Mutagenetix > Incidental Mutation

Incidental Mutation 'R8079:Limch1'

629194

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.187) question?

Stock #

R8079 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

66745827-67057158 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 67046753 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 878 (I878V)

Ref Sequence

ENSEMBL: ENSMUSP00000043163 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000153174]

AlphaFold

Q3UH68

Predicted Effect

possibly damaging
Transcript: ENSMUST00000038188
AA Change: I878V

PolyPhen 2 Score 0.730 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: I878V

Domain	Start	End	E-Value	Type
low complexity region	41	57	N/A	INTRINSIC
low complexity region	67	80	N/A	INTRINSIC
low complexity region	129	140	N/A	INTRINSIC
coiled coil region	192	241	N/A	INTRINSIC
low complexity region	411	430	N/A	INTRINSIC
coiled coil region	615	672	N/A	INTRINSIC
low complexity region	679	691	N/A	INTRINSIC
LIM	830	888	5.08e-7	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000101164
AA Change: I1034V

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: I1034V

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 damaging
Transcript: ENSMUST00000117601
AA Change: I875V

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: I875V

Domain	Start	End	E-Value	Type
CH	23	124	1e-15	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	704	752	N/A	INTRINSIC
low complexity region	759	771	N/A	INTRINSIC
LIM	910	968	2.4e-9	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000118242
AA Change: I1045V

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: I1045V

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

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: I750V

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
Pfam:DUF4757	250	418	5.2e-66	PFAM
low complexity region	567	586	N/A	INTRINSIC
coiled coil region	771	828	N/A	INTRINSIC
low complexity region	835	847	N/A	INTRINSIC
low complexity region	989	1003	N/A	INTRINSIC
LIM	1012	1070	5.08e-7	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000153174
AA Change: I37V

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000118979
Gene: ENSMUSG00000037736
AA Change: I37V

