Mutagenetix > Incidental Mutation

Incidental Mutation 'R3762:Limch1'

270552

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: 0.121) question?

Stock #

R3762 (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 67186183 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 828 (Y828C)

Ref Sequence

ENSEMBL: ENSMUSP00000112732 (fasta)

Gene Model

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

AlphaFold

Q3UH68

Predicted Effect

probably damaging
Transcript: ENSMUST00000038188
AA Change: Y661C

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

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: Y661C

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: Y817C

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

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: Y817C

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: Y658C

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

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: Y658C

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: Y828C

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

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: Y828C

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: Y533C

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: Y533C

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 25 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arhgap35	A	T	7: 16,299,000 (GRCm39)	S22T	probably damaging	Het
Atp2b1	T	C	10: 98,845,351 (GRCm39)	I718T	probably damaging	Het
Cad	T	A	5: 31,232,890 (GRCm39)		probably null	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,619,782 (GRCm39)		probably benign	Het
Defa41	C	T	8: 21,691,753 (GRCm39)	S45F	probably damaging	Het
Dhx15	G	A	5: 52,324,074 (GRCm39)	P406L	probably benign	Het
Dnah17	T	A	11: 117,995,352 (GRCm39)	M999L	probably benign	Het
Dpysl4	A	G	7: 138,676,672 (GRCm39)	E374G	probably damaging	Het
Gatad2a	T	C	8: 70,368,930 (GRCm39)		probably null	Het
Gm826	C	A	2: 160,155,423 (GRCm39)		probably benign	Het
H2-M10.1	T	A	17: 36,636,216 (GRCm39)	H117L	probably damaging	Het
Klhl9	A	T	4: 88,639,830 (GRCm39)	V137D	possibly damaging	Het
Med1	T	C	11: 98,046,341 (GRCm39)		probably benign	Het
Muc5ac	A	T	7: 141,361,212 (GRCm39)	T1507S	possibly damaging	Het
Pak6	A	T	2: 118,526,958 (GRCm39)	Q651L	probably damaging	Het
Plscr2	T	A	9: 92,173,133 (GRCm39)	V90D	probably damaging	Het
Rbbp4	G	A	4: 129,228,344 (GRCm39)	T2I	probably damaging	Het
Rnf121	G	A	7: 101,673,244 (GRCm39)	T223M	probably damaging	Het
Rsph6a	A	G	7: 18,789,256 (GRCm39)	K196R	probably damaging	Het
Tex47	A	T	5: 7,355,529 (GRCm39)	I237L	probably benign	Het
Ulk1	C	T	5: 110,937,223 (GRCm39)	R691Q	probably benign	Het
Vmn1r30	C	A	6: 58,412,278 (GRCm39)	V185L	probably benign	Het
Vmn2r103	A	T	17: 20,032,411 (GRCm39)	E728D	probably damaging	Het
Vmn2r14	A	T	5: 109,368,033 (GRCm39)	Y320N	probably benign	Het
Zc3h14	T	A	12: 98,724,902 (GRCm39)	F188Y	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
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'- GCAGATGCTTTAGATTCCACATGG -3'
(R):5'- CTGTTAGACCGCAGACAACG -3'

Sequencing Primer
(F):5'- AGATTCCACATGGTCTCTCATGGAG -3'
(R):5'- GTTAGACCGCAGACAACGTGATC -3'

Posted On

2015-03-18