Mutagenetix > Incidental Mutation

Incidental Mutation 'R9176:Lims1'

696690

Institutional Source

Beutler Lab

Gene Symbol

Lims1

Ensembl Gene

ENSMUSG00000019920

Gene Name

LIM and senescent cell antigen-like domains 1

Synonyms

Lims1l, 4921524A02Rik, C430041B13Rik, 2310016J22Rik, PINCH1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9176 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

58159288-58260513 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 58254265 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Glycine at position 340 (C340G)

Ref Sequence

ENSEMBL: ENSMUSP00000020077 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020077] [ENSMUST00000020078] [ENSMUST00000105468]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000020077
AA Change: C340G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
AA Change: C340G

Domain	Start	End	E-Value	Type
LIM	71	124	3.78e-15	SMART
LIM	132	183	5.35e-15	SMART
LIM	196	246	1.01e-10	SMART
LIM	254	305	2.84e-19	SMART
LIM	313	365	3.84e-16	SMART
low complexity region	371	387	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000020078
AA Change: C290G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000020078
Gene: ENSMUSG00000019920
AA Change: C290G

Domain	Start	End	E-Value	Type
LIM	21	74	3.78e-15	SMART
LIM	82	133	5.35e-15	SMART
LIM	146	196	1.01e-10	SMART
LIM	204	255	2.84e-19	SMART
LIM	263	315	5.51e-17	SMART
low complexity region	317	334	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000105468
AA Change: C340G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
AA Change: C340G

Domain	Start	End	E-Value	Type
LIM	71	124	3.78e-15	SMART
LIM	132	183	5.35e-15	SMART
LIM	196	246	1.01e-10	SMART
LIM	254	305	2.84e-19	SMART
LIM	313	365	5.51e-17	SMART
low complexity region	367	384	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (70/70)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
PHENOTYPE: Homozygous null mice die shortly after implantation and have a disorganized egg cylinder by E5.5, which is degenerated by E6.5. E5.5 null embryos exhibit decreased cell proliferation and excessive cell death. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001J03Rik	T	C	5: 146,121,004 (GRCm39)	D119G	probably damaging	Het
1700123K08Rik	T	C	5: 138,561,155 (GRCm39)	D169G	probably damaging	Het
Abcd2	T	G	15: 91,075,623 (GRCm39)	R63S	probably benign	Het
Ankrd55	T	C	13: 112,459,610 (GRCm39)	V68A	possibly damaging	Het
Avil	T	C	10: 126,852,248 (GRCm39)	Y678H	probably damaging	Het
Bltp1	T	A	3: 37,010,852 (GRCm39)	V1750E	possibly damaging	Het
Cd300ld2	C	A	11: 114,904,772 (GRCm39)	E32*	probably null	Het
Chuk	A	T	19: 44,076,442 (GRCm39)	L423Q	probably damaging	Het
Cisd3	A	G	11: 97,579,127 (GRCm39)	T90A	probably damaging	Het
Cmpk2	T	A	12: 26,524,027 (GRCm39)	S275T	probably benign	Het
Cntnap5c	T	A	17: 58,620,730 (GRCm39)	N936K	probably damaging	Het
Col15a1	G	C	4: 47,288,200 (GRCm39)		probably benign	Het
Col4a4	G	T	1: 82,463,349 (GRCm39)	P1047Q	unknown	Het
Col6a4	A	G	9: 105,938,755 (GRCm39)	L1321P	probably damaging	Het
Crat	A	G	2: 30,297,892 (GRCm39)	F211L	probably damaging	Het
Csmd3	T	C	15: 47,864,937 (GRCm39)	Q27R		Het
Dapk1	T	C	13: 60,866,262 (GRCm39)	V205A	probably damaging	Het
Ddx20	T	C	3: 105,586,158 (GRCm39)	N729S	probably benign	Het
Derl2	A	G	11: 70,904,376 (GRCm39)	V139A	possibly damaging	Het
Dscam	C	T	16: 96,486,553 (GRCm39)	D1041N	probably benign	Het
Fbxo2	A	T	4: 148,250,147 (GRCm39)	R226W	probably damaging	Het
Fhip1b	A	C	7: 105,030,585 (GRCm39)	H180Q	probably benign	Het
Fhip2b	T	C	14: 70,826,540 (GRCm39)	K183E	probably benign	Het
Gpr19	A	G	6: 134,846,718 (GRCm39)	S322P	probably damaging	Het
Gvin2	T	C	7: 105,551,262 (GRCm39)	K597E	possibly damaging	Het
Herc6	A	G	6: 57,636,663 (GRCm39)	N793S	probably benign	Het
Ikbke	A	T	1: 131,191,025 (GRCm39)	S563T	probably benign	Het
Il1r2	T	C	1: 40,144,478 (GRCm39)	L55P	probably damaging	Het
Klhl8	C	A	5: 104,012,111 (GRCm39)	A575S	probably benign	Het
Loxl3	G	A	6: 83,026,292 (GRCm39)	C460Y	probably damaging	Het
Mapk9	T	A	11: 49,763,565 (GRCm39)	L152*	probably null	Het
Mef2d	T	C	3: 88,066,463 (GRCm39)	V144A	possibly damaging	Het
Mertk	A	G	2: 128,620,892 (GRCm39)	D578G	possibly damaging	Het
Mettl1	C	A	10: 126,881,250 (GRCm39)	Q254K	probably benign	Het
Naip2	T	C	13: 100,298,707 (GRCm39)	E443G	probably damaging	Het
Ndor1	A	G	2: 25,138,241 (GRCm39)	F484L	probably damaging	Het
Neurl1b	C	T	17: 26,660,055 (GRCm39)	T425I	possibly damaging	Het
Nomo1	G	A	7: 45,730,828 (GRCm39)	V1104M	possibly damaging	Het
Or13a19	G	T	7: 139,903,121 (GRCm39)	G170C	probably damaging	Het
Or13p8	T	A	4: 118,583,850 (GRCm39)	Y135*	probably null	Het
Or4c10b	T	C	2: 89,711,515 (GRCm39)	V115A	probably benign	Het
Or5b95	A	G	19: 12,657,600 (GRCm39)	M43V	probably benign	Het
Or5p57	A	G	7: 107,665,246 (GRCm39)	V223A	probably benign	Het
Or8g20	T	A	9: 39,396,247 (GRCm39)	M98L	probably benign	Het
Or9i2	A	G	19: 13,815,796 (GRCm39)	V247A	probably damaging	Het
Parp4	A	G	14: 56,873,274 (GRCm39)	K1173E	possibly damaging	Het
Phkb	T	A	8: 86,697,623 (GRCm39)	N477K	probably damaging	Het
Plekha7	T	G	7: 115,739,926 (GRCm39)	I812L	possibly damaging	Het
Plxnb1	A	G	9: 108,941,651 (GRCm39)	T1711A	probably damaging	Het
Polg	A	G	7: 79,109,857 (GRCm39)	V382A	probably benign	Het
Pomt2	T	A	12: 87,194,451 (GRCm39)		probably benign	Het
Prdm1	T	C	10: 44,316,123 (GRCm39)	H671R	probably damaging	Het
Prkca	G	A	11: 107,870,244 (GRCm39)	R15C	possibly damaging	Het
Prkch	T	A	12: 73,746,968 (GRCm39)	N282K	probably damaging	Het
Ptpn6	T	C	6: 124,702,249 (GRCm39)	R385G	probably benign	Het
Rad21	A	T	15: 51,841,455 (GRCm39)	M87K	probably damaging	Het
Safb2	ACTTCTTCT	ACTTCT	17: 56,878,292 (GRCm39)		probably benign	Het
Scn1a	A	T	2: 66,103,689 (GRCm39)	V1857E	probably damaging	Het
Shprh	A	G	10: 11,036,320 (GRCm39)	T386A	probably benign	Het
Slco1b2	T	C	6: 141,598,229 (GRCm39)	L94P	probably damaging	Het
Snx29	A	G	16: 11,236,728 (GRCm39)	N90D	probably benign	Het
Stt3a	A	T	9: 36,662,592 (GRCm39)	H222Q	probably damaging	Het
Tbc1d5	T	C	17: 51,089,363 (GRCm39)	T584A	probably benign	Het
Tktl2	T	C	8: 66,964,664 (GRCm39)	V74A	probably damaging	Het
Tpp2	A	G	1: 44,031,553 (GRCm39)	N1124D	probably null	Het
Trpv1	A	T	11: 73,130,481 (GRCm39)	T196S	probably benign	Het
Ulk4	T	C	9: 120,974,128 (GRCm39)	E968G	probably benign	Het
Zbtb8a	G	T	4: 129,254,221 (GRCm39)	T91K	probably damaging	Het
Zfp317	T	A	9: 19,559,163 (GRCm39)	V459E	probably damaging	Het
Zfp790	A	G	7: 29,529,387 (GRCm39)	T691A	probably benign	Het

