Mutagenetix > Incidental Mutation

Incidental Mutation 'R6207:Lims1'

503209

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

044341-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6207 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

58159288-58260513 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 58230386 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Methionine at position 49 (K49M)

Ref Sequence

ENSEMBL: ENSMUSP00000020077 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000020077
AA Change: K49M

PolyPhen 2 Score 0.764 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
AA Change: K49M

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

SMART Domains

Protein: ENSMUSP00000020078
Gene: ENSMUSG00000019920

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

possibly damaging
Transcript: ENSMUST00000105468
AA Change: K49M

PolyPhen 2 Score 0.674 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
AA Change: K49M

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: 99.5%
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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930451I11Rik	G	A	7: 126,430,065 (GRCm39)	P69S	probably damaging	Het
Abca15	A	G	7: 119,973,017 (GRCm39)	R864G	probably benign	Het
Acbd5	T	C	2: 22,959,490 (GRCm39)	C15R	possibly damaging	Het
Ahctf1	A	T	1: 179,604,955 (GRCm39)		probably null	Het
Ak3	T	A	19: 29,000,340 (GRCm39)	K190N	probably damaging	Het
B4galnt3	A	T	6: 120,183,575 (GRCm39)		probably null	Het
Calcrl	T	C	2: 84,163,874 (GRCm39)	H439R	probably benign	Het
Casp7	T	A	19: 56,429,452 (GRCm39)	D279E	possibly damaging	Het
Cckar	A	G	5: 53,857,186 (GRCm39)	V337A	probably benign	Het
Cep85l	T	C	10: 53,157,651 (GRCm39)	Y684C	probably benign	Het
Cmtm1	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	8: 105,036,102 (GRCm39)		probably benign	Homo
Commd7	T	C	2: 153,474,530 (GRCm39)	N23S	possibly damaging	Het
Cpne9	A	T	6: 113,271,734 (GRCm39)	I365F	possibly damaging	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dot1l	C	T	10: 80,622,277 (GRCm39)	A831V	probably benign	Het
Entrep1	T	C	19: 23,950,802 (GRCm39)	E593G	probably damaging	Het
Epcam	C	A	17: 87,947,864 (GRCm39)	N111K	probably damaging	Het
Etnk1	A	G	6: 143,126,524 (GRCm39)	Q123R	probably damaging	Het
Fam170a	A	T	18: 50,415,017 (GRCm39)	E221V	probably damaging	Het
Fbl	T	C	7: 27,874,278 (GRCm39)	S88P	possibly damaging	Het
Fbxo36	T	A	1: 84,874,251 (GRCm39)	Y82*	probably null	Het
Fer1l5	A	G	1: 36,424,241 (GRCm39)	K285R	probably damaging	Het
Foxn3	G	T	12: 99,162,569 (GRCm39)	T444K	probably damaging	Het
Gak	C	T	5: 108,772,895 (GRCm39)		probably null	Het
Gprc6a	T	C	10: 51,502,931 (GRCm39)	I311V	probably benign	Het
Hrg	T	C	16: 22,773,288 (GRCm39)		probably null	Het
Htatip2	G	A	7: 49,420,567 (GRCm39)	V138I	probably benign	Het
Ighv1-4	A	T	12: 114,451,142 (GRCm39)		probably benign	Het
Kcnq2	T	C	2: 180,755,026 (GRCm39)	M174V	possibly damaging	Het
