Mutagenetix > Incidental Mutations

Incidental Mutation 'R6547:Limch1'

521264

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.177) question?

Stock #

R6547 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

66745827-67057158 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 67028774 bp

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Valine at position 806 (E806V)

Ref Sequence

ENSEMBL: ENSMUSP00000112732 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000038188
AA Change: E639V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: E639V

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: E795V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: E795V

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: E636V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: E636V

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: E806V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: E806V

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

unknown
Transcript: ENSMUST00000119854
AA Change: E511V

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: E511V

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

noncoding transcript
Transcript: ENSMUST00000140428

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201322

Meta Mutation Damage Score

0.1479

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.2%
20x: 97.4%

Validation Efficiency

98% (53/54)

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932414N04Rik	A	T	2: 68,659,907		probably benign	Het
9230113P08Rik	T	A	9: 35,908,485	M15K	probably null	Het
Abca13	T	A	11: 9,274,757	V490E	probably benign	Het
Abca2	G	T	2: 25,433,338	G106V	possibly damaging	Het
Ablim3	T	C	18: 61,823,929	T276A	probably benign	Het
Anxa7	A	G	14: 20,469,393	V119A	probably benign	Het
Arl9	A	G	5: 77,010,410		probably null	Het
Atm	T	C	9: 53,440,157	Y2964C	probably damaging	Het
Bbs9	T	C	9: 22,514,069	Y140H	probably benign	Het
Calcr	A	T	6: 3,717,177	D94E	probably damaging	Het
Celsr3	T	A	9: 108,829,128	Y937N	probably damaging	Het
Clca3a1	C	T	3: 144,736,947	A779T	probably damaging	Het
Clec9a	T	A	6: 129,416,376	V94D	probably benign	Het
Colec12	G	T	18: 9,840,351	L57F	probably damaging	Het
Fa2h	T	C	8: 111,348,020	Y317C	probably damaging	Het
Fam126a	T	C	5: 23,965,100	N417S	probably benign	Het
Flnc	A	G	6: 29,448,608	T1282A	probably damaging	Het
Gm10801	AAGT	AAGTAGT	2: 98,663,803		probably null	Het
Hcn2	G	T	10: 79,717,152	V162L	probably benign	Het
Kbtbd11	T	A	8: 15,027,641	V80E	possibly damaging	Het
Lama4	A	G	10: 39,073,656	D915G	probably damaging	Het
Mppe1	T	C	18: 67,228,988	I169V	probably benign	Het
Msc	A	C	1: 14,755,745	S2A	possibly damaging	Het
Nploc4	A	G	11: 120,428,522		probably null	Het
Nr3c2	A	T	8: 76,908,809	I180F	possibly damaging	Het
Nrap	G	T	19: 56,351,566	H840N	probably benign	Het
Olfr151	T	A	9: 37,730,495	M163L	probably benign	Het
Pdlim1	G	A	19: 40,223,120	T243I	probably damaging	Het
Pfkl	T	A	10: 77,995,354	M318L	probably benign	Het
Rap1gds1	C	A	3: 138,955,338	R426L	probably damaging	Het
Ric1	A	G	19: 29,594,826	N674D	probably damaging	Het
Rp1	G	A	1: 4,170,305	T875I	unknown	Het
Rtn1	G	T	12: 72,308,761	S137Y	possibly damaging	Het
Scn2a	A	G	2: 65,715,897	I935V	probably benign	Het
Serpina1a	C	T	12: 103,855,921	V251M	probably damaging	Het
Slc19a3	A	G	1: 83,022,900	V132A	probably damaging	Het
Slc26a6	T	A	9: 108,860,782		probably null	Het
Slc2a5	T	A	4: 150,135,619	V164D	possibly damaging	Het
Slc4a1	T	A	11: 102,356,735	T441S	probably damaging	Het
Stk33	T	C	7: 109,320,835	I366V	possibly damaging	Het
Syt14	G	T	1: 192,901,869	H696N	possibly damaging	Het
Tcaim	T	A	9: 122,814,466	V77D	probably benign	Het
Tefm	T	G	11: 80,140,384		probably null	Het
Tekt3	T	A	11: 63,070,478	S158T	possibly damaging	Het
Tmem2	A	T	19: 21,844,831	T1197S	probably benign	Het
Tspan11	T	A	6: 127,949,803	M238K	possibly damaging	Het
Unc5c	A	T	3: 141,790,019	T476S	probably benign	Het
Usp9y	A	T	Y: 1,444,612	L109Q	probably damaging	Homo
Vmn2r111	T	C	17: 22,559,051	N549S	possibly damaging	Het
Vps13c	C	A	9: 67,973,365	Q3495K	probably damaging	Het
Zbtb10	G	A	3: 9,251,703	A192T	probably benign	Het
Zfp316	A	T	5: 143,254,197	V689D	probably damaging	Het
Zswim1	A	G	2: 164,824,796		probably benign	Het
Zswim5	T	C	4: 116,986,903	L1046P	probably damaging	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
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
R8079:Limch1	UTSW	5	67046753	missense	possibly damaging	0.73
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
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'- ACCCAAGAGTATGTGTCTTTTGTG -3'
(R):5'- TAGACCGCAGACAACGTGATC -3'

Sequencing Primer
(F):5'- GCGGTGCAGATGCTTTAGATTCC -3'
(R):5'- GCAGACAACGTGATCCTCTTAAAGAG -3'

Posted On

2018-06-06