Mutagenetix > Incidental Mutation

Incidental Mutation 'R7878:Lima1'

608598

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

045930-MU

Accession Numbers

Essential gene?

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

Stock #

R7878 (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 99717431 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 192 (V192I)

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: V192I

PolyPhen 2 Score 0.115 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000073371
Gene: ENSMUSG00000023022
AA Change: V192I

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: V32I

PolyPhen 2 Score 0.115 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000104652
Gene: ENSMUSG00000023022
AA Change: V32I

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

probably benign
Transcript: ENSMUST00000231121

Coding Region Coverage

1x: 100.0%
3x: 99.9%
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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ahi1	G	A	10: 20,857,330 (GRCm39)		probably null	Het
Ak7	T	A	12: 105,733,008 (GRCm39)	I584N	probably damaging	Het
Akip1	A	T	7: 109,306,609 (GRCm39)	Y102F	probably damaging	Het
Alg9	T	C	9: 50,754,083 (GRCm39)	Y588H	probably benign	Het
Arid1a	A	T	4: 133,414,582 (GRCm39)	N831K	unknown	Het
Bcl2l11	T	A	2: 127,970,608 (GRCm39)	L19*	probably null	Het
Btn1a1	T	C	13: 23,643,214 (GRCm39)	T412A	possibly damaging	Het
Ccbe1	T	C	18: 66,209,462 (GRCm39)	N193D	possibly damaging	Het
Ccdc168	T	C	1: 44,095,174 (GRCm39)	S1975G	probably benign	Het
Cd96	A	G	16: 45,938,139 (GRCm39)	S109P	probably damaging	Het
Cdh23	A	C	10: 60,149,979 (GRCm39)	I2622S	possibly damaging	Het
Cmya5	G	T	13: 93,226,265 (GRCm39)	T2941K	probably damaging	Het
Cntn1	T	C	15: 92,192,934 (GRCm39)	Y679H	probably damaging	Het
Cpsf1	A	G	15: 76,484,700 (GRCm39)	V619A	probably damaging	Het
Elp5	T	A	11: 69,861,425 (GRCm39)	I185F	probably damaging	Het
Frem1	A	G	4: 82,938,917 (GRCm39)	V55A	probably benign	Het
Kif1b	A	T	4: 149,299,454 (GRCm39)	Y985N	probably damaging	Het
Lao1	A	G	4: 118,824,619 (GRCm39)	N234D	probably benign	Het
Lrp2	T	G	2: 69,338,153 (GRCm39)	D1209A	probably damaging	Het
Lrp2	C	A	2: 69,338,154 (GRCm39)	D1209Y	probably damaging	Het
Luzp1	A	G	4: 136,269,163 (GRCm39)	H462R	probably benign	Het
Mab21l1	A	T	3: 55,691,438 (GRCm39)	T342S	probably benign	Het
Mst1	T	C	9: 107,961,812 (GRCm39)	V657A	probably benign	Het
Mtmr11	A	G	3: 96,076,515 (GRCm39)	K490R	probably benign	Het
Myh3	A	G	11: 66,978,077 (GRCm39)	D383G	probably damaging	Het
Nectin1	G	A	9: 43,715,198 (GRCm39)	G478D	probably benign	Het
Nrip1	A	G	16: 76,091,554 (GRCm39)	M1T	probably null	Het
Odad1	A	G	7: 45,573,984 (GRCm39)	E17G	possibly damaging	Het
Odad2	G	T	18: 7,217,801 (GRCm39)	H638N	probably benign	Het
Or1j10	A	G	2: 36,267,145 (GRCm39)	D119G	probably damaging	Het
Or52z15	A	T	7: 103,332,471 (GRCm39)	H182L	probably damaging	Het
Pnisr	C	A	4: 21,874,370 (GRCm39)	F704L	unknown	Het
Ptpn21	T	A	12: 98,681,387 (GRCm39)	K82N	probably damaging	Het
Pyroxd2	T	G	19: 42,731,104 (GRCm39)		probably null	Het
Pzp	A	G	6: 128,489,274 (GRCm39)	S446P	possibly damaging	Het
Rbck1	T	A	2: 152,160,330 (GRCm39)	I450F	probably damaging	Het
Rnase4	T	A	14: 51,342,333 (GRCm39)	L19Q	probably damaging	Het
Rrp9	A	G	9: 106,358,516 (GRCm39)	E118G	probably damaging	Het
Sec22a	A	G	16: 35,168,005 (GRCm39)	S169P	probably benign	Het
Sema5b	G	A	16: 35,481,996 (GRCm39)	S957N	probably benign	Het
Serpina3g	A	T	12: 104,204,361 (GRCm39)		probably benign	Het
Skint2	A	T	4: 112,506,942 (GRCm39)	I322F	possibly damaging	Het
Spata31h1	G	A	10: 82,119,856 (GRCm39)	R4385W	probably benign	Het
Sspo	G	A	6: 48,469,460 (GRCm39)	C4471Y	probably damaging	Het
Stk16	T	A	1: 75,189,589 (GRCm39)	L167*	probably null	Het
Tanc2	G	A	11: 105,804,241 (GRCm39)	R245H		Het
Tdpoz1	G	A	3: 93,578,431 (GRCm39)	Q118*	probably null	Het
Tekt3	C	T	11: 62,961,277 (GRCm39)	R149*	probably null	Het
Tenm4	A	G	7: 96,501,564 (GRCm39)	E1256G	probably damaging	Het
Tie1	G	A	4: 118,335,621 (GRCm39)	R791C	probably damaging	Het
Tpr	T	A	1: 150,299,411 (GRCm39)	S1204T	possibly damaging	Het
Trim28	G	T	7: 12,758,289 (GRCm39)		probably benign	Het
Ucp1	A	G	8: 84,024,521 (GRCm39)	N282S	probably benign	Het
Unc80	T	A	1: 66,640,300 (GRCm39)	D1402E	possibly damaging	Het
Vmn1r69	T	A	7: 10,314,717 (GRCm39)	T5S	probably benign	Het
Zfyve28	T	A	5: 34,356,999 (GRCm39)	K733M	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
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'- GGGGACTCAAATCTCAGCATC -3'
(R):5'- CGGAAGCAGTTATCCAGAGC -3'

Sequencing Primer
(F):5'- GAGGCTTTTATGAACACAACTCG -3'
(R):5'- AGCAGTTATCCAGAGCCGGTATC -3'

Posted On

2019-12-20