Mutagenetix > Incidental Mutation

Incidental Mutation 'R4876:Limch1'

376856

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

MMRRC Submission

042485-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.152) question?

Stock #

R4876 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

66903232-67214502 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 67039270 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 66 (V66I)

Ref Sequence

ENSEMBL: ENSMUSP00000116126 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101164] [ENSMUST00000118242] [ENSMUST00000130228]

AlphaFold

Q3UH68

Predicted Effect

probably benign
Transcript: ENSMUST00000101164
AA Change: V66I

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: V66I

Domain	Start	End	E-Value	Type
CH	23	124	2.09e-13	SMART
low complexity region	197	213	N/A	INTRINSIC
low complexity region	223	236	N/A	INTRINSIC
low complexity region	285	296	N/A	INTRINSIC
coiled coil region	348	397	N/A	INTRINSIC
low complexity region	567	586	N/A	INTRINSIC
coiled coil region	771	828	N/A	INTRINSIC
low complexity region	835	847	N/A	INTRINSIC
LIM	986	1044	5.08e-7	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000118242
AA Change: V66I

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: V66I

Domain	Start	End	E-Value	Type
CH	23	124	2.09e-13	SMART
low complexity region	197	213	N/A	INTRINSIC
low complexity region	223	236	N/A	INTRINSIC
low complexity region	285	296	N/A	INTRINSIC
coiled coil region	336	385	N/A	INTRINSIC
low complexity region	555	574	N/A	INTRINSIC
coiled coil region	782	839	N/A	INTRINSIC
low complexity region	846	858	N/A	INTRINSIC
LIM	997	1055	5.08e-7	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000130228
AA Change: V66I

PolyPhen 2 Score 0.640 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000116126
Gene: ENSMUSG00000037736
AA Change: V66I

Domain	Start	End	E-Value	Type
Pfam:CH	25	77	2.2e-7	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201852

Meta Mutation Damage Score

0.1267

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.5%

Validation Efficiency

99% (97/98)

