Mutagenetix > Incidental Mutation

Incidental Mutation 'R3926:Lims2'

308307

Institutional Source

Beutler Lab

Gene Symbol

Lims2

Ensembl Gene

ENSMUSG00000024395

Gene Name

LIM and senescent cell antigen like domains 2

Synonyms

PINCH2

MMRRC Submission

040821-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3926 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

32055346-32091673 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 32090996 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 327 (S327G)

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: S327G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000025254
Gene: ENSMUSG00000024395
AA Change: S327G

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

noncoding transcript
Transcript: ENSMUST00000225125

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225400

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226112

Predicted Effect

probably benign
Transcript: ENSMUST00000225404

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225470

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 93.6%

Validation Efficiency

98% (55/56)

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700012B07Rik	G	T	11: 109,684,980 (GRCm39)	C172*	probably null	Het
Ahnak	G	A	19: 8,983,692 (GRCm39)	D1659N	probably benign	Het
Arfgap2	C	T	2: 91,105,150 (GRCm39)	R405W	probably damaging	Het
Asb14	T	C	14: 26,619,695 (GRCm39)	I48T	possibly damaging	Het
Astn1	A	T	1: 158,407,227 (GRCm39)	I559F	possibly damaging	Het
Atg7	C	T	6: 114,650,639 (GRCm39)	T83M	possibly damaging	Het
Bco1	T	C	8: 117,854,211 (GRCm39)	S379P	probably benign	Het
Becn2	T	C	1: 175,748,852 (GRCm39)	V306A	probably benign	Het
Bst1	T	C	5: 43,997,796 (GRCm39)	V265A	possibly damaging	Het
Car11	T	C	7: 45,349,915 (GRCm39)	F45L	probably benign	Het
Cdkl2	T	C	5: 92,180,998 (GRCm39)	I214V	possibly damaging	Het
Cluap1	T	A	16: 3,729,398 (GRCm39)	S141T	probably damaging	Het
Col11a1	C	T	3: 113,883,773 (GRCm39)		probably benign	Het
Col1a2	G	A	6: 4,518,822 (GRCm39)		probably benign	Het
Corin	T	G	5: 72,529,473 (GRCm39)	D294A	probably damaging	Het
Crct1	C	A	3: 92,922,014 (GRCm39)		probably benign	Het
Ddx41	A	G	13: 55,679,083 (GRCm39)	L559P	probably damaging	Het
Ddx59	T	A	1: 136,344,482 (GRCm39)	V51D	probably benign	Het
Dennd1b	A	G	1: 139,071,697 (GRCm39)	N397D	probably benign	Het
Evc2	T	A	5: 37,540,574 (GRCm39)	L590Q	probably damaging	Het
Fhl5	A	T	4: 25,214,790 (GRCm39)		probably benign	Het
Flg2	A	G	3: 93,110,522 (GRCm39)	Y850C	unknown	Het
Gal3st2b	G	T	1: 93,868,512 (GRCm39)	V246L	probably benign	Het
Jam3	A	T	9: 27,017,701 (GRCm39)	I29K	possibly damaging	Het
Klhl1	A	T	14: 96,584,316 (GRCm39)	C305S	possibly damaging	Het
Lynx1	A	G	15: 74,623,205 (GRCm39)	Y76H	probably damaging	Het
Mycbp2	G	A	14: 103,441,936 (GRCm39)	P1943L	probably damaging	Het
Myo3a	A	G	2: 22,455,053 (GRCm39)	D86G	probably damaging	Het
Nkx3-2	T	A	5: 41,919,223 (GRCm39)	Q255L	probably damaging	Het
Notch3	C	T	17: 32,372,531 (GRCm39)	R641H	possibly damaging	Het
Nr2c2	T	A	6: 92,137,382 (GRCm39)	M431K	probably damaging	Het
Ogfod3	T	C	11: 121,074,255 (GRCm39)	T265A	probably damaging	Het
Pcdh9	G	T	14: 94,124,246 (GRCm39)	Y641*	probably null	Het
Pcdha9	T	A	18: 37,132,465 (GRCm39)	D511E	probably damaging	Het
Pcdhgb8	A	G	18: 37,895,443 (GRCm39)	Y171C	probably damaging	Het
Pcnx1	T	C	12: 82,005,505 (GRCm39)	C1075R	probably damaging	Het
Pik3c3	C	A	18: 30,444,382 (GRCm39)		probably benign	Het
Pkhd1	T	C	1: 20,621,097 (GRCm39)	T854A	probably benign	Het
Pycr1	T	C	11: 120,532,961 (GRCm39)	T100A	probably benign	Het
Rhof	T	C	5: 123,242,593 (GRCm39)		probably null	Het
Scn9a	T	A	2: 66,357,217 (GRCm39)	D1028V	possibly damaging	Het
Serpina3f	T	C	12: 104,185,740 (GRCm39)	I315T	possibly damaging	Het
Slc1a6	T	A	10: 78,648,715 (GRCm39)	S479T	possibly damaging	Het
Tmcc1	T	C	6: 116,019,874 (GRCm39)	D166G	probably damaging	Het
Trav3-3	A	G	14: 53,903,828 (GRCm39)	K49E	probably benign	Het
Usp28	T	C	9: 48,942,223 (GRCm39)		probably null	Het
Utrn	C	T	10: 12,573,786 (GRCm39)	V1095I	probably benign	Het
Zfp217	T	C	2: 169,954,438 (GRCm39)	D1038G	probably damaging	Het
Zfp709	A	G	8: 72,644,397 (GRCm39)	R609G	probably damaging	Het
Zfp729a	T	A	13: 67,768,310 (GRCm39)	K640*	probably null	Het
Zfp986	A	T	4: 145,619,090 (GRCm39)		probably benign	Het
Zkscan6	A	T	11: 65,719,051 (GRCm39)	H357L	probably benign	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
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
R9234:Lims2	UTSW	18	32,090,943 (GRCm39)	missense	probably benign	0.12
X0027:Lims2	UTSW	18	32,087,599 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

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

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

Posted On

2015-04-17