Mutagenetix > Incidental Mutation

Incidental Mutation 'R1968:Lima1'

219318

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

039981-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.123) question?

Stock #

R1968 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

99676351-99773292 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 99717565 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 147 (N147S)

Ref Sequence

ENSEMBL: ENSMUSP00000073371 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073691] [ENSMUST00000109024] [ENSMUST00000231121]

AlphaFold

Q9ERG0

Predicted Effect

probably benign
Transcript: ENSMUST00000073691
AA Change: N147S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000073371
Gene: ENSMUSG00000023022
AA Change: N147S

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

probably benign
Transcript: ENSMUST00000109024

SMART Domains

Protein: ENSMUSP00000104652
Gene: ENSMUSG00000023022

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: ENSMUST00000169887

Predicted Effect

probably benign
Transcript: ENSMUST00000231121

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.2%

Validation Efficiency

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: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4fm4	A	G	4: 144,397,193 (GRCm39)	Y180H	possibly damaging	Het
Abcc10	A	T	17: 46,633,125 (GRCm39)	L528Q	probably damaging	Het
Adam18	T	A	8: 25,136,463 (GRCm39)	T353S	probably benign	Het
Aldh1a3	A	G	7: 66,061,248 (GRCm39)		probably null	Het
Aldh3b2	T	A	19: 4,030,705 (GRCm39)	M390K	probably benign	Het
Arhgap45	T	C	10: 79,863,536 (GRCm39)	I793T	probably damaging	Het
Arsb	A	G	13: 93,944,067 (GRCm39)	M253V	probably benign	Het
Atcay	T	C	10: 81,048,312 (GRCm39)	D258G	possibly damaging	Het
Atf1	G	T	15: 100,152,395 (GRCm39)		probably null	Het
Atp1a4	C	T	1: 172,067,731 (GRCm39)	E511K	probably benign	Het
Atp8a1	A	G	5: 67,825,000 (GRCm39)	V777A	probably benign	Het
Baz1a	T	C	12: 54,947,122 (GRCm39)	T1173A	possibly damaging	Het
Bdh2	A	T	3: 134,991,370 (GRCm39)	D15V	probably benign	Het
Cacna1e	T	C	1: 154,576,240 (GRCm39)	Y69C	probably damaging	Het
Caskin2	A	G	11: 115,694,440 (GRCm39)	L387P	probably benign	Het
Cat	T	C	2: 103,315,334 (GRCm39)	E17G	probably benign	Het
Ccdc15	T	C	9: 37,259,091 (GRCm39)	I54M	probably benign	Het
Ccn1	T	C	3: 145,353,965 (GRCm39)	Y275C	probably damaging	Het
Cdhr1	T	G	14: 36,801,682 (GRCm39)	I754L	probably benign	Het
Cep120	G	A	18: 53,856,313 (GRCm39)	T368I	probably benign	Het
Cep126	C	A	9: 8,100,909 (GRCm39)	D542Y	probably damaging	Het
Cep135	T	C	5: 76,772,594 (GRCm39)	S660P	possibly damaging	Het
Cfap70	A	T	14: 20,470,879 (GRCm39)	S455R	possibly damaging	Het
Chd8	A	G	14: 52,458,450 (GRCm39)	M886T	probably damaging	Het
Ckap5	T	C	2: 91,416,688 (GRCm39)	S1098P	probably benign	Het
Clec4e	A	T	6: 123,260,533 (GRCm39)	I204N	probably damaging	Het
Cntnap5c	G	A	17: 58,666,291 (GRCm39)	R1107H	probably damaging	Het
Cramp1	T	C	17: 25,183,913 (GRCm39)	D1234G	probably damaging	Het
Csf1r	A	T	18: 61,245,867 (GRCm39)	I275L	probably benign	Het
Cyp27a1	A	G	1: 74,776,435 (GRCm39)	E457G	probably benign	Het
Cyp2d11	T	C	15: 82,273,749 (GRCm39)	T410A	probably benign	Het
Cyp2d22	G	C	15: 82,257,373 (GRCm39)	T264S	probably benign	Het
Daam2	G	A	17: 49,790,088 (GRCm39)	R390W	probably damaging	Het
Decr2	T	C	17: 26,302,053 (GRCm39)	S226G	probably benign	Het
Dennd6b	T	C	15: 89,074,544 (GRCm39)	D91G	possibly damaging	Het
Dglucy	T	C	12: 100,825,903 (GRCm39)	V515A	possibly damaging	Het
Dlg5	A	T	14: 24,214,187 (GRCm39)	L734*	probably null	Het
Dop1b	A	G	16: 93,579,307 (GRCm39)	N1690D	probably damaging	Het
Exoc5	A	G	14: 49,272,347 (GRCm39)	Y356H	probably benign	Het
Fut7	T	A	2: 25,315,738 (GRCm39)	V332D	probably benign	Het