Allele List at MGI

Other mutations in this stock

Total: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930562C15Rik	T	C	16: 4,667,536 (GRCm39)	F309S	unknown	Het
A630001G21Rik	C	T	1: 85,646,761 (GRCm39)	V167M	probably damaging	Het
Anks6	C	T	4: 47,030,795 (GRCm39)	G601S	probably damaging	Het
Ano4	A	G	10: 88,948,697 (GRCm39)	F138L	probably damaging	Het
Aoc1	T	C	6: 48,883,681 (GRCm39)	V519A	possibly damaging	Het
Arhgef37	A	T	18: 61,631,310 (GRCm39)	Y558*	probably null	Het
Atxn3	T	A	12: 101,914,638 (GRCm39)	S29C	probably damaging	Het
Bbs2	T	C	8: 94,796,788 (GRCm39)		probably benign	Het
Bicral	A	T	17: 47,136,502 (GRCm39)	I236N	probably damaging	Het
Cabcoco1	A	G	10: 68,377,599 (GRCm39)	V30A	probably benign	Het
Cap2	A	G	13: 46,684,497 (GRCm39)	M1V	probably null	Het
Ccdc153	T	C	9: 44,152,305 (GRCm39)	M1T	probably null	Het
Ccnf	A	T	17: 24,449,311 (GRCm39)	V489D	probably damaging	Het
Cdin1	A	C	2: 115,500,539 (GRCm39)	H159P	probably damaging	Het
Cntnap3	T	C	13: 64,935,520 (GRCm39)	T448A	probably benign	Het
Cpa4	G	A	6: 30,590,814 (GRCm39)	D371N	probably benign	Het
Csl	T	A	10: 99,594,402 (GRCm39)	Y221F	possibly damaging	Het
Dalrd3	T	C	9: 108,448,635 (GRCm39)		probably benign	Het
Dennd4a	T	A	9: 64,803,872 (GRCm39)	N1070K	probably benign	Het
Dipk2a	C	T	9: 94,419,630 (GRCm39)	R100H	probably damaging	Het
Dmwd	A	T	7: 18,814,472 (GRCm39)	D374V	probably damaging	Het
Eea1	G	T	10: 95,831,475 (GRCm39)	A189S	probably benign	Het
Fasn	A	G	11: 120,703,138 (GRCm39)	V1629A	probably damaging	Het
Fcgbpl1	A	T	7: 27,842,225 (GRCm39)		probably benign	Het
Fndc1	T	C	17: 7,990,471 (GRCm39)	D1075G	unknown	Het
Fsip2	A	G	2: 82,805,202 (GRCm39)	N507S	possibly damaging	Het
Gabra5	T	G	7: 57,063,413 (GRCm39)	E337A	probably damaging	Het
Gsg1l	A	G	7: 125,490,841 (GRCm39)	Y288H	probably benign	Het
H2-M11	A	T	17: 36,858,401 (GRCm39)	D65V	probably benign	Het
Hmgxb3	A	T	18: 61,279,606 (GRCm39)	C736S	possibly damaging	Het
Hsd3b3	A	T	3: 98,649,960 (GRCm39)	I121N	probably damaging	Het
Ikbke	GCC	G	1: 131,203,004 (GRCm39)		probably null	Het
Il16	A	C	7: 83,322,302 (GRCm39)	S338A	probably benign	Het
Itpr1	G	A	6: 108,459,867 (GRCm39)	A2054T	probably damaging	Het
Lamp3	T	A	16: 19,474,220 (GRCm39)	I385F	probably damaging	Het
Lmod2	A	G	6: 24,604,278 (GRCm39)	R418G	probably benign	Het
Ly6g6c	A	T	17: 35,288,416 (GRCm39)	D96V	probably damaging	Het
Map2k2	G	A	10: 80,950,947 (GRCm39)	V131M	probably damaging	Het
Mapk9	T	C	11: 49,745,152 (GRCm39)	V22A	probably damaging	Het
Mettl2	T	C	11: 105,019,894 (GRCm39)	I177T	probably damaging	Het
Mob4	C	T	1: 55,191,995 (GRCm39)		probably benign	Het
Mybpc1	A	T	10: 88,372,286 (GRCm39)	N781K	probably benign	Het
Mybpc1	T	C	10: 88,358,853 (GRCm39)	I1113V	probably benign	Het
Myom1	A	G	17: 71,384,405 (GRCm39)	T707A	probably damaging	Het
