Mutagenetix > Incidental Mutation

Incidental Mutation 'R2103:Limch1'

230670

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

MMRRC Submission

040107-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.121) question?

Stock #

R2103 (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 67156072 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 394 (K394R)

Ref Sequence

ENSEMBL: ENSMUSP00000098723 (fasta)

Gene Model

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

AlphaFold

Q3UH68

Predicted Effect

probably benign
Transcript: ENSMUST00000038188
AA Change: K238R

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: K238R

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 benign
Transcript: ENSMUST00000101164
AA Change: K394R

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: K394R

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 benign
Transcript: ENSMUST00000117601
AA Change: K235R

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: K235R

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 benign
Transcript: ENSMUST00000118242
AA Change: K382R

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: K382R

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: K110R

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: K110R

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
AA Change: K226R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736
AA Change: K226R

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
AA Change: K247R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736
AA Change: K247R

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: ENSMUST00000201322

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137394

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147050

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.2%
20x: 94.9%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadac	C	A	3: 59,947,235 (GRCm39)	P311Q	probably damaging	Het
Acoxl	T	A	2: 127,814,526 (GRCm39)	M314K	probably damaging	Het
Agmat	A	T	4: 141,483,214 (GRCm39)	D216V	probably damaging	Het
Aida	A	T	1: 183,094,627 (GRCm39)	E107D	probably benign	Het
Ano5	A	G	7: 51,187,561 (GRCm39)	K50R	possibly damaging	Het
Anxa2	A	T	9: 69,391,098 (GRCm39)	D95V	probably damaging	Het
Aspm	G	A	1: 139,419,403 (GRCm39)	V3023M	probably damaging	Het
Atg16l2	A	G	7: 100,939,568 (GRCm39)		probably null	Het
B3galt4	G	A	17: 34,169,813 (GRCm39)	R142C	probably damaging	Het
B3galt5	A	T	16: 96,117,225 (GRCm39)	K286M	probably damaging	Het
Best3	A	C	10: 116,838,499 (GRCm39)	I186L	probably benign	Het
Blm	G	T	7: 80,155,697 (GRCm39)		probably null	Het
Cat	A	T	2: 103,293,660 (GRCm39)	D389E	probably damaging	Het
Cert1	T	A	13: 96,771,394 (GRCm39)	N550K	probably damaging	Het
Cluh	C	A	11: 74,550,355 (GRCm39)	C222*	probably null	Het
Cntnap2	G	A	6: 47,275,522 (GRCm39)	E1325K	probably damaging	Het
Col14a1	A	T	15: 55,313,336 (GRCm39)	D1320V	unknown	Het
Cpne7	A	G	8: 123,854,176 (GRCm39)	K288E	possibly damaging	Het
Cyp26b1	A	G	6: 84,552,032 (GRCm39)	S369P	possibly damaging	Het
Cyp2j9	T	A	4: 96,460,201 (GRCm39)	K434M	probably damaging	Het
Dpyd	G	C	3: 118,858,601 (GRCm39)	S605T	probably benign	Het
Dst	A	G	1: 34,229,339 (GRCm39)	T1986A	probably benign	Het
Ebf2	T	A	14: 67,625,391 (GRCm39)	V233D	probably damaging	Het
Ecm2	A	G	13: 49,683,732 (GRCm39)	D570G	probably benign	Het
Efhc1	T	A	1: 21,059,784 (GRCm39)	C611*	probably null	Het
Epop	T	C	11: 97,519,480 (GRCm39)	T210A	probably benign	Het
Fdxacb1	A	T	9: 50,682,946 (GRCm39)	N101I	probably benign	Het
Fezf1	A	G	6: 23,247,331 (GRCm39)	F248S	possibly damaging	Het
Galnt16	A	G	12: 80,630,430 (GRCm39)	D262G	probably damaging	Het
Gm9507	T	A	10: 77,647,500 (GRCm39)		probably benign	Het
Grin2b	A	T	6: 135,757,138 (GRCm39)	I441N	probably benign	Het
