Mutagenetix > Incidental Mutation

Incidental Mutation 'R7373:Lims1'

572228

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

045456-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7373 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

58159288-58260513 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 58245442 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 157 (F157S)

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: F157S

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
AA Change: F157S

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: F107S

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000020078
Gene: ENSMUSG00000019920
AA Change: F107S

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: F157S

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

SMART Domains

Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
AA Change: F157S

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

Meta Mutation Damage Score

0.9677

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

98% (57/58)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts2	G	A	11: 50,686,262 (GRCm39)	A1027T	probably benign	Het
Aldh7a1	G	A	18: 56,675,389 (GRCm39)	T260M	possibly damaging	Het
Anks3	T	C	16: 4,773,735 (GRCm39)	Y187C	probably benign	Het
Atp2c2	A	T	8: 120,456,991 (GRCm39)	I198F	probably benign	Het
Bsn	T	C	9: 107,990,683 (GRCm39)	T1690A	probably damaging	Het
Catsper3	T	C	13: 55,955,945 (GRCm39)	I350T	possibly damaging	Het
Cdcp1	C	T	9: 123,006,965 (GRCm39)	R594H	probably damaging	Het
Cfap57	C	T	4: 118,472,128 (GRCm39)	V84I	probably benign	Het
Cldn1	G	T	16: 26,179,606 (GRCm39)	P154T	probably damaging	Het
Cntnap5a	A	T	1: 116,508,367 (GRCm39)	N1293I	probably benign	Het
Cpsf4l	C	T	11: 113,590,657 (GRCm39)		probably null	Het
Crybg1	T	C	10: 43,880,136 (GRCm39)	T351A	probably benign	Het
Csmd1	T	C	8: 16,042,713 (GRCm39)	N2340S	probably damaging	Het
Dennd4a	C	A	9: 64,804,551 (GRCm39)	Q1297K	probably benign	Het
Dll3	A	G	7: 27,994,057 (GRCm39)	V460A	probably benign	Het
Dnah8	T	C	17: 30,986,939 (GRCm39)		probably null	Het
Dst	G	T	1: 34,227,472 (GRCm39)	L1688F	probably benign	Het
Ehmt1	A	G	2: 24,809,585 (GRCm39)	M1T	probably null	Het
Fasn	A	T	11: 120,704,802 (GRCm39)	L1261Q	possibly damaging	Het
Fat1	A	G	8: 45,479,702 (GRCm39)	D2916G	probably damaging	Het
Fgfr3	C	A	5: 33,885,034 (GRCm39)	F49L	probably benign	Het
Hlx	T	C	1: 184,463,062 (GRCm39)	T197A	probably benign	Het
Hormad1	A	T	3: 95,483,628 (GRCm39)	T147S	probably damaging	Het
Igf1r	T	A	7: 67,844,826 (GRCm39)	Y866*	probably null	Het
Itgb8	A	G	12: 119,166,210 (GRCm39)	V107A	probably benign	Het
Kat2a	C	T	11: 100,599,392 (GRCm39)	A533T	probably benign	Het
Kif20b	T	C	19: 34,913,071 (GRCm39)	L328P	probably damaging	Het
Lrp2	G	T	2: 69,331,036 (GRCm39)	H1673Q	probably damaging	Het
Lrrc46	C	A	11: 96,929,706 (GRCm39)	M43I	probably benign	Het
Lrrk2	T	C	15: 91,584,207 (GRCm39)		probably null	Het
Meox2	A	T	12: 37,158,797 (GRCm39)		probably benign	Het
Mff	A	G	1: 82,714,838 (GRCm39)		probably null	Het
Mfsd5	T	A	15: 102,189,427 (GRCm39)	F266L	probably damaging	Het
Miga2	A	G	2: 30,272,083 (GRCm39)	T468A	probably damaging	Het
Mmel1	T	A	4: 154,973,665 (GRCm39)	L316Q	not run	Het
Ndufa9	C	A	6: 126,811,421 (GRCm39)	G232C	probably damaging	Het
Obox2	A	T	7: 15,131,145 (GRCm39)	K84*	probably null	Het
Or4f58	T	A	2: 111,851,787 (GRCm39)	R137S	probably benign	Het
Or51a39	T	A	7: 102,363,306 (GRCm39)	I105F	possibly damaging	Het
Otogl	G	T	10: 107,737,112 (GRCm39)	Q101K	probably damaging	Het
Pcnx2	C	T	8: 126,534,766 (GRCm39)	V1288M	probably damaging	Het
Pde10a	T	A	17: 9,161,824 (GRCm39)	W220R	probably benign	Het
Recql5	T	C	11: 115,819,198 (GRCm39)	T123A	possibly damaging	Het
Rpl28	T	C	7: 4,796,602 (GRCm39)	V61A	probably benign	Het
Secisbp2l	A	T	2: 125,599,191 (GRCm39)	M494K	probably damaging	Het
Sh3bgr	G	A	16: 96,007,035 (GRCm39)	E2K	unknown	Het
Shcbp1l	C	A	1: 153,300,986 (GRCm39)	T6K	probably benign	Het
Slc22a15	A	C	3: 101,785,213 (GRCm39)	L353R	possibly damaging	Het
Sqle	T	C	15: 59,189,658 (GRCm39)	I100T	probably benign	Het
Tas2r106	A	T	6: 131,655,317 (GRCm39)	L178H	probably damaging	Het
Tll1	A	T	8: 64,504,391 (GRCm39)	N668K	probably damaging	Het
Tm7sf2	A	G	19: 6,116,676 (GRCm39)	S118P	probably benign	Het
Tmco5	G	T	2: 116,717,226 (GRCm39)	V169L	probably benign	Het
Trpv1	A	G	11: 73,131,499 (GRCm39)	K346E	probably damaging	Het
Ttk	G	A	9: 83,736,930 (GRCm39)	R463H	probably benign	Het
Vmn2r120	G	T	17: 57,816,406 (GRCm39)	L650I	probably benign	Het
Vmn2r58	C	T	7: 41,487,212 (GRCm39)	C561Y	probably damaging	Het
Vmn2r-ps117	A	T	17: 19,044,948 (GRCm39)	Q455L	probably benign	Het
Zfr	T	A	15: 12,140,645 (GRCm39)	S231T	unknown	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
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
R9176:Lims1	UTSW	10	58,254,265 (GRCm39)	missense	probably damaging	1.00
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'- TTAGGGGTAAGGCAGTAGCTTC -3'
(R):5'- GGCAGTAACAGACTCTGTGAC -3'

Sequencing Primer
(F):5'- CTTCTATGGGAGGAACACTAGAGTC -3'
(R):5'- AGACTCTGTGACCAAGCTCTG -3'

Posted On

2019-09-13