	11: 119,340,943 (GRCm39)	M3529K		Het
Ror2	C	A	13: 53,265,374 (GRCm39)	D573Y	probably damaging	Het
Shank1	A	G	7: 43,962,579 (GRCm39)	T98A	unknown	Het
Shcbp1	A	T	8: 4,798,800 (GRCm39)	I373K	possibly damaging	Het
Slc25a42	A	G	8: 70,642,736 (GRCm39)	S64P	probably damaging	Het
Smco3	T	A	6: 136,808,410 (GRCm39)	I155F	probably damaging	Het
Snx4	C	A	16: 33,087,161 (GRCm39)	S102*	probably null	Het
Snx4	T	A	16: 33,108,069 (GRCm39)	S288T	probably benign	Het
Socs4	A	G	14: 47,527,716 (GRCm39)	N217S	probably benign	Het
Tatdn2	G	A	6: 113,679,683 (GRCm39)		probably null	Het
Tmprss2	A	G	16: 97,379,821 (GRCm39)	Y160H	probably damaging	Het
Trim37	T	C	11: 87,036,393 (GRCm39)	I158T	possibly damaging	Het
Trip11	C	T	12: 101,811,990 (GRCm39)		probably null	Het
Ubr3	G	A	2: 69,727,990 (GRCm39)	A118T	probably benign	Het
Ubxn7	T	C	16: 32,178,895 (GRCm39)		probably null	Het
Unc5cl	C	T	17: 48,770,658 (GRCm39)	H369Y	probably damaging	Het
Unc5d	A	T	8: 29,250,877 (GRCm39)	N263K	probably damaging	Het
Vmn2r59	A	G	7: 41,661,907 (GRCm39)	I636T	possibly damaging	Het
Vps13d	G	T	4: 144,875,792 (GRCm39)	Q1578K		Het
Wnk2	T	C	13: 49,224,274 (GRCm39)	D1171G	probably damaging	Het
Zfpm2	A	G	15: 40,966,470 (GRCm39)	Y985C	probably damaging	Het
Zpbp2	A	T	11: 98,443,398 (GRCm39)	N77I	probably damaging	Het

Other mutations in Lims2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01153:Lims2	APN	18	32,090,370 (GRCm39)	splice site	probably null
R0180:Lims2	UTSW	18	32,089,368 (GRCm39)	missense	probably benign	0.12
R0268:Lims2	UTSW	18	32,077,573 (GRCm39)	missense	probably benign	0.16
R0344:Lims2	UTSW	18	32,077,573 (GRCm39)	missense	probably benign	0.16
R1920:Lims2	UTSW	18	32,088,395 (GRCm39)	nonsense	probably null
R2138:Lims2	UTSW	18	32,088,460 (GRCm39)	missense	possibly damaging	0.90
R3415:Lims2	UTSW	18	32,077,208 (GRCm39)	missense	probably damaging	0.99
R3926:Lims2	UTSW	18	32,090,996 (GRCm39)	missense	probably benign	0.00
R4273:Lims2	UTSW	18	32,089,390 (GRCm39)	missense	probably benign	0.25
R4693:Lims2	UTSW	18	32,077,552 (GRCm39)	missense	probably benign	0.02
R4893:Lims2	UTSW	18	32,074,864 (GRCm39)	splice site	probably null
R5599:Lims2	UTSW	18	32,090,324 (GRCm39)	missense	probably benign	0.01
R6376:Lims2	UTSW	18	32,087,515 (GRCm39)	missense	possibly damaging	0.74
R7202:Lims2	UTSW	18	32,090,017 (GRCm39)	missense	probably benign	0.13
R7216:Lims2	UTSW	18	32,090,315 (GRCm39)	missense	probably damaging	0.99
R7848:Lims2	UTSW	18	32,091,301 (GRCm39)	makesense	probably null
X0027:Lims2	UTSW	18	32,087,599 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCTCACCCTGGAATCTAGCC -3'
(R):5'- AAATGCCTGTGAGGTGGGTC -3'

Sequencing Primer
(F):5'- TGGAATCTAGCCCGCTGG -3'
(R):5'- TACATAGCCCGAGGTGGACTG -3'

Posted On

2022-03-25