Mutagenetix > Incidental Mutation

Incidental Mutation 'R0599:Lima1'

55254

Institutional Source

Beutler Lab

Gene Symbol

Lima1

Ensembl Gene

ENSMUSG00000023022

Gene Name

LIM domain and actin binding 1

Synonyms

3526402A12Rik, EPLIN, epithelial protein lost in neoplasm, 1110021C24Rik

MMRRC Submission

038788-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.141) question?

Stock #

R0599 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

99676351-99773292 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 99700040 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 146 (N146K)

Ref Sequence

ENSEMBL: ENSMUSP00000104652 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073691] [ENSMUST00000109024]

AlphaFold

Q9ERG0

Predicted Effect

probably damaging
Transcript: ENSMUST00000073691
AA Change: N306K

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000073371
Gene: ENSMUSG00000023022
AA Change: N306K

Domain	Start	End	E-Value	Type
LIM	387	439	5.14e-17	SMART
low complexity region	534	546	N/A	INTRINSIC
low complexity region	570	587	N/A	INTRINSIC
low complexity region	598	609	N/A	INTRINSIC
low complexity region	613	626	N/A	INTRINSIC
low complexity region	747	753	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000083709

Predicted Effect

probably damaging
Transcript: ENSMUST00000109024
AA Change: N146K

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000104652
Gene: ENSMUSG00000023022
AA Change: N146K

Domain	Start	End	E-Value	Type
LIM	227	279	5.14e-17	SMART
low complexity region	374	386	N/A	INTRINSIC
low complexity region	410	427	N/A	INTRINSIC
low complexity region	438	449	N/A	INTRINSIC
low complexity region	453	466	N/A	INTRINSIC
low complexity region	587	593	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230033