Krt39	G	T	11: 99,412,041 (GRCm39)	P15Q	probably damaging	Het
L1td1	G	A	4: 98,625,655 (GRCm39)	D617N	possibly damaging	Het
Lgalsl	T	A	11: 20,779,382 (GRCm39)	K88*	probably null	Het
Man2a1	T	C	17: 65,020,600 (GRCm39)	V792A	probably benign	Het
Mcm2	G	T	6: 88,862,844 (GRCm39)	D749E	probably benign	Het
Mdga1	G	A	17: 30,057,491 (GRCm39)	T775M	probably damaging	Het
Myb	A	G	10: 21,021,221 (GRCm39)	S403P	probably benign	Het
Nek6	T	C	2: 38,447,846 (GRCm39)	S37P	possibly damaging	Het
Or10d1b	T	C	9: 39,613,606 (GRCm39)	H153R	probably benign	Het
Or14c46	A	C	7: 85,918,968 (GRCm39)	F10V	probably damaging	Het
Or52a33	A	G	7: 103,289,209 (GRCm39)	V46A	probably benign	Het
Or56b2j	G	A	7: 104,352,818 (GRCm39)	V15M	probably damaging	Het
Peg10	GAT	GATCAT	6: 4,756,449 (GRCm39)		probably benign	Het
Prpf40a	T	C	2: 53,047,927 (GRCm39)	M197V	probably benign	Het
Prune2	T	A	19: 17,095,480 (GRCm39)	I328N	probably damaging	Het
Psap	T	A	10: 60,136,317 (GRCm39)	C484S	probably damaging	Het
Pus1	T	C	5: 110,925,580 (GRCm39)	D80G	probably benign	Het
Rasa3	T	C	8: 13,648,251 (GRCm39)	T138A	possibly damaging	Het
Scaf1	G	T	7: 44,657,047 (GRCm39)		probably benign	Het
Skap1	T	A	11: 96,594,959 (GRCm39)	Y143*	probably null	Het
Slc22a20	A	G	19: 6,035,969 (GRCm39)	L67P	probably damaging	Het
Slc25a17	T	C	15: 81,213,265 (GRCm39)	Y146C	probably damaging	Het
Slfn4	C	T	11: 83,079,951 (GRCm39)	T154I	possibly damaging	Het
Snai1	T	A	2: 167,380,229 (GRCm39)	V7D	probably damaging	Het
Snrnp200	T	A	2: 127,052,655 (GRCm39)	M84K	probably benign	Het
Spop	G	T	11: 95,362,063 (GRCm39)	K31N	possibly damaging	Het
Surf1	T	C	2: 26,804,819 (GRCm39)	T145A	probably benign	Het
Tbkbp1	T	C	11: 97,037,165 (GRCm39)	E278G	probably damaging	Het
Thumpd2	G	A	17: 81,363,266 (GRCm39)	A67V	probably damaging	Het
Timd4	A	T	11: 46,706,353 (GRCm39)	M52L	probably damaging	Het
Trav16	A	T	14: 53,981,045 (GRCm39)	N78I	probably damaging	Het
Tspan12	T	C	6: 21,799,907 (GRCm39)	T147A	probably damaging	Het
Tulp1	A	T	17: 28,577,651 (GRCm39)		probably benign	Het
Ubqlnl	A	T	7: 103,797,915 (GRCm39)	N527K	possibly damaging	Het
Ubr4	G	A	4: 139,148,559 (GRCm39)	C1681Y	probably damaging	Het
Unc13c	T	C	9: 73,665,910 (GRCm39)	K1037E	possibly damaging	Het
Vmn2r111	T	C	17: 22,778,032 (GRCm39)	N549S	possibly damaging	Het
Vmn2r4	G	A	3: 64,313,926 (GRCm39)	H352Y	probably damaging	Het
Vmn2r61	A	T	7: 41,909,616 (GRCm39)	H47L	probably benign	Het
Vwa5a	A	G	9: 38,633,968 (GRCm39)	E57G	probably damaging	Het
Zfp180	A	T	7: 23,804,510 (GRCm39)	R310*	probably null	Het
Zfp672	T	C	11: 58,208,349 (GRCm39)		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
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
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'- TATCCTGCTCGGCATCACAG -3'
(R):5'- ATGTCCTCTGGTGGAAGTTTATAAG -3'

Sequencing Primer
(F):5'- AGGACTCTGAACTCTCAAGCTTG -3'
(R):5'- CCTCTGGTGGAAGTTTATAAGACAAG -3'

Posted On

2018-02-27