Other mutations in Lims1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
P0027:Lims1	UTSW	10	58,254,277 (GRCm39)	missense	probably benign	0.00
R4271:Lims1	UTSW	10	58,246,026 (GRCm39)	critical splice donor site	probably null
R4528:Lims1	UTSW	10	58,245,882 (GRCm39)	missense	probably damaging	1.00
R4546:Lims1	UTSW	10	58,254,612 (GRCm39)	intron	probably benign
R4992:Lims1	UTSW	10	58,246,063 (GRCm39)	intron	probably benign
R5380:Lims1	UTSW	10	58,252,492 (GRCm39)	missense	probably damaging	0.99
R6207:Lims1	UTSW	10	58,230,386 (GRCm39)	missense	possibly damaging	0.76
R6543:Lims1	UTSW	10	58,248,273 (GRCm39)	nonsense	probably null
R6684:Lims1	UTSW	10	58,234,835 (GRCm39)	splice site	probably null
R6762:Lims1	UTSW	10	58,248,367 (GRCm39)	missense	probably damaging	1.00
R7373:Lims1	UTSW	10	58,245,442 (GRCm39)	missense	probably damaging	1.00
R7434:Lims1	UTSW	10	58,230,301 (GRCm39)	missense	probably benign
R7597:Lims1	UTSW	10	58,248,263 (GRCm39)	missense	probably damaging	0.99
R8035:Lims1	UTSW	10	58,246,263 (GRCm39)	intron	probably benign
R8039:Lims1	UTSW	10	58,245,494 (GRCm39)	missense	probably benign	0.03
R8860:Lims1	UTSW	10	58,243,925 (GRCm39)	nonsense	probably null
T0722:Lims1	UTSW	10	58,254,277 (GRCm39)	missense	probably benign	0.00
Z1177:Lims1	UTSW	10	58,245,478 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TCTCAGGAAAGAAGGCTTGAGC -3'
(R):5'- GCAGACTGGCTTTAGATCAATTTC -3'

Sequencing Primer
(F):5'- TGAAATGCTCCCGTGTGA -3'
(R):5'- CAACAAACTTATCCCTTTGAGTGG -3'

Posted On

2022-02-07