Ncam2	G	A	16: 81,287,234 (GRCm39)	A383T	probably benign	Het
Nomo1	T	C	7: 45,715,915 (GRCm39)	S761P	probably damaging	Het
Nsd3	T	A	8: 26,181,161 (GRCm39)	S921T	possibly damaging	Het
Omp	A	T	7: 97,794,233 (GRCm39)	D131E	probably benign	Het
Or10d1c	A	T	9: 38,893,922 (GRCm39)	C139*	probably null	Het
Or4f7d-ps1	C	G	2: 111,675,040 (GRCm39)		noncoding transcript	Het
Or8d4	C	T	9: 40,038,514 (GRCm39)	V248I	probably damaging	Het
Pard3	T	C	8: 128,287,950 (GRCm39)		probably benign	Het
Parg	A	G	14: 31,993,625 (GRCm39)	T286A	probably damaging	Het
Parp1	T	A	1: 180,396,600 (GRCm39)	M1K	probably null	Het
Pclo	T	A	5: 14,861,694 (GRCm39)	S4882R	unknown	Het
Pcnx2	C	T	8: 126,498,847 (GRCm39)	E1551K	probably damaging	Het
Pcyox1l	A	G	18: 61,832,565 (GRCm39)	Y161H	probably damaging	Het
Pdzd8	A	T	19: 59,289,236 (GRCm39)	C721*	probably null	Het
Piwil4	T	C	9: 14,651,761 (GRCm39)	D90G	probably benign	Het
Plxdc2	T	A	2: 16,708,129 (GRCm39)	C306S	probably damaging	Het
Plxna2	T	A	1: 194,326,083 (GRCm39)	F6I	probably benign	Het
Prkaa1	T	C	15: 5,203,886 (GRCm39)	M265T	probably benign	Het
Prrc2b	T	C	2: 32,104,212 (GRCm39)	V1230A	probably benign	Het
Rfx2	T	C	17: 57,091,706 (GRCm39)	E329G	probably benign	Het
Scg2	T	C	1: 79,413,636 (GRCm39)	I322M	probably damaging	Het
Scly	T	A	1: 91,247,850 (GRCm39)	N399K	probably damaging	Het
Sec23b	T	A	2: 144,428,281 (GRCm39)		probably null	Het
Sephs2	A	T	7: 126,872,219 (GRCm39)	Y291*	probably null	Het
Slc45a3	T	C	1: 131,909,285 (GRCm39)	I494T	possibly damaging	Het
Slc6a21	C	A	7: 44,929,535 (GRCm39)	Y76*	probably null	Het
Slfn14	T	A	11: 83,167,098 (GRCm39)	I806L	possibly damaging	Het
Slfn4	T	A	11: 83,077,844 (GRCm39)	S211T	probably benign	Het
Sptbn4	A	G	7: 27,071,577 (GRCm39)	V1624A	probably damaging	Het
Sugp1	T	A	8: 70,523,834 (GRCm39)	M567K	probably damaging	Het
Tmem121	A	T	12: 113,152,348 (GRCm39)	M189L	probably benign	Het
Tmem201	A	G	4: 149,806,727 (GRCm39)	S444P	probably damaging	Het
Tmem63a	T	C	1: 180,800,751 (GRCm39)	V744A	probably benign	Het
Tnrc18	G	A	5: 142,717,380 (GRCm39)	S2358F	unknown	Het
Ubash3b	A	G	9: 40,929,405 (GRCm39)	V404A	probably benign	Het
Unc13c	A	T	9: 73,656,821 (GRCm39)	C1127S	probably damaging	Het
Unc5a	T	C	13: 55,145,042 (GRCm39)	V253A	probably benign	Het
Vmn1r-ps123	C	T	13: 23,180,535 (GRCm39)		noncoding transcript	Het
Wdr74	A	G	19: 8,716,849 (GRCm39)	E253G	possibly damaging	Het
Wwox	T	C	8: 115,174,988 (GRCm39)	Y107H	probably damaging	Het
Zdhhc22	A	T	12: 87,035,012 (GRCm39)	Y147N	probably damaging	Het
Zfp131	T	C	13: 120,250,491 (GRCm39)	H44R	possibly damaging	Het
Zfp235	A	G	7: 23,840,384 (GRCm39)	T268A	probably benign	Het
Zfp280d	T	C	9: 72,206,140 (GRCm39)		probably benign	Het
Zfp358	T	C	8: 3,546,170 (GRCm39)	S251P	probably damaging	Het

