Mutagenetix > Incidental Mutation

Incidental Mutation 'R5223:Lrch3'

402461

Institutional Source

Beutler Lab

Gene Symbol

Lrch3

Ensembl Gene

ENSMUSG00000022801

Gene Name

leucine-rich repeats and calponin homology (CH) domain containing 3

Synonyms

2210409B11Rik, LOC385628

MMRRC Submission

042796-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.123) question?

Stock #

R5223 (G1)

Quality Score

141

Status

Not validated

Chromosome

Chromosomal Location

32914100-33015647 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 32914397 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 86 (R86W)

Ref Sequence

ENSEMBL: ENSMUSP00000130009 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023491] [ENSMUST00000135193] [ENSMUST00000164486] [ENSMUST00000165616] [ENSMUST00000170201] [ENSMUST00000170899]

AlphaFold

Q8BVU0

Predicted Effect

probably damaging
Transcript: ENSMUST00000023491
AA Change: R86W

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: R86W

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	482	493	N/A	INTRINSIC
low complexity region	539	554	N/A	INTRINSIC
CH	651	754	9.24e-15	SMART
low complexity region	759	774	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000135193
AA Change: R86W

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: R86W

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	482	493	N/A	INTRINSIC
low complexity region	539	554	N/A	INTRINSIC
CH	651	755	6.79e-13	SMART
transmembrane domain	771	793	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156928

Predicted Effect

probably damaging
Transcript: ENSMUST00000164486
AA Change: R86W

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000131416
Gene: ENSMUSG00000022801
AA Change: R86W

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000165616
AA Change: R86W

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: R86W

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
Blast:LRR	89	113	1e-6	BLAST
Blast:LRR	114	137	3e-7	BLAST
low complexity region	328	339	N/A	INTRINSIC
low complexity region	385	400	N/A	INTRINSIC
CH	497	600	9.24e-15	SMART
low complexity region	605	620	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000170201
AA Change: R86W

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: R86W

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	482	493	N/A	INTRINSIC
low complexity region	539	554	N/A	INTRINSIC
CH	615	718	9.24e-15	SMART
low complexity region	723	738	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000170899
AA Change: R86W

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
AA Change: R86W

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	489	504	N/A	INTRINSIC
CH	565	668	9.24e-15	SMART
low complexity region	673	688	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.2%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	C	T	11: 120,013,452	V273M	possibly damaging	Het
Acin1	CCGC	CC	14: 54,642,941		probably null	Het
Acvr1b	T	A	15: 101,193,976	C46S	probably damaging	Het
Ahi1	A	T	10: 20,970,919	H416L	possibly damaging	Het
Aspm	T	A	1: 139,478,334	L1653Q	probably damaging	Het
Cacna1a	G	A	8: 84,587,195	V1533M	possibly damaging	Het
Ccdc33	C	T	9: 58,032,984	E502K	possibly damaging	Het
Ctnnd1	C	T	2: 84,616,789	V371M	probably damaging	Het
Cyp2a12	A	T	7: 27,036,463		probably null	Het
Ep400	A	G	5: 110,668,630	V2675A	probably damaging	Het
Foxh1	T	A	15: 76,668,729		probably null	Het
Gad1-ps	G	A	10: 99,445,147		noncoding transcript	Het
Gm10093	A	G	17: 78,492,438	E286G	probably benign	Het
Gm13078	T	A	4: 143,728,021	S296R	probably benign	Het
Gpnmb	C	T	6: 49,056,205	T539M	probably benign	Het
Hspa9	A	G	18: 34,952,671		probably null	Het
Hspg2	T	C	4: 137,543,914	L2454P	probably damaging	Het
Ift140	T	A	17: 25,035,812	I422N	probably benign	Het
Igkv6-32	T	C	6: 70,074,223	S50G	probably benign	Het
Il23r	T	A	6: 67,486,170	Y113F	probably benign	Het
Kcnt1	A	G	2: 25,903,422	D636G	probably benign	Het
Klhl41	G	A	2: 69,679,827	W569*	probably null	Het
Klra4	T	A	6: 130,062,147	D94V	probably damaging	Het
Lca5	T	A	9: 83,398,613	H378L	probably benign	Het
Lhx8	T	A	3: 154,321,644	T254S	probably damaging	Het
Lrp2	T	A	2: 69,524,053	N477I	probably damaging	Het
Man2a1	T	A	17: 64,712,271	I710K	probably benign	Het
Ncor1	A	T	11: 62,339,000	Y881N	probably damaging	Het
Nhsl1	T	A	10: 18,526,326	V1100E	probably damaging	Het
Olfr1208	T	C	2: 88,897,334	T88A	probably benign	Het
Olfr486	A	G	7: 108,172,708	V12A	probably benign	Het
Olfr855	T	C	9: 19,585,026	V163A	probably benign	Het
Oprk1	T	C	1: 5,589,296	V83A	probably benign	Het
Pacs1	C	T	19: 5,145,141	V472I	probably benign	Het
Pard3b	T	C	1: 62,344,113	Y789H	probably damaging	Het
Pcdha2	T	C	18: 36,940,791	Y492H	probably damaging	Het
Pcnt	T	C	10: 76,380,272	N2261D	probably damaging	Het
Pex5l	A	T	3: 32,958,796	S15T	probably damaging	Het
Plekhg4	A	G	8: 105,378,949	N682S	probably benign	Het
Poc5	A	T	13: 96,402,955	M335L	probably benign	Het
Polr1a	C	T	6: 71,967,907	R1316W	possibly damaging	Het
Pp2d1	T	C	17: 53,507,845	H617R	probably benign	Het
Prpsap1	T	C	11: 116,488,148	K65E	probably benign	Het
Ptgfrn	T	C	3: 101,045,593	E775G	probably benign	Het
Ptprc	T	A	1: 138,117,862	I87F	probably benign	Het
Rbbp8	C	A	18: 11,721,690	A324E	probably benign	Het
Rfx6	G	T	10: 51,677,996	G63*	probably null	Het
Rpl37a	T	C	1: 72,712,149	M47T	probably benign	Het
Samm50	T	G	15: 84,200,630	N187K	probably benign	Het
Skiv2l	A	G	17: 34,845,166		probably null	Het
Slamf9	T	C	1: 172,476,232	I48T	possibly damaging	Het
Slc2a12	A	G	10: 22,702,032	K576E	probably damaging	Het
Slc4a10	G	A	2: 62,253,366	G388S	probably damaging	Het
Smtn	G	T	11: 3,529,530	N512K	probably benign	Het
Sntb1	C	G	15: 55,642,795	G461R	probably damaging	Het
Sspo	A	G	6: 48,478,324	Y3040C	probably damaging	Het
Stat1	T	A	1: 52,144,242	V389E	probably damaging	Het
Sult5a1	A	T	8: 123,145,422	M227K	probably damaging	Het
Thsd4	T	C	9: 60,057,042	D389G	probably damaging	Het
Tnxb	T	C	17: 34,704,078	V2545A	possibly damaging	Het
Tpo	T	A	12: 30,092,590	I712F	probably damaging	Het
Trim62	T	C	4: 128,909,411	V418A	probably damaging	Het
Uqcrc1	C	A	9: 108,942,156	H95N	probably damaging	Het
Vmn2r114	ATTT	ATT	17: 23,290,932		probably null	Het
Vmn2r66	T	C	7: 85,007,885	D104G	probably benign	Het
Wdr26	T	C	1: 181,187,686	I371V	probably benign	Het
Wdr78	T	A	4: 103,049,403	S738C	possibly damaging	Het
Zfp273	T	G	13: 67,826,179	C475W	probably damaging	Het
Zfp738	G	T	13: 67,673,063	T55K	probably damaging	Het
Zmym2	A	G	14: 56,946,514	I978V	probably benign	Het