Meta Mutation Damage Score

0.0949

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.5%
20x: 95.0%

Validation Efficiency

98% (80/82)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a cytoskeleton-associated protein that inhibits actin filament depolymerization and cross-links filaments in bundles. It is downregulated in some cancer cell lines. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and expression of some of the variants maybe independently regulated. [provided by RefSeq, Aug 2011]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	A	G	6: 128,529,208 (GRCm39)	L978P	probably damaging	Het
Abcb1a	C	T	5: 8,748,539 (GRCm39)	T290M	probably benign	Het
Abcd3	A	T	3: 121,558,742 (GRCm39)	F585I	probably damaging	Het
Abtb3	G	A	10: 85,494,200 (GRCm39)	G1106D	probably damaging	Het
Acan	A	G	7: 78,761,038 (GRCm39)		probably benign	Het
Anxa6	T	C	11: 54,870,292 (GRCm39)	D667G	possibly damaging	Het
Ap3m2	G	T	8: 23,283,128 (GRCm39)	A208D	possibly damaging	Het
Arhgap17	A	T	7: 122,903,013 (GRCm39)		probably benign	Het
Bptf	A	G	11: 106,959,208 (GRCm39)	V1838A	probably damaging	Het
Brip1	T	A	11: 86,043,563 (GRCm39)	M334L	probably benign	Het
Btbd10	C	T	7: 112,934,516 (GRCm39)		probably benign	Het
Cdh20	C	A	1: 109,980,696 (GRCm39)	T208K	probably damaging	Het
Cnga4	A	G	7: 105,055,025 (GRCm39)	Y100C	probably damaging	Het
Dnah10	G	A	5: 124,878,017 (GRCm39)	V2644M	probably damaging	Het
Dnah9	T	C	11: 65,856,515 (GRCm39)	D2882G	probably damaging	Het
Eapp	T	A	12: 54,732,747 (GRCm39)	K117M	probably damaging	Het
Eml3	T	C	19: 8,916,427 (GRCm39)	V673A	probably benign	Het
Ephb4	G	A	5: 137,368,117 (GRCm39)	C754Y	probably damaging	Het
Eps8l1	A	G	7: 4,480,956 (GRCm39)	D33G	possibly damaging	Het
Farsa	A	G	8: 85,594,212 (GRCm39)	K321E	probably damaging	Het
Fry	G	A	5: 150,360,624 (GRCm39)	R2090Q	probably damaging	Het
Gm10283	A	G	8: 60,954,258 (GRCm39)		probably benign	Het
Grm4	A	G	17: 27,650,464 (GRCm39)	I844T	probably benign	Het
Gtf2h3	A	G	5: 124,726,691 (GRCm39)	D124G	probably benign	Het
Gulo	A	T	14: 66,227,890 (GRCm39)	D347E	probably damaging	Het
Hmcn1	A	G	1: 150,485,552 (GRCm39)	F4350S	possibly damaging	Het
Hspg2	A	G	4: 137,239,712 (GRCm39)	D473G	probably damaging	Het
Il17ra	T	A	6: 120,458,466 (GRCm39)	I539N	probably damaging	Het
Insrr	A	G	3: 87,720,440 (GRCm39)	E1026G	probably damaging	Het
Itga2	A	T	13: 114,993,186 (GRCm39)		probably benign	Het
Kdm1b	A	T	13: 47,212,286 (GRCm39)	D190V	possibly damaging	Het
Mnt	G	T	11: 74,733,122 (GRCm39)	V85L	probably benign	Het
Mon2	T	A	10: 122,861,970 (GRCm39)		probably benign	Het
Mtf1	T	C	4: 124,713,994 (GRCm39)		probably benign	Het
Mylk4	T	C	13: 32,896,737 (GRCm39)		probably null	Het
Myo18b	A	C	5: 113,013,616 (GRCm39)	L780R	probably damaging	Het
Myo1e	A	G	9: 70,283,942 (GRCm39)		probably benign	Het
Obscn	A	G	11: 58,964,522 (GRCm39)	S705P	probably damaging	Het
Ocrl	A	T	X: 47,024,963 (GRCm39)		probably benign	Het
Or1e34	A	T	11: 73,778,730 (GRCm39)	M156K	probably benign	Het
Or4c35	T	C	2: 89,808,545 (GRCm39)	F141S	probably benign	Het
Or51k1	A	T	7: 103,661,395 (GRCm39)	C171*	probably null	Het
Or52ab4	A	G	7: 102,987,393 (GRCm39)	N44S	probably damaging	Het
Otof	T	A	5: 30,528,049 (GRCm39)	K1931N	probably damaging	Het
Plcxd3	A	G	15: 4,546,349 (GRCm39)	S118G	probably damaging	Het
Plcz1	T	A	6: 139,974,268 (GRCm39)	Q58L	probably benign	Het
Proser1	C	A	3: 53,386,485 (GRCm39)	P789Q	probably benign	Het
Rassf4	T	C	6: 116,622,897 (GRCm39)	E38G	probably damaging	Het
Ros1	A	T	10: 51,999,396 (GRCm39)	Y1164N	probably damaging	Het
Rpgrip1l	A	G	8: 92,031,628 (GRCm39)	I83T	probably damaging	Het
Scn9a	T	G	2: 66,357,143 (GRCm39)	K1053Q	probably damaging	Het
Sgsm1	G	T	5: 113,392,894 (GRCm39)	Q1087K	probably damaging	Het
Slc16a10	T	C	10: 40,017,914 (GRCm39)	D40G	probably benign	Het
Slc27a6	A	G	18: 58,689,885 (GRCm39)	D117G	probably damaging	Het
Slc2a9	T	A	5: 38,637,487 (GRCm39)		probably benign	Het
Slc4a1	A	G	11: 102,248,741 (GRCm39)		probably benign	Het
Smarca1	T	A	X: 46,912,303 (GRCm39)	Q982L	probably benign	Het
Sp100	T	A	1: 85,608,831 (GRCm39)	I320N	possibly damaging	Het
Stx8	A	T	11: 68,000,188 (GRCm39)	R209S	probably null	Het
Sulf2	T	C	2: 165,925,799 (GRCm39)	T453A	possibly damaging	Het
Syne2	AGAGTGAG	AGAGTGAGTGAG	12: 76,144,734 (GRCm39)		probably null	Het
Tenm2	T	A	11: 35,915,607 (GRCm39)	I1976F	possibly damaging	Het
Tenm3	G	A	8: 48,730,745 (GRCm39)	S1341L	probably damaging	Het
Tmem130	C	T	5: 144,674,619 (GRCm39)	V369M	probably damaging	Het
Tmem200c	A	G	17: 69,147,506 (GRCm39)	K30E	probably damaging	Het
Tmem225	A	G	9: 40,061,043 (GRCm39)	I117V	possibly damaging	Het
Tmt1a3	A	T	15: 100,233,264 (GRCm39)	N152Y	possibly damaging	Het
Top2a	A	G	11: 98,892,243 (GRCm39)	I1073T	probably damaging	Het
Trps1	A	C	15: 50,695,256 (GRCm39)	Y296*	probably null	Het
Tubg1	T	C	11: 101,016,162 (GRCm39)	M377T	probably benign	Het
Tut7	A	G	13: 59,957,301 (GRCm39)	V7A	probably damaging	Het
Vmn1r35	G	A	6: 66,656,497 (GRCm39)	H58Y	probably benign	Het
Vmn1r56	G	A	7: 5,199,429 (GRCm39)	H63Y	probably benign	Het
Vmn1r75	T	C	7: 11,615,189 (GRCm39)		probably null	Het
Vnn3	T	C	10: 23,741,603 (GRCm39)	S303P	possibly damaging	Het
Wdr49	C	T	3: 75,338,383 (GRCm39)		probably null	Het
Wdr49	T	C	3: 75,357,197 (GRCm39)		probably null	Het
Zzef1	T	C	11: 72,804,004 (GRCm39)	L2582P	probably damaging	Het

