Mutagenetix > Incidental Mutation

Incidental Mutation 'R8039:Lims1'

618424

Institutional Source

Beutler Lab

Gene Symbol

Lims1

Ensembl Gene

ENSMUSG00000019920

Gene Name

LIM and senescent cell antigen-like domains 1

Synonyms

4921524A02Rik, PINCH1, C430041B13Rik, Lims1l, 2310016J22Rik

MMRRC Submission

067476-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8039 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

58323466-58424691 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 58409672 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 174 (N174K)

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 benign
Transcript: ENSMUST00000020077
AA Change: N174K

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
AA Change: N174K

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 benign
Transcript: ENSMUST00000020078
AA Change: N124K

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000020078
Gene: ENSMUSG00000019920
AA Change: N124K

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 benign
Transcript: ENSMUST00000105468
AA Change: N174K

PolyPhen 2 Score 0.129 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
AA Change: N174K

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: 99.6%
20x: 98.5%

Validation Efficiency

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932438A13Rik	T	A	3: 36,943,214	V1140E	probably benign	Het
Abca17	T	C	17: 24,328,725	H225R	probably damaging	Het
Adgrb2	T	A	4: 130,022,268	L1451Q	probably damaging	Het
Afdn	T	C	17: 13,899,141	L1713P	probably damaging	Het
Agr2	A	T	12: 35,995,559	I15F	probably benign	Het
Agrn	T	C	4: 156,169,011	T1808A	probably benign	Het
Akap6	A	G	12: 53,141,676	I1958V	probably benign	Het
Ankrd60	C	A	2: 173,572,491		probably null	Het
Anpep	A	G	7: 79,839,400		probably null	Het
Apoa4	A	T	9: 46,242,293	D64V	possibly damaging	Het
Arhgef26	C	A	3: 62,339,930	T145N	probably benign	Het
Art1	A	T	7: 102,106,845	Q81L	probably benign	Het
Astl	A	T	2: 127,343,983	S71C	probably damaging	Het
Atp2a1	A	G	7: 126,448,805	I611T	probably damaging	Het
Cacna2d2	T	A	9: 107,527,433	V1139D	possibly damaging	Het
Chst10	T	A	1: 38,866,031	K198*	probably null	Het
Ckmt2	G	A	13: 91,863,312	H60Y	possibly damaging	Het
Coq7	G	C	7: 118,533,246	S2R	possibly damaging	Het
Cspp1	T	A	1: 10,113,013	D814E	probably benign	Het
Cyp2c54	CCTCTTTCATAGCTCT	CCTCT	19: 40,073,732		probably null	Het
Daam2	C	A	17: 49,464,538	G860V	probably damaging	Het
Ecm2	A	T	13: 49,514,850	I10F	probably benign	Het
Epb41l1	A	T	2: 156,506,412	D312V	probably damaging	Het
Epsti1	G	A	14: 77,931,301	R126H	probably damaging	Het
Erc1	A	T	6: 119,773,665	Y367*	probably null	Het
Erh	T	A	12: 80,637,578	R42W	probably damaging	Het
Fam124a	C	T	14: 62,605,876	Q278*	probably null	Het
Fam155a	T	C	8: 9,207,892	T419A	probably benign	Het
Fbxo3	T	A	2: 104,054,941	L385Q	probably damaging	Het
Fbxo31	T	A	8: 121,559,055	T219S	probably damaging	Het
Fstl5	T	G	3: 76,648,418	V534G	possibly damaging	Het
Gatsl3	G	T	11: 4,221,639	A288S	probably damaging	Het
Gbp2b	A	T	3: 142,618,164	I577F	probably benign	Het
Gbp8	A	T	5: 105,050,917	L44*	probably null	Het
Gck	C	T	11: 5,910,301	A114T	probably benign	Het
Gm16486	T	C	8: 70,710,906	V916A	probably benign	Het
Gtf2i	A	G	5: 134,255,834	V537A	possibly damaging	Het
Iqcm	C	A	8: 75,763,105	H400Q	probably damaging	Het
Itpr1	T	C	6: 108,386,628	L737P	probably damaging	Het
Jakmip1	A	G	5: 37,100,772	E254G	probably damaging	Het
Kif15	A	T	9: 123,007,425	R1095W	possibly damaging	Het
Klhdc8a	G	A	1: 132,303,108	R237Q	probably benign	Het
Klhl38	T	C	15: 58,322,862	E157G	probably benign	Het
Klrk1	T	A	6: 129,612,823	N221I	probably benign	Het
Lhx8	A	T	3: 154,306,939	H345Q	probably damaging	Het
Madd	T	A	2: 91,167,061	Q754L	probably benign	Het
Mau2	T	C	8: 70,019,790	D581G	probably damaging	Het
Miga1	A	T	3: 152,276,756	I561N	probably benign	Het
Mmp1a	TG	TGG	9: 7,465,083		probably null	Het
Mob3c	T	C	4: 115,831,687	V139A	probably benign	Het
Nadk	G	T	4: 155,577,067	D17Y	probably benign	Het
Ncapd2	C	T	6: 125,181,026	V380I	probably damaging	Het
Nes	G	A	3: 87,977,008	R858K	probably benign	Het
Nphp3	T	C	9: 104,031,963	S791P	probably benign	Het
Nup210	T	C	6: 91,070,233	T496A	probably benign	Het
Ogfr	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	2: 180,595,266		probably benign	Het
Olfr1186	C	T	2: 88,525,871	T96I	probably benign	Het
Olfr220	T	A	1: 174,449,596	S324R	unknown	Het
Olfr914	T	A	9: 38,607,389	M308K	probably benign	Het
Ovgp1	T	A	3: 105,976,023	S105T	probably benign	Het
Pbld2	T	A	10: 63,047,992	C79S	probably damaging	Het
Pik3cd	T	A	4: 149,659,866	M143L	possibly damaging	Het
Plat	G	T	8: 22,772,232	G91W	probably damaging	Het
Poln	A	G	5: 34,122,672	V282A	probably benign	Het
Ppp1r11	T	C	17: 36,951,446	T21A	probably damaging	Het
Prpf8	T	A	11: 75,502,542	I1664N	possibly damaging	Het
Prr29	C	T	11: 106,376,912	A161V	probably benign	Het
Rasa3	T	C	8: 13,588,931	D292G	probably damaging	Het
Rnf25	T	C	1: 74,593,964	T411A	probably damaging	Het
Rraga	C	T	4: 86,575,980	T21I	probably damaging	Het
Setdb2	T	A	14: 59,402,375	Y673F	probably damaging	Het
Sf3a1	C	T	11: 4,167,787	T183I	probably damaging	Het
Shank3	A	T	15: 89,505,439	H413L	probably damaging	Het
Slc30a5	A	G	13: 100,813,681		probably null	Het
Slc6a18	T	C	13: 73,665,626	S523G	probably benign	Het
Spaca1	C	T	4: 34,044,207	V96I	probably damaging	Het
Sycp2	C	T	2: 178,374,585	A695T	probably benign	Het
Tnrc18	C	A	5: 142,732,052	G2216C	unknown	Het
Trak2	T	C	1: 58,946,288	N17S	probably benign	Het
Ttn	T	A	2: 76,878,432	N8792I	unknown	Het
Ttyh1	T	C	7: 4,122,541	V64A	probably benign	Het
Usb1	T	A	8: 95,333,413	S50R	probably damaging	Het
Ush2a	T	A	1: 188,957,373	I5044N	probably damaging	Het
Vmn1r84	A	T	7: 12,362,008	F253I	possibly damaging	Het
Vmn2r99	T	C	17: 19,380,040	I442T	probably benign	Het
Vsig1	C	T	X: 140,933,126	H232Y	probably benign	Het