Other mutations in Limch1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00583:Limch1	APN	5	67,111,022 (GRCm39)	missense	probably damaging	0.99
IGL00644:Limch1	APN	5	67,173,895 (GRCm39)	missense	probably benign	0.01
IGL00705:Limch1	APN	5	67,150,496 (GRCm39)	nonsense	probably null
IGL01154:Limch1	APN	5	66,903,301 (GRCm39)	nonsense	probably null	0.00
IGL01865:Limch1	APN	5	67,131,923 (GRCm39)	nonsense	probably null
IGL02529:Limch1	APN	5	67,159,956 (GRCm39)	missense	possibly damaging	0.89
IGL03171:Limch1	APN	5	67,191,537 (GRCm39)	missense	possibly damaging	0.80
IGL03308:Limch1	APN	5	67,159,901 (GRCm39)	missense	possibly damaging	0.92
IGL03396:Limch1	APN	5	67,111,016 (GRCm39)	missense	probably damaging	1.00
R0067:Limch1	UTSW	5	67,131,965 (GRCm39)	missense	probably damaging	0.99
R0067:Limch1	UTSW	5	67,131,965 (GRCm39)	missense	probably damaging	0.99
R0114:Limch1	UTSW	5	67,193,427 (GRCm39)	intron	probably benign
R0129:Limch1	UTSW	5	67,116,933 (GRCm39)	missense	probably damaging	0.96
R0193:Limch1	UTSW	5	67,184,882 (GRCm39)	missense	probably damaging	1.00
R0194:Limch1	UTSW	5	67,156,616 (GRCm39)	missense	probably benign	0.05
R0367:Limch1	UTSW	5	67,015,297 (GRCm39)	critical splice donor site	probably null
R0558:Limch1	UTSW	5	67,126,498 (GRCm39)	missense	probably damaging	1.00
R0927:Limch1	UTSW	5	67,154,576 (GRCm39)	missense	probably damaging	1.00
R1190:Limch1	UTSW	5	67,126,540 (GRCm39)	missense	probably damaging	1.00
R1316:Limch1	UTSW	5	67,156,586 (GRCm39)	missense	probably damaging	1.00
R1469:Limch1	UTSW	5	67,039,323 (GRCm39)	splice site	probably benign
R1647:Limch1	UTSW	5	67,156,599 (GRCm39)	missense	probably damaging	1.00
R1648:Limch1	UTSW	5	67,156,599 (GRCm39)	missense	probably damaging	1.00
R1944:Limch1	UTSW	5	67,156,442 (GRCm39)	missense	probably damaging	1.00
R2103:Limch1	UTSW	5	67,156,072 (GRCm39)	missense	probably benign	0.05
R2126:Limch1	UTSW	5	67,187,103 (GRCm39)	missense	probably damaging	1.00
R2248:Limch1	UTSW	5	67,201,742 (GRCm39)	missense	probably damaging	1.00
R2415:Limch1	UTSW	5	67,131,977 (GRCm39)	missense	probably damaging	1.00
R3762:Limch1	UTSW	5	67,186,183 (GRCm39)	missense	probably damaging	1.00
R3797:Limch1	UTSW	5	67,126,422 (GRCm39)	missense	probably damaging	1.00
R4659:Limch1	UTSW	5	67,184,900 (GRCm39)	missense	probably damaging	1.00
R4773:Limch1	UTSW	5	67,184,850 (GRCm39)	missense	probably damaging	0.99
R5062:Limch1	UTSW	5	67,126,578 (GRCm39)	missense	probably damaging	1.00
R5191:Limch1	UTSW	5	67,184,904 (GRCm39)	missense	probably damaging	1.00
R5202:Limch1	UTSW	5	67,150,516 (GRCm39)	missense	probably damaging	1.00
R5335:Limch1	UTSW	5	67,039,300 (GRCm39)	missense	probably damaging	1.00
R5436:Limch1	UTSW	5	67,131,909 (GRCm39)	missense	possibly damaging	0.72
R5994:Limch1	UTSW	5	67,131,965 (GRCm39)	missense	probably damaging	1.00
R6049:Limch1	UTSW	5	67,188,203 (GRCm39)	missense	probably benign	0.32
R6228:Limch1	UTSW	5	67,173,845 (GRCm39)	missense	probably damaging	1.00
R6547:Limch1	UTSW	5	67,186,117 (GRCm39)	missense	probably damaging	1.00
R6600:Limch1	UTSW	5	66,903,281 (GRCm39)	missense	probably benign
R6888:Limch1	UTSW	5	67,179,269 (GRCm39)	missense	probably benign	0.21
R7111:Limch1	UTSW	5	67,182,519 (GRCm39)	splice site	probably null
R7132:Limch1	UTSW	5	67,111,028 (GRCm39)	missense	probably damaging	1.00
R7144:Limch1	UTSW	5	67,175,001 (GRCm39)	missense	probably benign	0.10
R7302:Limch1	UTSW	5	67,116,942 (GRCm39)	missense	probably benign	0.02
R7341:Limch1	UTSW	5	67,191,545 (GRCm39)	missense	probably benign	0.06
R7491:Limch1	UTSW	5	67,211,580 (GRCm39)	missense	probably damaging	0.99
R8079:Limch1	UTSW	5	67,204,096 (GRCm39)	missense	possibly damaging	0.73
R8229:Limch1	UTSW	5	67,186,138 (GRCm39)	missense	probably damaging	1.00
R8348:Limch1	UTSW	5	67,159,825 (GRCm39)	missense	probably damaging	0.98
R8395:Limch1	UTSW	5	67,126,394 (GRCm39)	missense	probably damaging	0.96
R8416:Limch1	UTSW	5	67,156,649 (GRCm39)	missense	probably benign
R8448:Limch1	UTSW	5	67,159,825 (GRCm39)	missense	probably damaging	0.98
R8477:Limch1	UTSW	5	67,131,908 (GRCm39)	missense	probably benign	0.01
R8924:Limch1	UTSW	5	67,190,475 (GRCm39)	missense	probably benign	0.01
R9080:Limch1	UTSW	5	67,174,992 (GRCm39)	missense	probably benign	0.00
R9619:Limch1	UTSW	5	67,015,284 (GRCm39)	missense	probably damaging	1.00
R9681:Limch1	UTSW	5	67,126,422 (GRCm39)	missense	probably damaging	1.00
R9715:Limch1	UTSW	5	67,156,360 (GRCm39)	missense	probably damaging	1.00
X0022:Limch1	UTSW	5	67,179,295 (GRCm39)	missense	probably benign	0.00
X0027:Limch1	UTSW	5	67,159,963 (GRCm39)	missense	probably damaging	1.00
Z1177:Limch1	UTSW	5	67,186,142 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AAGTCAACGTTGGCAGAGC -3'
(R):5'- CTCTTAGCTCAGTGGAGTCG -3'

Sequencing Primer
(F):5'- CAACGTTGGCAGAGCTTGTTACC -3'
(R):5'- GGTGTGTTCTCATTCCAGGAGTATAC -3'

Posted On

2016-03-17