Mutagenetix > Incidental Mutation

Incidental Mutation 'R4992:Lims1'

386273

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

042586-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4992 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

58159288-58260513 bp(+) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

A to C at 58246063 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000101108 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000020077

SMART Domains

Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920

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

probably benign
Transcript: ENSMUST00000105468

SMART Domains

Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124312

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.7%

Validation Efficiency

98% (84/86)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930407I10Rik	G	A	15: 81,948,203 (GRCm39)	R700Q	possibly damaging	Het
4930444P10Rik	T	A	1: 16,151,101 (GRCm39)	E27V	probably damaging	Het
Acsm4	T	A	7: 119,310,640 (GRCm39)	I509N	probably benign	Het
Asb18	T	C	1: 89,880,585 (GRCm39)	M143V	probably benign	Het
Birc6	A	G	17: 74,996,251 (GRCm39)	D4475G	probably benign	Het
Bsn	A	T	9: 107,992,747 (GRCm39)	S1002T	probably damaging	Het
Bub3	T	C	7: 131,162,535 (GRCm39)	S33P	probably damaging	Het
Ccna1	T	A	3: 54,957,311 (GRCm39)	R35S	probably damaging	Het
Cdc23	T	A	18: 34,779,972 (GRCm39)	M119L	probably benign	Het
Ces1a	A	G	8: 93,771,650 (GRCm39)	V49A	probably benign	Het
Chi3l1	A	T	1: 134,116,364 (GRCm39)	E282D	probably benign	Het
Crocc	G	A	4: 140,773,977 (GRCm39)	A220V	probably damaging	Het
Cstf1	A	G	2: 172,219,720 (GRCm39)	Y277C	probably damaging	Het
D930020B18Rik	C	G	10: 121,490,666 (GRCm39)	P89A	probably damaging	Het
D930020B18Rik	C	T	10: 121,490,667 (GRCm39)	P89L	probably damaging	Het
Dennd5a	A	G	7: 109,493,919 (GRCm39)	S1262P	probably damaging	Het
Dnajb5	G	A	4: 42,953,386 (GRCm39)		probably null	Het
E330034G19Rik	A	G	14: 24,357,064 (GRCm39)	K200R	unknown	Het
Ect2l	A	G	10: 18,048,477 (GRCm39)	F156S	probably benign	Het
Egf	T	C	3: 129,505,179 (GRCm39)		probably null	Het
Elmo1	T	C	13: 20,526,689 (GRCm39)	F413S	probably damaging	Het
Elmo3	T	A	8: 106,036,133 (GRCm39)	Y607*	probably null	Het
Eno3	A	G	11: 70,549,473 (GRCm39)	D98G	probably damaging	Het
Ephb2	A	G	4: 136,388,150 (GRCm39)	V651A	probably damaging	Het
Fbp1	C	T	13: 63,012,888 (GRCm39)	V102I	probably benign	Het
Gcn1	T	C	5: 115,737,225 (GRCm39)	V1321A	probably benign	Het
Gimd1	A	T	3: 132,340,718 (GRCm39)	Y78F	probably benign	Het
Glmn	T	G	5: 107,705,167 (GRCm39)	D483A	probably damaging	Het
Gsr	C	T	8: 34,183,941 (GRCm39)	T401I	probably damaging	Het
Htr3b	G	A	9: 48,870,518 (GRCm39)	H62Y	possibly damaging	Het
Ifna6	T	C	4: 88,745,777 (GRCm39)	V42A	probably benign	Het
Igkv4-80	A	C	6: 68,993,649 (GRCm39)	S81A	probably benign	Het
Inpp4b	A	T	8: 82,759,837 (GRCm39)	R627S	probably damaging	Het
Kif13a	C	T	13: 46,930,639 (GRCm39)	V142M	probably damaging	Het
Ltn1	T	C	16: 87,202,475 (GRCm39)	T1059A	possibly damaging	Het
Lyst	T	C	13: 13,835,748 (GRCm39)	L1810P	probably damaging	Het