Domain	Start	End	E-Value	Type
Pfam:LIM	1	52	2e-9	PFAM

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 99.0%
20x: 96.5%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb9	A	G	5: 124,083,123	I255T	possibly damaging	Het
Ablim1	A	T	19: 57,182,224		probably null	Het
Akap10	G	A	11: 61,930,054	P8L	possibly damaging	Het
Ankle2	C	T	5: 110,231,316	A27V	probably damaging	Het
Anxa8	A	G	14: 34,094,812	T246A	probably benign	Het
Arhgap5	A	G	12: 52,567,205	N1460S	probably benign	Het
Arid5b	T	G	10: 68,098,356	D572A	possibly damaging	Het
Atrn	T	A	2: 131,013,641	L1278Q	probably null	Het
AU040320	G	T	4: 126,832,160	K454N	possibly damaging	Het
Baz2b	T	A	2: 59,900,768	R2085W	probably damaging	Het
Bbx	A	T	16: 50,210,458	N649K	probably damaging	Het
BC034090	G	A	1: 155,225,286	P411S	probably damaging	Het
Calcoco2	A	T	11: 96,107,537	F20Y	probably damaging	Het
Carmil2	A	G	8: 105,686,761	R50G	probably damaging	Het
Catspere2	A	G	1: 178,046,959	T131A	probably benign	Het
Cdcp1	C	A	9: 123,173,790	V739L	probably damaging	Het
Chit1	A	G	1: 134,144,027	T92A	possibly damaging	Het
Clstn3	A	G	6: 124,459,804	I185T	probably damaging	Het
Dctpp1	C	A	7: 127,259,389	V61L	probably damaging	Het
Dip2a	T	C	10: 76,287,321	T760A	probably benign	Het
Dock10	C	T	1: 80,578,704	V552I	probably benign	Het
Dpcr1	T	C	17: 35,638,192	T172A	unknown	Het
Dpp8	A	G	9: 65,043,735	E151G	probably damaging	Het
Dvl2	G	C	11: 70,007,518	R367P	possibly damaging	Het
Fem1b	A	T	9: 62,796,361	I539N	probably damaging	Het
Frat2	A	T	19: 41,847,838	L25H	probably damaging	Het
Garnl3	A	T	2: 33,018,499		probably null	Het
Gh	T	C	11: 106,301,427	H47R	possibly damaging	Het
Glmp	T	C	3: 88,325,738	V61A	probably damaging	Het
Gm6614	T	G	6: 141,987,734	M462L	probably benign	Het
Gm9925	T	C	18: 74,065,487	V129A	unknown	Het
H2-M9	T	A	17: 36,642,133	E94V	probably benign	Het
Hira	A	T	16: 18,925,757	Q408L	probably benign	Het
Hook3	A	G	8: 26,088,058		probably null	Het
Ifi206	G	A	1: 173,481,158	P424L		Het
Impdh2	T	C	9: 108,563,325	V270A	probably benign	Het
Klhl14	A	G	18: 21,651,965	I135T	probably benign	Het
Klra10	C	A	6: 130,275,775	V179L	probably benign	Het
Kmt2c	T	C	5: 25,302,732	S3236G	probably damaging	Het
Krt76	G	T	15: 101,888,390	A358D	possibly damaging	Het
Lacc1	C	A	14: 77,029,552	G424C	probably damaging	Het
Lipi	C	T	16: 75,565,530		probably null	Het
Lrrc17	C	T	5: 21,561,071	R184W	probably damaging	Het
Mllt10	A	G	2: 18,123,756	N183D	probably damaging	Het
Mterf2	C	T	10: 85,120,163	G199D	probably damaging	Het
Nat8f4	A	T	6: 85,900,994	S182R	probably benign	Het
Ndrg3	C	A	2: 156,937,532	E238*	probably null	Het
Nop14	A	T	5: 34,654,461	L194H	probably damaging	Het
Obscn	T	C	11: 59,081,905	E2105G	possibly damaging	Het
Olfr1009	A	T	2: 85,722,043	T213S	probably benign	Het
Olfr1079	T	A	2: 86,538,381	H176L	possibly damaging	Het
Olfr1457	A	C	19: 13,095,284	Y121*	probably null	Het
Olfr829	A	T	9: 18,857,429	Y259F	possibly damaging	Het
Pbx3	C	T	2: 34,178,228	A320T	probably benign	Het
Pcdhac2	A	T	18: 37,146,144	S726C	probably damaging	Het
Pcdhgb2	A	G	18: 37,690,763	D269G	probably damaging	Het
Pcgf6	A	T	19: 47,045,832	S257T	probably damaging	Het
Pclo	A	T	5: 14,540,458	H924L	unknown	Het
Per3	T	A	4: 151,042,678	T129S	possibly damaging	Het
Pi4ka	A	T	16: 17,303,060	M1270K		Het
Plec	G	A	15: 76,179,550	Q2277*	probably null	Het
Pnma1	T	A	12: 84,147,335	K198M	probably damaging	Het
Prc1	T	A	7: 80,304,767	F196L	possibly damaging	Het
Prkcz	T	C	4: 155,357,505	T57A	probably damaging	Het
Repin1	G	T	6: 48,597,345	E403*	probably null	Het
Robo4	A	G	9: 37,402,635	M61V	possibly damaging	Het
Rps12	C	T	10: 23,785,677	V79I	probably benign	Het
Rsph3a	A	G	17: 7,979,188	K466E	probably benign	Het
Scly	A	T	1: 91,308,367	I168F	probably damaging	Het
Setd1a	T	A	7: 127,785,053	F359I	unknown	Het
Sh3tc1	A	G	5: 35,706,857	L662P	possibly damaging	Het
Slc12a5	T	C	2: 164,992,452	W798R	probably damaging	Het
Slc16a6	C	T	11: 109,473,455	R13Q	unknown	Het
Smarcad1	A	G	6: 65,052,782	D118G	possibly damaging	Het
Sos2	T	C	12: 69,607,215	T788A	probably damaging	Het
Syvn1	A	G	19: 6,048,366	E75G	probably null	Het
Thpo	T	C	16: 20,726,394	E103G	probably benign	Het
Trav7d-3	A	T	14: 52,744,736	E78V	possibly damaging	Het
Uap1	A	G	1: 170,158,763	S217P	probably damaging	Het
Unc45a	T	G	7: 80,331,562	R497S	probably damaging	Het
Upf1	A	G	8: 70,338,884		probably null	Het
Usp47	A	T	7: 112,046,970	K28M	probably damaging	Het
Wdr72	A	C	9: 74,218,772	T1062P	probably damaging	Het
Wnt7b	A	T	15: 85,537,445	C339S	probably damaging	Het
Zfp954	G	T	7: 7,115,471	T358K	probably benign	Het
Zmynd15	G	T	11: 70,459,452		probably benign	Het