Gnas	T	C	2: 174,140,526 (GRCm39)	S232P	probably damaging	Het
Gramd4	A	G	15: 86,017,106 (GRCm39)	E522G	probably damaging	Het
Gys1	A	G	7: 45,092,970 (GRCm39)	T297A	probably damaging	Het
Herc4	T	C	10: 63,109,304 (GRCm39)	S180P	probably benign	Het
Hivep3	C	T	4: 119,953,435 (GRCm39)	P584S	possibly damaging	Het
Irag2	T	A	6: 145,115,499 (GRCm39)	S310T	probably damaging	Het
Itpk1	G	T	12: 102,641,729 (GRCm39)		probably null	Het
Jmjd1c	A	T	10: 67,061,219 (GRCm39)	S1191C	probably damaging	Het
Map4k5	G	A	12: 69,865,266 (GRCm39)	T506I	probably damaging	Het
Mat1a	A	T	14: 40,832,991 (GRCm39)	E58V	probably damaging	Het
Mfsd13a	T	C	19: 46,360,492 (GRCm39)	L348P	probably damaging	Het
Mon2	A	G	10: 122,845,470 (GRCm39)	Y1413H	probably damaging	Het
Mpp3	C	A	11: 101,909,378 (GRCm39)		probably benign	Het
Mpp4	T	A	1: 59,183,961 (GRCm39)	I260F	probably damaging	Het
Myocd	C	A	11: 65,091,733 (GRCm39)	G70C	probably damaging	Het
Nckap1	C	T	2: 80,348,286 (GRCm39)	S889N	probably benign	Het
Nckap5	T	A	1: 125,942,367 (GRCm39)	D209V	probably damaging	Het
Nlrp9a	A	G	7: 26,264,366 (GRCm39)	K707R	probably benign	Het
Npr3	A	G	15: 11,905,055 (GRCm39)	L224S	probably benign	Het
Or5m9b	T	A	2: 85,905,549 (GRCm39)	L155Q	probably damaging	Het
Or5w20	T	A	2: 87,727,383 (GRCm39)	V280E	probably damaging	Het
Or6c74	A	G	10: 129,869,602 (GRCm39)	S36G	probably damaging	Het
Otof	C	T	5: 30,545,998 (GRCm39)	D467N	probably damaging	Het
Paxx	T	C	2: 25,350,640 (GRCm39)		probably benign	Het
Pcmt1	G	A	10: 7,516,474 (GRCm39)	R179*	probably null	Het
Phkb	T	A	8: 86,697,580 (GRCm39)	V463D	probably benign	Het
Prkcq	T	C	2: 11,250,208 (GRCm39)	V175A	probably damaging	Het
Rasl11b	T	G	5: 74,356,797 (GRCm39)	I58S	probably damaging	Het
Rb1cc1	A	T	1: 6,318,419 (GRCm39)		probably null	Het
Reck	T	A	4: 43,913,771 (GRCm39)		probably null	Het
Riox1	G	T	12: 83,998,156 (GRCm39)	D231Y	probably damaging	Het
Rlf	T	A	4: 121,005,617 (GRCm39)	N1231I	probably damaging	Het
Rpn1	A	G	6: 88,072,530 (GRCm39)	D291G	possibly damaging	Het
Samsn1	C	T	16: 75,742,461 (GRCm39)		noncoding transcript	Het
Scara5	T	C	14: 65,927,249 (GRCm39)	C49R	possibly damaging	Het
Serpini1	A	G	3: 75,521,785 (GRCm39)	D92G	probably benign	Het
Setdb2	A	T	14: 59,656,858 (GRCm39)	L153Q	probably damaging	Het
Sh3rf3	C	T	10: 58,649,809 (GRCm39)	T138M	probably benign	Het
Shkbp1	C	T	7: 27,054,825 (GRCm39)		probably null	Het
Slc22a29	G	A	19: 8,195,707 (GRCm39)	P111S	probably benign	Het
Smarca1	A	G	X: 46,941,564 (GRCm39)	V618A	probably damaging	Het
Spef2	T	A	15: 9,609,602 (GRCm39)	M1308L	probably damaging	Het
Spink5	A	G	18: 44,123,775 (GRCm39)	N354S	probably benign	Het
Srrm2	T	C	17: 24,040,465 (GRCm39)	S2370P	probably damaging	Het
Ssxb3	A	T	X: 8,454,905 (GRCm39)	I28N	probably damaging	Het
Sucla2	A	G	14: 73,831,119 (GRCm39)	T411A	probably damaging	Het
Tex38	A	C	4: 115,637,537 (GRCm39)	S89A	probably benign	Het
Tjp2	A	T	19: 24,088,437 (GRCm39)	D723E	probably damaging	Het
Tln2	A	T	9: 67,163,183 (GRCm39)	N1121K	probably damaging	Het
Tti1	T	C	2: 157,850,966 (GRCm39)	E91G	possibly damaging	Het
Wbp2	A	T	11: 115,973,191 (GRCm39)	M72K	possibly damaging	Het
Wdfy4	C	A	14: 32,828,001 (GRCm39)	C1062F	possibly damaging	Het
Wiz	A	G	17: 32,578,346 (GRCm39)	Y389H	probably damaging	Het
Zcchc3	T	C	2: 152,256,012 (GRCm39)	K229R	probably damaging	Het
Zmat3	C	A	3: 32,415,131 (GRCm39)	D60Y	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
R0599:Lima1	UTSW	15	99,700,040 (GRCm39)	missense	probably damaging	1.00
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
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'- TTCCTGCAGTGAGCTCTACAC -3'
(R):5'- GGGCAGAATTCCACACAGAC -3'

Sequencing Primer
(F):5'- ACCGGGCTCTTACCTTGG -3'
(R):5'- TACCCTCCTGCTGAAGT -3'

Posted On

2014-08-25