Other mutations in Lims1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
P0027:Lims1	UTSW	10	58418455	missense	probably benign	0.00
R4271:Lims1	UTSW	10	58410204	critical splice donor site	probably null
R4528:Lims1	UTSW	10	58410060	missense	probably damaging	1.00
R4546:Lims1	UTSW	10	58418790	intron	probably benign
R4992:Lims1	UTSW	10	58410241	intron	probably benign
R5380:Lims1	UTSW	10	58416670	missense	probably damaging	0.99
R6207:Lims1	UTSW	10	58394564	missense	possibly damaging	0.76
R6543:Lims1	UTSW	10	58412451	nonsense	probably null
R6684:Lims1	UTSW	10	58399013	splice site	probably null
R6762:Lims1	UTSW	10	58412545	missense	probably damaging	1.00
R7373:Lims1	UTSW	10	58409620	missense	probably damaging	1.00
R7434:Lims1	UTSW	10	58394479	missense	probably benign
R7597:Lims1	UTSW	10	58412441	missense	probably damaging	0.99
R8035:Lims1	UTSW	10	58410441	intron	probably benign
R8860:Lims1	UTSW	10	58408103	nonsense	probably null
R9176:Lims1	UTSW	10	58418443	missense	probably damaging	1.00
T0722:Lims1	UTSW	10	58418455	missense	probably benign	0.00
Z1177:Lims1	UTSW	10	58409656	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GGAACACTAGAGTCAGTCCCTC -3'
(R):5'- TCCCTCTCCTAGCAGAACAG -3'

Sequencing Primer
(F):5'- GAGTCAGTCCCTCCATAAACACTTC -3'
(R):5'- TCTCCTAGCAGAACAGGAGGC -3'

Posted On

2020-01-23