Other mutations in Limch1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00583:Limch1	APN	5	66953679	missense	probably damaging	0.99
IGL00644:Limch1	APN	5	67016552	missense	probably benign	0.01
IGL00705:Limch1	APN	5	66993153	nonsense	probably null
IGL01154:Limch1	APN	5	66745958	nonsense	probably null	0.00
IGL01865:Limch1	APN	5	66974580	nonsense	probably null
IGL02529:Limch1	APN	5	67002613	missense	possibly damaging	0.89
IGL03171:Limch1	APN	5	67034194	missense	possibly damaging	0.80
IGL03308:Limch1	APN	5	67002558	missense	possibly damaging	0.92
IGL03396:Limch1	APN	5	66953673	missense	probably damaging	1.00
R0067:Limch1	UTSW	5	66974622	missense	probably damaging	0.99
R0067:Limch1	UTSW	5	66974622	missense	probably damaging	0.99
R0114:Limch1	UTSW	5	67036084	intron	probably benign
R0129:Limch1	UTSW	5	66959590	missense	probably damaging	0.96
R0193:Limch1	UTSW	5	67027539	missense	probably damaging	1.00
R0194:Limch1	UTSW	5	66999273	missense	probably benign	0.05
R0367:Limch1	UTSW	5	66857954	critical splice donor site	probably null
R0558:Limch1	UTSW	5	66969155	missense	probably damaging	1.00
R0927:Limch1	UTSW	5	66997233	missense	probably damaging	1.00
R1190:Limch1	UTSW	5	66969197	missense	probably damaging	1.00
R1316:Limch1	UTSW	5	66999243	missense	probably damaging	1.00
R1469:Limch1	UTSW	5	66881980	splice site	probably benign
R1647:Limch1	UTSW	5	66999256	missense	probably damaging	1.00
R1648:Limch1	UTSW	5	66999256	missense	probably damaging	1.00
R1944:Limch1	UTSW	5	66999099	missense	probably damaging	1.00
R2103:Limch1	UTSW	5	66998729	missense	probably benign	0.05
R2126:Limch1	UTSW	5	67029760	missense	probably damaging	1.00
R2248:Limch1	UTSW	5	67044399	missense	probably damaging	1.00
R2415:Limch1	UTSW	5	66974634	missense	probably damaging	1.00
R3762:Limch1	UTSW	5	67028840	missense	probably damaging	1.00
R3797:Limch1	UTSW	5	66969079	missense	probably damaging	1.00
R4659:Limch1	UTSW	5	67027557	missense	probably damaging	1.00
R4773:Limch1	UTSW	5	67027507	missense	probably damaging	0.99
R4876:Limch1	UTSW	5	66881927	missense	possibly damaging	0.64
R5062:Limch1	UTSW	5	66969235	missense	probably damaging	1.00
R5191:Limch1	UTSW	5	67027561	missense	probably damaging	1.00
R5202:Limch1	UTSW	5	66993173	missense	probably damaging	1.00
R5335:Limch1	UTSW	5	66881957	missense	probably damaging	1.00
R5436:Limch1	UTSW	5	66974566	missense	possibly damaging	0.72
R5994:Limch1	UTSW	5	66974622	missense	probably damaging	1.00
R6049:Limch1	UTSW	5	67030860	missense	probably benign	0.32
R6228:Limch1	UTSW	5	67016502	missense	probably damaging	1.00
R6547:Limch1	UTSW	5	67028774	missense	probably damaging	1.00
R6600:Limch1	UTSW	5	66745938	missense	probably benign
R6888:Limch1	UTSW	5	67021926	missense	probably benign	0.21
R7111:Limch1	UTSW	5	67025176	splice site	probably null
R7132:Limch1	UTSW	5	66953685	missense	probably damaging	1.00
R7144:Limch1	UTSW	5	67017658	missense	probably benign	0.10
R7302:Limch1	UTSW	5	66959599	missense	probably benign	0.02
R7341:Limch1	UTSW	5	67034202	missense	probably benign	0.06
R7491:Limch1	UTSW	5	67054237	missense	probably damaging	0.99
R8229:Limch1	UTSW	5	67028795	missense	probably damaging	1.00
R8348:Limch1	UTSW	5	67002482	missense	probably damaging	0.98
R8395:Limch1	UTSW	5	66969051	missense	probably damaging	0.96
R8416:Limch1	UTSW	5	66999306	missense	probably benign
R8448:Limch1	UTSW	5	67002482	missense	probably damaging	0.98
R8477:Limch1	UTSW	5	66974565	missense	probably benign	0.01
R8924:Limch1	UTSW	5	67033132	missense	probably benign	0.01
R9080:Limch1	UTSW	5	67017649	missense	probably benign	0.00
R9619:Limch1	UTSW	5	66857941	missense	probably damaging	1.00
R9681:Limch1	UTSW	5	66969079	missense	probably damaging	1.00
R9715:Limch1	UTSW	5	66999017	missense	probably damaging	1.00
X0022:Limch1	UTSW	5	67021952	missense	probably benign	0.00
X0027:Limch1	UTSW	5	67002620	missense	probably damaging	1.00
Z1177:Limch1	UTSW	5	67028799	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TAGGTGTACCCCTGTTTGGCTC -3'
(R):5'- AAGAAGCAGCTGGTTGTTGG -3'

Sequencing Primer
(F):5'- GTACTGTATATCCTGAACCACGGG -3'
(R):5'- GGCTTTGTATTTTCTTTGACAGCC -3'

Posted On

2020-06-30