Mutagenetix > Incidental Mutation

Incidental Mutation 'R5436:Limch1'

428327

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

MMRRC Submission

043001-MU

Accession Numbers

Essential gene?

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

Stock #

R5436 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

66903232-67214502 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 67131909 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 133 (V133A)

Ref Sequence

ENSEMBL: ENSMUSP00000123337 (fasta)

Gene Model

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

AlphaFold

Q3UH68

Predicted Effect

possibly damaging
Transcript: ENSMUST00000038188
AA Change: V124A

PolyPhen 2 Score 0.460 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: V124A

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

possibly damaging
Transcript: ENSMUST00000101164
AA Change: V280A

PolyPhen 2 Score 0.516 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: V280A

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: V121A

PolyPhen 2 Score 0.694 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: V121A

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

possibly damaging
Transcript: ENSMUST00000118242
AA Change: V280A

PolyPhen 2 Score 0.655 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: V280A

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: V8A

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: V8A

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: V124A

PolyPhen 2 Score 0.250 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736
AA Change: V124A

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

possibly damaging
Transcript: ENSMUST00000132991
AA Change: V133A

PolyPhen 2 Score 0.721 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736
AA Change: V133A

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: ENSMUST00000201852

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202048

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201848

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147050

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201322

Meta Mutation Damage Score

0.1122

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

99% (106/107)

