Mutagenetix > Incidental Mutations

Incidental Mutation 'R1648:Limch1'

174010

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

MMRRC Submission

039684-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.135) question?

Stock #

R1648 (G1)

Quality Score

201

Status

Validated

Chromosome

Chromosomal Location

66745827-67057158 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 66999256 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 511 (S511R)

Ref Sequence

ENSEMBL: ENSMUSP00000098723 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000127184] [ENSMUST00000132991]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000038188
AA Change: S355R

PolyPhen 2 Score 0.860 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: S355R

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: S511R

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: S511R

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

possibly damaging
Transcript: ENSMUST00000117601
AA Change: S352R

PolyPhen 2 Score 0.781 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: S352R

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: S499R

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: S499R

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: S227R

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: S227R

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 benign
Transcript: ENSMUST00000127184

SMART Domains

Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736

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	180	229	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000132991

SMART Domains

Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736

Domain	Start	End	E-Value	Type
low complexity region	50	66	N/A	INTRINSIC
low complexity region	76	89	N/A	INTRINSIC
Pfam:DUF4757	103	269	2.6e-63	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137394

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140428

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147050

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201322

Meta Mutation Damage Score

0.0795

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 95.9%
20x: 91.4%

Validation Efficiency

95% (73/77)

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 138,069,420	N1457D	probably benign	Het
Adgb	A	G	10: 10,395,371	F817L	probably damaging	Het
Akap6	A	T	12: 53,142,006	K2068*	probably null	Het
Alms1	T	C	6: 85,678,402	L3310P	probably damaging	Het
Ankrd27	T	A	7: 35,603,853	D219E	probably benign	Het
Atp10a	T	C	7: 58,784,827	V283A	probably damaging	Het
Atp11a	C	T	8: 12,847,495	S270L	probably damaging	Het
Casp3	T	C	8: 46,638,074	S254P	probably benign	Het
Cep104	G	A	4: 153,979,096		probably null	Het
Cep170b	C	T	12: 112,736,372	T423I	probably damaging	Het
Cfap58	A	G	19: 47,955,405	E348G	probably benign	Het
Chd6	A	G	2: 161,042,058	L89S	probably damaging	Het
Cyp2a22	T	C	7: 26,932,368	S488G	probably damaging	Het
D130040H23Rik	C	A	8: 69,302,981	H363Q	probably benign	Het
Dcaf7	T	A	11: 106,051,802	F192I	probably damaging	Het
Ddx20	T	C	3: 105,679,188	I614V	probably benign	Het
Ehbp1	G	A	11: 22,096,000	T558I	probably damaging	Het
Eif2ak3	T	A	6: 70,883,631	V397D	possibly damaging	Het
Eif2b5	T	C	16: 20,502,585	V296A	possibly damaging	Het
Esr1	A	G	10: 5,001,260	E546G	possibly damaging	Het
Fras1	T	A	5: 96,726,613		probably null	Het
G930045G22Rik	T	C	6: 50,846,718		noncoding transcript	Het
Gemin5	A	T	11: 58,147,979	L568*	probably null	Het
Gm22697+Rbm27	AGGTCCAGGCCCAGGCCCTGGTCCTGGCCCTGGCCCTGGTCCCGGCCCAGGCCC	AGGTCCCGGCCCAGGCCC	18: 42,301,883		probably benign	Het
Gpr155	T	C	2: 73,364,164		probably null	Het
Has1	A	G	17: 17,849,985	Y225H	probably damaging	Het
Hk3	A	G	13: 55,014,461	F110S	probably damaging	Het
Iars	A	G	13: 49,723,002	K848E	possibly damaging	Het
Kif17	A	G	4: 138,269,895	Y43C	probably damaging	Het
Kif20b	A	T	19: 34,936,790	T355S	possibly damaging	Het
Kif21a	T	C	15: 90,994,367	T237A	probably damaging	Het
Klc1	T	C	12: 111,776,887	L216P	probably damaging	Het
Krt7	A	C	15: 101,412,567	S32R	probably damaging	Het
Lama3	A	G	18: 12,532,199	D2330G	possibly damaging	Het
Luzp2	T	A	7: 55,264,270		probably null	Het
Macc1	T	C	12: 119,446,421	M308T	probably benign	Het
Mroh9	T	G	1: 163,046,056	E510A	probably damaging	Het
Myo1h	G	T	5: 114,336,275	L458F	probably damaging	Het
Neto1	A	T	18: 86,500,054	Y528F	probably damaging	Het
Nlrp9b	T	A	7: 20,026,544	C187S	possibly damaging	Het
Nup160	T	C	2: 90,710,088	Y854H	probably damaging	Het
Odc1	T	C	12: 17,548,537		probably benign	Het
Olfr1436	T	A	19: 12,298,659	I158L	probably benign	Het
Olfr519	A	G	7: 108,893,765	I214T	probably damaging	Het
Olfr642	A	G	7: 104,050,169	Y62H	probably damaging	Het
Plcb2	A	T	2: 118,723,780	M64K	possibly damaging	Het
Plcxd3	A	T	15: 4,375,809	I33F	probably benign	Het
Postn	A	G	3: 54,376,101	T534A	probably damaging	Het
Prkd2	T	A	7: 16,857,807	F588I	possibly damaging	Het
Prrg4	C	A	2: 104,832,743	A173S	probably benign	Het
Rinl	C	T	7: 28,797,632	A519V	probably damaging	Het
Rpgrip1l	A	C	8: 91,252,889	V975G	probably damaging	Het
Rps6ka4	C	A	19: 6,839,362	V118L	probably benign	Het
Rtkn	T	C	6: 83,135,994	S16P	probably damaging	Het
Sbspon	C	A	1: 15,883,759	R99L	probably damaging	Het
Sdf4	G	A	4: 155,999,429	A119T	probably damaging	Het
Sgpp1	T	A	12: 75,716,216	H397L	possibly damaging	Het
Shc2	T	A	10: 79,626,111	M367L	probably benign	Het
Slc26a5	T	A	5: 21,813,976	K590*	probably null	Het
Slc39a12	T	C	2: 14,451,992	V597A	probably benign	Het
Smcp	A	T	3: 92,584,481	C20S	unknown	Het
Tdrd6	A	C	17: 43,627,109	V1016G	possibly damaging	Het
Tmem132c	T	A	5: 127,463,056		probably benign	Het
Tmem170b	A	T	13: 41,606,262	Q16L	probably null	Het
Tmem30a	A	G	9: 79,793,029	F61S	probably damaging	Het
Tnfsf13b	T	C	8: 10,031,534	M232T	probably damaging	Het
Trip11	T	A	12: 101,884,392	K853*	probably null	Het
Tusc3	C	A	8: 39,046,567	S64*	probably null	Het
Vmn2r111	A	T	17: 22,569,061	D436E	probably benign	Het
Zfp607a	T	C	7: 27,879,068	V521A	probably benign	Het
Zfp704	A	T	3: 9,471,039	S140R	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
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	intron	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
X0022:Limch1	UTSW	5	67021952	missense	probably benign	0.00
X0027:Limch1	UTSW	5	67002620	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCAGTACATCGAGAGGTTCACCATC -3'
(R):5'- ACAAGCTACCCACAATTCGGTTTCC -3'

Sequencing Primer
(F):5'- AGGTTCACCATCAGTGAGGC -3'
(R):5'- tcctcctcctcctcctcc -3'

Posted On

2014-04-24