Other mutations in Lima1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00668:Lima1	APN	15	99,700,038 (GRCm39)	missense	possibly damaging	0.47
IGL01104:Lima1	APN	15	99,741,581 (GRCm39)	missense	probably damaging	1.00
IGL02618:Lima1	APN	15	99,700,097 (GRCm39)	splice site	probably benign
IGL03124:Lima1	APN	15	99,694,615 (GRCm39)	splice site	probably benign
R0312:Lima1	UTSW	15	99,678,968 (GRCm39)	missense	possibly damaging	0.69
R0601:Lima1	UTSW	15	99,678,353 (GRCm39)	missense	probably damaging	0.98
R1423:Lima1	UTSW	15	99,717,626 (GRCm39)	nonsense	probably null
R1704:Lima1	UTSW	15	99,717,617 (GRCm39)	missense	probably benign	0.00
R1784:Lima1	UTSW	15	99,678,344 (GRCm39)	missense	possibly damaging	0.93
R1819:Lima1	UTSW	15	99,717,817 (GRCm39)	missense	probably benign	0.01
R1968:Lima1	UTSW	15	99,717,565 (GRCm39)	missense	probably benign
R2352:Lima1	UTSW	15	99,692,396 (GRCm39)	missense	probably benign	0.02
R2908:Lima1	UTSW	15	99,699,991 (GRCm39)	critical splice donor site	probably null
R4582:Lima1	UTSW	15	99,678,873 (GRCm39)	missense	possibly damaging	0.65
R4672:Lima1	UTSW	15	99,741,590 (GRCm39)	missense	probably damaging	1.00
R4858:Lima1	UTSW	15	99,717,457 (GRCm39)	missense	probably benign	0.23
R6140:Lima1	UTSW	15	99,678,939 (GRCm39)	missense	probably damaging	1.00
R6614:Lima1	UTSW	15	99,681,461 (GRCm39)	missense	probably damaging	1.00
R6898:Lima1	UTSW	15	99,679,148 (GRCm39)	missense	possibly damaging	0.61
R7598:Lima1	UTSW	15	99,717,577 (GRCm39)	missense	probably benign	0.01
R7601:Lima1	UTSW	15	99,717,577 (GRCm39)	missense	probably benign	0.01
R7878:Lima1	UTSW	15	99,717,431 (GRCm39)	missense	probably benign	0.12
R8219:Lima1	UTSW	15	99,678,671 (GRCm39)	missense	probably damaging	1.00
R8348:Lima1	UTSW	15	99,678,753 (GRCm39)	missense	probably benign	0.00
R8733:Lima1	UTSW	15	99,678,699 (GRCm39)	missense	probably damaging	1.00
R8821:Lima1	UTSW	15	99,704,306 (GRCm39)	missense	probably benign	0.00
R9285:Lima1	UTSW	15	99,678,687 (GRCm39)	missense	probably damaging	1.00
R9300:Lima1	UTSW	15	99,704,320 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TGCCACCAAATTCCTAGACGCTG -3'
(R):5'- CACAAGCTGTGCTGCTAGAAGAGAG -3'

Sequencing Primer
(F):5'- GCAGCCTAGAGTCAGACTTTC -3'
(R):5'- CTGATGAGCATCCAGTTTGAGAC -3'

Posted On

2013-07-11