Mutagenetix > Incidental Mutation

Incidental Mutation 'R9300:Lima1'

704899

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

Accession Numbers

Essential gene?

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

Stock #

R9300 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

99676351-99773292 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 99704320 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Asparagine at position 283 (S283N)

Ref Sequence

ENSEMBL: ENSMUSP00000073371 (fasta)

Gene Model

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

AlphaFold

Q9ERG0

Predicted Effect

probably benign
Transcript: ENSMUST00000073691
AA Change: S283N

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000073371
Gene: ENSMUSG00000023022
AA Change: S283N

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
AA Change: S123N

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000104652
Gene: ENSMUSG00000023022
AA Change: S123N

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1b	G	A	5: 8,875,614 (GRCm39)	V596I	probably benign	Het
Acad8	A	T	9: 26,888,928 (GRCm39)	H371Q	probably damaging	Het
Actn3	G	T	19: 4,921,656 (GRCm39)	R175S	probably benign	Het
Adamts9	G	T	6: 92,864,371 (GRCm39)	D780E	probably benign	Het
AK157302	C	A	13: 21,679,537 (GRCm39)	T21K	probably benign	Het
Ank3	A	T	10: 69,706,872 (GRCm39)	H329L	unknown	Het
Ankrd36	A	G	11: 5,519,979 (GRCm39)	H18R	possibly damaging	Het
Anks1b	T	A	10: 90,412,966 (GRCm39)	V38D	possibly damaging	Het
Apbb2	A	T	5: 66,470,677 (GRCm39)	L520H	probably damaging	Het
Arid1b	C	A	17: 5,293,274 (GRCm39)	P731T	probably damaging	Het
Atp1a4	A	G	1: 172,067,398 (GRCm39)	F578S	probably damaging	Het
Atp6v0a2	A	T	5: 124,789,312 (GRCm39)	I360F	probably damaging	Het
Bcas3	A	T	11: 85,448,184 (GRCm39)	I600F	probably damaging	Het
C1qtnf7	T	G	5: 43,766,441 (GRCm39)	C20W	possibly damaging	Het
Cadm1	A	T	9: 47,708,821 (GRCm39)	K184*	probably null	Het
Ccdc138	A	T	10: 58,343,448 (GRCm39)	H101L	probably benign	Het
Cep120	T	A	18: 53,852,369 (GRCm39)	N503I	probably damaging	Het
Chil4	T	C	3: 106,109,874 (GRCm39)	T380A	probably benign	Het
Clip2	A	G	5: 134,526,942 (GRCm39)		probably null	Het
Cyp3a11	G	A	5: 145,799,164 (GRCm39)	P341L	possibly damaging	Het
Cyp3a41a	G	C	5: 145,656,906 (GRCm39)		probably benign	Het
Dcaf1	A	G	9: 106,725,042 (GRCm39)	I509M	possibly damaging	Het
Dcaf13	T	C	15: 39,010,102 (GRCm39)	S429P	probably damaging	Het
Eln	A	G	5: 134,758,220 (GRCm39)	V151A	unknown	Het
Endou	T	G	15: 97,610,954 (GRCm39)	M377L	probably benign	Het
Etfa	A	G	9: 55,396,152 (GRCm39)	I138T	probably damaging	Het
Fbxw10	T	A	11: 62,768,109 (GRCm39)	S982T	probably benign	Het
Gm9602	A	T	14: 15,933,435 (GRCm39)	R47*	probably null	Het
Hectd4	G	A	5: 121,486,952 (GRCm39)	V3316I	probably benign	Het
Hif1a	T	C	12: 73,987,302 (GRCm39)	L477S	probably benign	Het
Icam5	G	C	9: 20,946,846 (GRCm39)	G458A	probably benign	Het
Itm2b	A	T	14: 73,603,896 (GRCm39)	D106E	probably benign	Het
Kdm4d	G	A	9: 14,375,336 (GRCm39)	T174M	probably damaging	Het
Kif16b	G	T	2: 142,541,207 (GRCm39)	D1364E	probably benign	Het
Lbhd1	G	A	19: 8,861,550 (GRCm39)	V61M	probably damaging	Het
Lclat1	T	A	17: 73,546,919 (GRCm39)	S279T	probably benign	Het
Lhx4	G	A	1: 155,580,956 (GRCm39)	L190F	probably damaging	Het
Magi1	C	A	6: 93,724,209 (GRCm39)	D496Y	probably damaging	Het