H2-Eb2	A	G	17: 34,553,278 (GRCm39)	I155V	probably benign	Het
Hectd4	C	A	5: 121,493,692 (GRCm39)	D3811E	probably benign	Het
Herc4	T	C	10: 63,081,889 (GRCm39)	S71P	probably benign	Het
Hhipl1	A	G	12: 108,293,977 (GRCm39)	T628A	probably benign	Het
Hoga1	A	C	19: 42,048,459 (GRCm39)		probably null	Het
Igf2bp1	A	G	11: 95,866,122 (GRCm39)	V122A	probably damaging	Het
Il10ra	C	A	9: 45,167,109 (GRCm39)	A481S	probably benign	Het
Klk1b26	A	T	7: 43,666,324 (GRCm39)	T256S	probably damaging	Het
Kndc1	C	T	7: 139,501,150 (GRCm39)	T813I	probably benign	Het
Lrrc37a	T	C	11: 103,391,087 (GRCm39)	E1446G	probably benign	Het
Lrrc47	C	T	4: 154,100,350 (GRCm39)	R287W	probably damaging	Het
Mdn1	T	A	4: 32,738,712 (GRCm39)	L3555Q	possibly damaging	Het
Mei1	A	G	15: 81,987,405 (GRCm39)	H399R	possibly damaging	Het
Mei1	G	T	15: 81,991,237 (GRCm39)	V472F	probably damaging	Het
Mrps34	T	A	17: 25,114,464 (GRCm39)		probably null	Het
Myom3	A	G	4: 135,503,723 (GRCm39)	T391A	probably benign	Het
Nfib	G	A	4: 82,248,645 (GRCm39)	T314I	possibly damaging	Het
Or5b99	T	C	19: 12,976,866 (GRCm39)	V172A	possibly damaging	Het
Or5p73	A	G	7: 108,064,810 (GRCm39)	N93S	probably benign	Het
Or6c5	T	C	10: 129,074,368 (GRCm39)	S117P	probably damaging	Het
Or9a2	A	G	6: 41,748,939 (GRCm39)	I98T	probably benign	Het
Pdia3	G	C	2: 121,264,474 (GRCm39)	G346A	probably damaging	Het
Plce1	T	C	19: 38,766,368 (GRCm39)	F2117S	probably damaging	Het
Plec	A	G	15: 76,057,743 (GRCm39)	F4055L	probably damaging	Het
Ppip5k1	A	T	2: 121,152,134 (GRCm39)		probably null	Het
Psma6	T	C	12: 55,454,842 (GRCm39)	I57T	probably benign	Het
Psme2	A	T	14: 55,828,297 (GRCm39)		probably null	Het
Reln	A	T	5: 22,174,358 (GRCm39)	D1948E	possibly damaging	Het
Rsf1	GGCG	GGCGACGGCAGCG	7: 97,229,113 (GRCm39)		probably benign	Het
Sbno1	G	T	5: 124,532,000 (GRCm39)	S727R	probably damaging	Het
Serpina3m	C	A	12: 104,355,958 (GRCm39)	Y208*	probably null	Het
Serpind1	T	C	16: 17,160,808 (GRCm39)	V446A	probably benign	Het
Shc3	T	A	13: 51,596,872 (GRCm39)	M384L	probably benign	Het
Slc38a11	A	G	2: 65,160,683 (GRCm39)	F304L	probably benign	Het
Slc4a5	A	C	6: 83,201,663 (GRCm39)	D4A	probably benign	Het
Slc4a5	G	A	6: 83,274,360 (GRCm39)	A1076T	probably benign	Het
Slpi	C	T	2: 164,197,463 (GRCm39)	C28Y	probably damaging	Het
Sptan1	T	C	2: 29,920,483 (GRCm39)	S2320P	probably damaging	Het
Stim2	A	G	5: 54,262,591 (GRCm39)	T278A	possibly damaging	Het
Sympk	T	A	7: 18,788,041 (GRCm39)	S1186T	probably benign	Het
Tbrg1	T	C	9: 37,560,715 (GRCm39)	D387G	probably benign	Het
Tns2	A	T	15: 102,021,100 (GRCm39)		probably null	Het
Tnxb	A	G	17: 34,901,225 (GRCm39)	Y1013C	probably damaging	Het
Tpsg1	T	C	17: 25,592,267 (GRCm39)	S41P	possibly damaging	Het
Trim36	T	C	18: 46,329,149 (GRCm39)	N85S	probably benign	Het
Trpm6	A	T	19: 18,773,648 (GRCm39)	H380L	probably benign	Het
Tssk4	A	G	14: 55,888,997 (GRCm39)	I174M	probably damaging	Het
Ttn	C	T	2: 76,776,735 (GRCm39)		probably null	Het
Vmn2r114	ATTT	ATT	17: 23,509,906 (GRCm39)		probably null	Het
Vmn2r4	T	A	3: 64,322,704 (GRCm39)	N5I	possibly damaging	Het
Vps11	G	A	9: 44,270,524 (GRCm39)	H183Y	probably damaging	Het
Vsig10l	A	G	7: 43,116,892 (GRCm39)	T476A	possibly damaging	Het
Vwa8	C	T	14: 79,145,670 (GRCm39)	R116C	probably damaging	Het
Vwf	G	A	6: 125,623,293 (GRCm39)	V1797I	probably benign	Het
Wasl	A	T	6: 24,618,377 (GRCm39)	S447T	unknown	Het
Whamm	C	T	7: 81,241,519 (GRCm39)	R277*	probably null	Het
Zfp874a	T	A	13: 67,590,623 (GRCm39)	I354F	probably benign	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
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'- TTAGCGCTTATAGGTCCGTGAG -3'
(R):5'- GCAGAGATTCCAACCAAGGTAG -3'

Sequencing Primer
(F):5'- CTTATAGGTCCGTGAGTCACAGGC -3'
(R):5'- GATTCCAACCAAGGTAGAGTAAAAAC -3'

Posted On

2014-09-18