Mutagenetix > Incidental Mutation

Incidental Mutation 'R1190:Limch1'

100727

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

MMRRC Submission

039262-MU

Accession Numbers

Essential gene?

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

Stock #

R1190 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

66903232-67214502 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 67126540 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 56 (D56G)

Ref Sequence

ENSEMBL: ENSMUSP00000123337 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000122812] [ENSMUST00000127184] [ENSMUST00000132991]

AlphaFold

Q3UH68

Predicted Effect

probably damaging
Transcript: ENSMUST00000038188
AA Change: D47G

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

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: D47G

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: D203G

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

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: D203G

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: D44G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: D44G

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: D203G

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

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: D203G

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

probably damaging
Transcript: ENSMUST00000119854
AA Change: D203G

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

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: D203G

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: ENSMUST00000122812

Predicted Effect

probably damaging
Transcript: ENSMUST00000127184
AA Change: D47G

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

SMART Domains

Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736
AA Change: D47G

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 damaging
Transcript: ENSMUST00000132991
AA Change: D56G

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

SMART Domains

Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736
AA Change: D56G

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: ENSMUST00000140428

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202048

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201848

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201852

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201322

Coding Region Coverage

1x: 99.0%
3x: 98.0%
10x: 95.3%
20x: 89.8%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 20 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Antxrl	T	C	14: 33,791,207 (GRCm39)	F367L	probably benign	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
Atp8a2	T	C	14: 60,097,719 (GRCm39)	K770E	probably benign	Het
Dnah17	G	A	11: 117,933,001 (GRCm39)	R3586W	probably damaging	Het
Dpysl2	A	G	14: 67,061,850 (GRCm39)	V252A	probably benign	Het
Dus2	T	C	8: 106,771,497 (GRCm39)	S208P	possibly damaging	Het
Elk3	T	C	10: 93,101,058 (GRCm39)	N231S	probably benign	Het
Ephx1	A	T	1: 180,821,494 (GRCm39)	M280K	probably benign	Het
Fstl4	T	C	11: 52,959,373 (GRCm39)	M138T	probably benign	Het
Iqsec1	A	T	6: 90,666,659 (GRCm39)	Y593N	probably damaging	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Lep	G	T	6: 29,071,173 (GRCm39)	E166*	probably null	Het
Or4d10c	G	T	19: 12,066,051 (GRCm39)	T35K	possibly damaging	Het
Pkn2	A	T	3: 142,517,286 (GRCm39)		probably null	Het
Plxna4	A	G	6: 32,228,071 (GRCm39)	Y512H	probably damaging	Het
Tekt1	A	T	11: 72,246,039 (GRCm39)	I161N	probably damaging	Het
Tex14	T	G	11: 87,385,934 (GRCm39)		probably null	Het
Trpc3	T	C	3: 36,725,497 (GRCm39)	N160D	probably benign	Het
Zfp369	T	C	13: 65,440,107 (GRCm39)	S264P	probably damaging	Het
Zfp747	G	A	7: 126,973,726 (GRCm39)	A148V	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
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
R4876:Limch1	UTSW	5	67,039,270 (GRCm39)	missense	possibly damaging	0.64
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'- TTTCCACACAGATCCTCCATGCAAG -3'
(R):5'- TAGAATTACCAGGCTCCAGCCAGG -3'

Sequencing Primer
(F):5'- TTGCAGACCACTGGAAGC -3'
(R):5'- CTCCAGCCAGGTGGATATG -3'

Posted On

2014-01-15