Mutagenetix > Incidental Mutations

Incidental Mutation 'R3797:Limch1'

272791

Institutional Source

Beutler Lab

Gene Symbol

Limch1

Ensembl Gene

ENSMUSG00000037736

Gene Name

LIM and calponin homology domains 1

Synonyms

3732412D22Rik

MMRRC Submission

040758-MU

Accession Numbers

Is this an essential gene?

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

Stock #

R3797 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

66745827-67057158 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 66969079 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 8 (T8A)

Ref Sequence

ENSEMBL: ENSMUSP00000043163 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000038188
AA Change: T8A

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

SMART Domains

Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: T8A

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: T164A

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: T164A

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: T5A

PolyPhen 2 Score 0.428 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: T5A

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: T164A

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: T164A

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 benign
Transcript: ENSMUST00000119854
AA Change: T164A

PolyPhen 2 Score 0.273 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: T164A

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 damaging
Transcript: ENSMUST00000122812
AA Change: T5A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

Predicted Effect

probably benign
Transcript: ENSMUST00000127184
AA Change: T8A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736
AA Change: T8A

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: T17A

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

SMART Domains

Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736
AA Change: T17A

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: ENSMUST00000201848

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201852

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202048

Meta Mutation Damage Score

0.0618

Coding Region Coverage

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

Validation Efficiency

100% (39/39)

Allele List at MGI

Other mutations in this stock

Total: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrf3	T	C	5: 30,196,823	I736V	possibly damaging	Het
Alpk3	C	A	7: 81,092,753	P773T	probably benign	Het
B4galt1	G	A	4: 40,807,258	T376I	probably benign	Het
Basp1	C	A	15: 25,364,312		probably benign	Het
Capn5	C	T	7: 98,125,829	G535R	probably null	Het
Ccdc170	G	A	10: 4,560,920	V660I	possibly damaging	Het
Cdc73	A	T	1: 143,677,723	D215E	probably benign	Het
Clec14a	G	A	12: 58,267,909	A309V	probably benign	Het
Clns1a	G	A	7: 97,696,835	G36R	probably benign	Het
Cops7a	C	T	6: 124,959,832	R252H	probably damaging	Het
Csmd2	C	T	4: 128,517,595	P2469S	probably benign	Het
Dsp	T	A	13: 38,177,284		probably null	Het
Eif3d	A	G	15: 77,968,569	F4S	probably damaging	Het
Ephb1	T	C	9: 101,971,267	T611A	probably damaging	Het
Fam43b	G	C	4: 138,395,098	R304G	probably benign	Het
Fgfr1	G	A	8: 25,572,437	D663N	probably damaging	Het
Gm5592	G	A	7: 41,157,835		probably benign	Het
Itgb8	T	C	12: 119,163,469	I683M	possibly damaging	Het
Kcnip3	A	G	2: 127,482,014	S32P	probably benign	Het
Lmf1	G	A	17: 25,654,471	V317M	probably damaging	Het
Ltbp1	A	G	17: 75,362,630	Q1455R	probably damaging	Het
Marc2	T	C	1: 184,841,308	E131G	possibly damaging	Het
Olfr620	C	T	7: 103,611,447	R302Q	probably benign	Het
Pak7	T	C	2: 136,100,826	I465V	probably benign	Het
Pcdhgb8	T	C	18: 37,762,675	I266T	probably benign	Het
Pde4d	T	C	13: 109,632,897	S40P	probably benign	Het
Phrf1	C	T	7: 141,259,918	R243*	probably null	Het
Polk	A	T	13: 96,486,982		probably benign	Het
Ppl	T	C	16: 5,104,550		probably benign	Het
Rab11fip3	A	G	17: 26,068,526	C218R	possibly damaging	Het
Setd2	T	C	9: 110,549,571	V818A	probably benign	Het
Skida1	C	A	2: 18,045,897	E815*	probably null	Het
Slc35g3	A	G	11: 69,760,917	F103L	probably benign	Het
Svil	T	A	18: 5,060,534	C802S	probably benign	Het
Trim7	A	G	11: 48,845,670		probably null	Het
Ugt3a1	G	A	15: 9,310,641	W336*	probably null	Het
Vmn2r72	T	C	7: 85,738,077	S760G	probably benign	Het
Vps13a	T	C	19: 16,745,947		probably null	Het
Wdfy4	A	T	14: 33,140,645	I590N	probably damaging	Het
Xdh	T	C	17: 73,907,658	E764G	probably damaging	Het
Xpnpep1	A	T	19: 53,006,342	V285D	probably benign	Het
Zfp934	T	C	13: 62,517,888	K313R	probably benign	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
R1648: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
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	splice site	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
R8079:Limch1	UTSW	5	67046753	missense	possibly damaging	0.73
R8229:Limch1	UTSW	5	67028795	missense	probably damaging	1.00
R8348:Limch1	UTSW	5	67002482	missense	probably damaging	0.98
R8395:Limch1	UTSW	5	66969051	missense	probably damaging	0.96
R8416:Limch1	UTSW	5	66999306	missense	probably benign
R8448:Limch1	UTSW	5	67002482	missense	probably damaging	0.98
R8477:Limch1	UTSW	5	66974565	missense	probably benign	0.01
X0022:Limch1	UTSW	5	67021952	missense	probably benign	0.00
X0027:Limch1	UTSW	5	67002620	missense	probably damaging	1.00
Z1177:Limch1	UTSW	5	67028799	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACAACTTTATGGGATGTGAGTTGC -3'
(R):5'- TCACTGCTTCCCCTGAGAAC -3'

Sequencing Primer
(F):5'- TGCTATACTAATTGAAAGGATGGAGC -3'
(R):5'- CCTGAGAACTACATCTGGCG -3'

Posted On

2015-03-25