Map1a	T	C	2: 121,133,446 (GRCm39)	S1421P	probably damaging	Het
Map3k20	C	T	2: 72,202,257 (GRCm39)	H163Y	probably damaging	Het
Mier3	T	G	13: 111,822,890 (GRCm39)		probably null	Het
Mllt3	G	A	4: 87,692,284 (GRCm39)	Q560*	probably null	Het
Mmp25	T	A	17: 23,851,728 (GRCm39)	D327V	probably benign	Het
Nckap5	G	A	1: 125,909,423 (GRCm39)	Q1603*	probably null	Het
Nell1	G	A	7: 49,712,368 (GRCm39)	V63I	probably benign	Het
Or10al3	C	T	17: 38,011,815 (GRCm39)	P85S	probably damaging	Het
Or2ag2b	A	T	7: 106,418,111 (GRCm39)	I274F	probably benign	Het
Or8a1	A	C	9: 37,641,578 (GRCm39)	S234A	probably benign	Het
Pde12	C	T	14: 26,386,931 (GRCm39)	E526K	probably damaging	Het
Pfn4	T	C	12: 4,825,442 (GRCm39)	V93A	possibly damaging	Het
Poglut2	A	G	1: 44,156,362 (GRCm39)	I75T	possibly damaging	Het
Ppp2r3d	A	G	9: 124,423,977 (GRCm38)	S60P	unknown	Het
Prelp	T	C	1: 133,842,257 (GRCm39)	H296R	probably damaging	Het
Prickle1	T	C	15: 93,398,749 (GRCm39)	E693G	possibly damaging	Het
Rars1	A	G	11: 35,706,488 (GRCm39)	L477P	probably damaging	Het
Rasal1	G	A	5: 120,802,172 (GRCm39)	R328H	probably damaging	Het
Rasef	A	G	4: 73,659,393 (GRCm39)	F220S	probably benign	Het
Rif1	C	T	2: 52,001,151 (GRCm39)	S1535L	probably damaging	Het
Rnf17	T	C	14: 56,697,495 (GRCm39)	I463T	possibly damaging	Het
Ryr3	A	T	2: 112,690,695 (GRCm39)	D1138E	probably benign	Het
Scn9a	T	A	2: 66,335,236 (GRCm39)	Y1251F	probably benign	Het
Sdk2	A	G	11: 113,715,856 (GRCm39)	W1568R	possibly damaging	Het
Senp6	A	G	9: 80,049,433 (GRCm39)	E1019G	probably damaging	Het
Shh	A	G	5: 28,663,461 (GRCm39)	Y236H	probably damaging	Het
Sin3a	A	G	9: 57,014,744 (GRCm39)	D655G	probably damaging	Het
Slc35a4	C	T	18: 36,815,274 (GRCm39)	P35S	probably damaging	Het
Slc35g1	T	C	19: 38,384,633 (GRCm39)	L24P	probably benign	Het
Slc39a4	G	T	15: 76,498,759 (GRCm39)	Q312K	probably damaging	Het
Slc6a5	A	T	7: 49,601,175 (GRCm39)	I659F	probably damaging	Het
Slc7a4	T	C	16: 17,392,399 (GRCm39)	Y345C	probably benign	Het
Slco6c1	G	T	1: 96,993,809 (GRCm39)	R645S	probably benign	Het
Soat1	T	C	1: 156,268,923 (GRCm39)	Y209C	probably benign	Het
Tbc1d9b	T	C	11: 50,054,714 (GRCm39)	S953P	probably benign	Het
Tgm1	G	A	14: 55,942,303 (GRCm39)	H683Y	probably benign	Het
Tmem98	G	A	11: 80,708,432 (GRCm39)	R134Q	probably damaging	Het
Trpm3	A	C	19: 22,955,745 (GRCm39)	M1107L	possibly damaging	Het
Vmn1r11	G	A	6: 57,114,872 (GRCm39)	V179I	probably benign	Het
Vmn1r119	G	T	7: 20,745,638 (GRCm39)	T248K	probably damaging	Het
Vmn1r236	T	A	17: 21,506,945 (GRCm39)	I21N	possibly damaging	Het
Vmn2r24	A	G	6: 123,793,030 (GRCm39)	T786A	possibly damaging	Het
Vstm5	A	T	9: 15,168,585 (GRCm39)	I50F	probably damaging	Het
Wdr1	T	C	5: 38,685,255 (GRCm39)	D572G	probably damaging	Het
Xaf1	T	C	11: 72,192,517 (GRCm39)	F5S	probably benign	Het
Zan	A	T	5: 137,468,519 (GRCm39)		probably null	Het
Zfp697	T	C	3: 98,334,979 (GRCm39)	V248A	possibly damaging	Het
Zftraf1	C	A	15: 76,530,541 (GRCm39)	V260L	probably benign	Het
Zkscan3	T	A	13: 21,577,667 (GRCm39)	T249S	unknown	Het
Znfx1	A	G	2: 166,897,860 (GRCm39)	Y355H	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
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

Predicted Primers

PCR Primer
(F):5'- AATGTGCATGAGCTGGCAG -3'
(R):5'- TTAGATCGTAGTCACTCGGGAC -3'

Sequencing Primer
(F):5'- CTGGCAGAGCAGAATCAAGACC -3'
(R):5'- GTAGTCACTCGGGACTTAGAATCC -3'

Posted On

2022-03-25