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930449A18Rik	T	C	3: 59,754,114 (GRCm39)		noncoding transcript	Het
Abca9	G	A	11: 110,025,062 (GRCm39)	L994F	probably damaging	Het
Abl2	A	T	1: 156,457,450 (GRCm39)	S239C	probably damaging	Het
Acsl5	T	A	19: 55,267,997 (GRCm39)		probably null	Het
Aff1	C	T	5: 103,931,736 (GRCm39)	T126I	probably damaging	Het
Amtn	T	C	5: 88,529,485 (GRCm39)	L107P	probably damaging	Het
Ankrd45	A	G	1: 160,986,682 (GRCm39)		probably benign	Het
Arl6ip5	G	A	6: 97,187,887 (GRCm39)	V36I	probably damaging	Het
Ascc3	T	A	10: 50,535,079 (GRCm39)	D657E	probably damaging	Het
Ascl1	T	A	10: 87,328,808 (GRCm39)	Q48L	unknown	Het
Asic4	T	A	1: 75,427,963 (GRCm39)	V163E	probably benign	Het
Atm	A	T	9: 53,371,104 (GRCm39)	M2245K	probably benign	Het
Barx2	T	G	9: 31,824,285 (GRCm39)	T35P	probably damaging	Het
Bdh1	C	T	16: 31,275,475 (GRCm39)	R235C	probably damaging	Het
C8b	T	A	4: 104,657,546 (GRCm39)	Y404*	probably null	Het
Car5a	A	G	8: 122,643,981 (GRCm39)		probably benign	Het
Ccdc13	T	C	9: 121,628,109 (GRCm39)	I169M	probably benign	Het
Cd163	A	T	6: 124,304,923 (GRCm39)	D1100V	probably benign	Het
Cimap2	A	T	4: 106,467,690 (GRCm39)	H315Q	probably benign	Het
Cntfr	T	C	4: 41,663,322 (GRCm39)	N162D	probably damaging	Het
Cops3	T	G	11: 59,715,171 (GRCm39)	D289A	probably damaging	Het
Crbn	A	T	6: 106,772,861 (GRCm39)	S42R	probably damaging	Het
Cth	T	A	3: 157,600,463 (GRCm39)	H397L	probably benign	Het
Dact2	A	G	17: 14,416,010 (GRCm39)	L730P	probably damaging	Het
Dhx37	C	T	5: 125,506,867 (GRCm39)	G210R	probably benign	Het
Dnaaf9	C	A	2: 130,606,419 (GRCm39)	K415N	probably benign	Het
Dnah1	T	C	14: 31,038,704 (GRCm39)	I126V	probably benign	Het
Dnttip2	T	C	3: 122,072,418 (GRCm39)	I566T	probably damaging	Het
Ehbp1l1	G	T	19: 5,766,276 (GRCm39)	R412S	possibly damaging	Het
Fam110b	A	C	4: 5,799,104 (GRCm39)	Q174P	probably benign	Het
Fam149a	A	T	8: 45,801,508 (GRCm39)	S457T	probably benign	Het
Fat3	A	C	9: 15,871,810 (GRCm39)	V3527G	probably benign	Het
Fat4	A	G	3: 38,945,495 (GRCm39)	M1463V	probably benign	Het
Gak	T	A	5: 108,740,218 (GRCm39)	I566F	possibly damaging	Het
Gdf10	T	A	14: 33,654,213 (GRCm39)	I240N	probably damaging	Het
Gprc6a	T	A	10: 51,502,798 (GRCm39)	H355L	probably benign	Het
Gxylt1	T	C	15: 93,145,780 (GRCm39)	K338R	probably damaging	Het
Hexim2	A	T	11: 103,029,095 (GRCm39)	E49V	probably null	Het
Hfm1	T	C	5: 107,040,638 (GRCm39)	D709G	possibly damaging	Het
Ighv1-49	T	C	12: 115,019,081 (GRCm39)	K19R	probably damaging	Het
Il17a	T	A	1: 20,803,870 (GRCm39)	Y88*	probably null	Het
Iqsec1	A	T	6: 90,822,343 (GRCm39)		probably benign	Het
Itih2	T	C	2: 10,110,007 (GRCm39)	D582G	probably benign	Het
Klc3	T	C	7: 19,131,884 (GRCm39)		probably null	Het
Larp4	T	A	15: 99,883,995 (GRCm39)	N78K	probably damaging	Het
Larp4b	A	G	13: 9,218,936 (GRCm39)	D526G	possibly damaging	Het
Lmbr1l	G	A	15: 98,802,672 (GRCm39)	R426C	probably damaging	Het
Lox	T	A	18: 52,662,175 (GRCm39)	D76V	probably benign	Het
Lrrc8d	T	A	5: 105,960,418 (GRCm39)	I276N	probably damaging	Het
Ltbr	G	A	6: 125,289,757 (GRCm39)	R146W	probably damaging	Het
Marchf10	A	T	11: 105,292,991 (GRCm39)	Y139N	possibly damaging	Het
Mrc1	T	G	2: 14,271,326 (GRCm39)	I410S	probably damaging	Het
Mrto4	A	T	4: 139,075,276 (GRCm39)	C176S	probably damaging	Het
Mtch1	G	T	17: 29,566,564 (GRCm39)	D66E	probably benign	Het
Nbas	T	G	12: 13,424,812 (GRCm39)	L1017R	probably damaging	Het
Nherf4	A	G	9: 44,159,652 (GRCm39)	V448A	possibly damaging	Het
Nim1k	A	G	13: 120,189,065 (GRCm39)		probably benign	Het
Nlrp6	T	A	7: 140,502,630 (GRCm39)	Y245*	probably null	Het
Or11g7	T	G	14: 50,691,184 (GRCm39)	V225G	probably damaging	Het
Or2t43	T	A	11: 58,457,763 (GRCm39)	H136L	probably benign	Het
Or4c3	T	A	2: 89,852,009 (GRCm39)	M134L	probably benign	Het
Or51q1	A	T	7: 103,628,473 (GRCm39)	I25F	probably benign	Het
Or5h24	C	T	16: 58,919,182 (GRCm39)	V58I	unknown	Het
Or8b1	A	C	9: 38,399,835 (GRCm39)	D170A	probably benign	Het
Pcare	A	T	17: 72,057,837 (GRCm39)	S613R	probably damaging	Het
Pcnx1	G	T	12: 81,907,180 (GRCm39)	G12V	probably damaging	Het
Pkp1	T	A	1: 135,846,656 (GRCm39)	K32M	probably damaging	Het
Poc5	T	C	13: 96,533,321 (GRCm39)	W150R	probably damaging	Het
Ppp1r16b	T	A	2: 158,599,253 (GRCm39)		probably benign	Het
Prune2	T	A	19: 16,998,007 (GRCm39)	M248K	probably damaging	Het
Rb1	A	T	14: 73,450,580 (GRCm39)		probably null	Het
Rhod	A	G	19: 4,476,615 (GRCm39)	C169R	probably benign	Het
Rif1	T	C	2: 52,010,983 (GRCm39)		probably benign	Het
Rnpc3	G	A	3: 113,418,648 (GRCm39)	A100V	probably damaging	Het
Rsf1	GCGGC	GCGGCGGCGTCGGC	7: 97,229,138 (GRCm39)		probably benign	Het
Scnn1a	A	T	6: 125,319,985 (GRCm39)	D528V	possibly damaging	Het
Sdhaf3	C	A	6: 7,038,855 (GRCm39)	T59K	probably benign	Het
Sec31a	C	A	5: 100,511,698 (GRCm39)	A330S	probably damaging	Het
Sgk3	A	G	1: 9,952,097 (GRCm39)	D241G	probably damaging	Het
Skint6	T	G	4: 112,953,788 (GRCm39)	I459L	probably benign	Het
Slco1a5	A	T	6: 142,200,118 (GRCm39)	V222E	probably damaging	Het
Slit3	T	A	11: 35,598,738 (GRCm39)	N1447K	probably benign	Het
Sorbs2	A	G	8: 46,249,038 (GRCm39)	H628R	probably damaging	Het
St6galnac2	A	G	11: 116,575,353 (GRCm39)		probably benign	Het
Tbc1d31	T	C	15: 57,816,267 (GRCm39)	V667A	probably benign	Het
Tbx20	A	T	9: 24,681,016 (GRCm39)	Y159N	probably damaging	Het
Tmprss11b	T	A	5: 86,810,092 (GRCm39)	Q296L	probably benign	Het
Ttc6	T	A	12: 57,721,380 (GRCm39)		probably null	Het
Ttn	T	A	2: 76,701,243 (GRCm39)		probably benign	Het
Tubgcp4	T	A	2: 121,018,617 (GRCm39)	L340H	probably damaging	Het
Tubgcp4	T	A	2: 121,024,663 (GRCm39)	F613I	probably benign	Het
Urb1	T	C	16: 90,589,650 (GRCm39)	Y377C	probably damaging	Het
Utp15	G	A	13: 98,397,354 (GRCm39)		probably null	Het
Vstm2b	A	G	7: 40,550,707 (GRCm39)		probably null	Het
Vwde	A	T	6: 13,190,627 (GRCm39)	V488D	probably damaging	Het
Wee1	TCCCC	TCCC	7: 109,723,776 (GRCm39)		probably null	Het
Zfp276	A	T	8: 123,992,021 (GRCm39)		probably benign	Het
Zfp318	T	A	17: 46,723,975 (GRCm39)	S1993T	possibly damaging	Het
Zfp959	T	C	17: 56,204,626 (GRCm39)	L218P	probably benign	Het
Zxdc	A	G	6: 90,347,542 (GRCm39)	D301G	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
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
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'- GATTCTATAGAGATGCCATTGGGTG -3'
(R):5'- AGCTCTCTGGGATGCATTGG -3'

Sequencing Primer
(F):5'- GGGTGTTTCTTCCAGCATCACAC -3'
(R):5'- GGGATGCATTGGCCACTTACATC -3'

Posted On

2016-09-01