Mboat1	T	G	13: 30,386,343 (GRCm39)	I119R	possibly damaging	Het
Mgat3	T	A	15: 80,096,743 (GRCm39)	D523E	probably benign	Het
Mphosph9	T	C	5: 124,442,253 (GRCm39)	E395G	probably damaging	Het
Mtcl1	G	T	17: 66,649,834 (GRCm39)	P1877Q	probably damaging	Het
Myo6	T	C	9: 80,190,792 (GRCm39)	V781A	possibly damaging	Het
Ncoa3	T	A	2: 165,911,859 (GRCm39)	M1395K	probably benign	Het
Nhlrc2	T	A	19: 56,558,966 (GRCm39)	D150E	probably benign	Het
Nlrp9a	T	C	7: 26,256,811 (GRCm39)	V54A	probably benign	Het
Or1e32	G	A	11: 73,705,146 (GRCm39)	T254I	probably damaging	Het
Or3a1d	A	G	11: 74,238,023 (GRCm39)	I129T	probably damaging	Het
Parp14	A	T	16: 35,661,512 (GRCm39)	C1479S	probably benign	Het
Pdcd1lg2	T	C	19: 29,423,484 (GRCm39)	V176A	probably damaging	Het
Pibf1	T	A	14: 99,388,103 (GRCm39)	N416K	probably damaging	Het
Pip4p1	A	G	14: 51,166,690 (GRCm39)	V179A	probably damaging	Het
Polb	A	T	8: 23,135,087 (GRCm39)	V115E	probably damaging	Het
Polq	T	A	16: 36,881,524 (GRCm39)	N1229K	possibly damaging	Het
Ppp1r21	A	T	17: 88,876,508 (GRCm39)	D440V	probably benign	Het
Ppp2ca	T	A	11: 52,004,033 (GRCm39)	H63Q	possibly damaging	Het
Prl7a1	C	T	13: 27,819,669 (GRCm39)		probably null	Het
Rgs1	C	A	1: 144,122,060 (GRCm39)	K77N	probably damaging	Het
Rnf112	T	A	11: 61,343,537 (GRCm39)	I100F	possibly damaging	Het
Rnf139	G	T	15: 58,770,325 (GRCm39)	E117*	probably null	Het
Robo1	G	A	16: 72,776,756 (GRCm39)	V743I	probably damaging	Het
Scarf1	T	C	11: 75,416,841 (GRCm39)	V761A	probably benign	Het
Scarf1	T	C	11: 75,413,056 (GRCm39)	L434P	probably damaging	Het
Sgsm1	A	T	5: 113,430,486 (GRCm39)	S300T	possibly damaging	Het
Slc26a7	T	G	4: 14,565,508 (GRCm39)	T192P	probably damaging	Het
Smarcc2	A	G	10: 128,310,579 (GRCm39)	K403E	probably damaging	Het
Snai3	G	A	8: 123,183,071 (GRCm39)	T158M	possibly damaging	Het
Spata31d1a	T	C	13: 59,850,965 (GRCm39)	N388D	probably benign	Het
Sptlc3	G	A	2: 139,437,923 (GRCm39)	V406I	probably benign	Het
Tgds	A	C	14: 118,355,175 (GRCm39)	Y197D	probably damaging	Het
Tll1	G	T	8: 64,546,978 (GRCm39)	R323S	probably damaging	Het
Trim14	A	G	4: 46,507,110 (GRCm39)	Y369H	probably damaging	Het
Ube2nl	C	T	7: 61,199,112 (GRCm39)		noncoding transcript	Het
Ube3a	T	A	7: 58,934,568 (GRCm39)	D560E	possibly damaging	Het
Vmn2r10	A	G	5: 109,145,592 (GRCm39)	V505A	possibly damaging	Het
Vmn2r114	T	G	17: 23,510,765 (GRCm39)	I572L	probably benign	Het
Vmn2r26	A	T	6: 124,003,070 (GRCm39)	Q160L	probably benign	Het
Vmn2r75	A	C	7: 85,815,375 (GRCm39)		probably null	Het
Vps8	A	G	16: 21,280,158 (GRCm39)	K336E	possibly damaging	Het
Zfp324	T	C	7: 12,703,300 (GRCm39)	S32P	probably benign	Het
Zfp366	T	C	13: 99,366,003 (GRCm39)	I388T	possibly damaging	Het
Zfp68	A	T	5: 138,605,599 (GRCm39)	N203K	possibly damaging	Het
Zhx2	A	T	15: 57,686,983 (GRCm39)	N784I	probably damaging	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
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
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'- TCGCCCATGTCATAATCGTG -3'
(R):5'- ACCTGATTTGGTGATGTTCCGC -3'

Sequencing Primer
(F):5'- TCGCCCATGTCATAATCGTGAAAAAG -3'
(R):5'- CCTTCTTCTAACACGAAAAGTTGGGG -3'

Posted On

2016-05-10