Other mutations in Lrch3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01129:Lrch3	APN	16	32994965	missense	probably benign	0.10
IGL01400:Lrch3	APN	16	32979541	missense	probably damaging	1.00
IGL02565:Lrch3	APN	16	33005714	missense	probably benign	0.00
IGL03076:Lrch3	APN	16	32981853	missense	possibly damaging	0.52
IGL03103:Lrch3	APN	16	32952137	missense	probably damaging	1.00
IGL03125:Lrch3	APN	16	32914277	missense	possibly damaging	0.83
IGL03349:Lrch3	APN	16	32955324	missense	probably damaging	1.00
eluted	UTSW	16	32986007	missense	probably null
leached	UTSW	16	32959463	missense	probably damaging	1.00
R0054:Lrch3	UTSW	16	32995852	intron	probably benign
R0123:Lrch3	UTSW	16	32961754	splice site	probably benign
R0225:Lrch3	UTSW	16	32961754	splice site	probably benign
R0326:Lrch3	UTSW	16	32979500	missense	probably damaging	1.00
R0455:Lrch3	UTSW	16	32986880	missense	probably damaging	0.99
R0734:Lrch3	UTSW	16	32997483	nonsense	probably null
R1204:Lrch3	UTSW	16	33009214	missense	probably damaging	1.00
R1470:Lrch3	UTSW	16	32988495	splice site	probably benign
R1526:Lrch3	UTSW	16	32950376	missense	probably damaging	1.00
R1597:Lrch3	UTSW	16	32950411	nonsense	probably null
R1850:Lrch3	UTSW	16	32986793	missense	probably benign	0.01
R1966:Lrch3	UTSW	16	32914385	missense	possibly damaging	0.94
R2241:Lrch3	UTSW	16	32995841	missense	probably damaging	0.99
R2313:Lrch3	UTSW	16	32961675	missense	probably damaging	1.00
R2902:Lrch3	UTSW	16	32950396	missense	probably damaging	1.00
R4723:Lrch3	UTSW	16	32988484	splice site	probably null
R4795:Lrch3	UTSW	16	33005704	missense	probably damaging	1.00
R4970:Lrch3	UTSW	16	32998513	missense	probably damaging	1.00
R5292:Lrch3	UTSW	16	32975807	missense	probably damaging	1.00
R5414:Lrch3	UTSW	16	32985965	splice site	probably null
R5470:Lrch3	UTSW	16	32998590	missense	probably damaging	1.00
R5594:Lrch3	UTSW	16	32914184	missense	probably damaging	0.99
R5843:Lrch3	UTSW	16	32998526	missense	probably damaging	1.00
R5862:Lrch3	UTSW	16	32995809	missense	probably damaging	1.00
R5911:Lrch3	UTSW	16	32959463	missense	probably damaging	1.00
R5932:Lrch3	UTSW	16	32975736	missense	probably damaging	1.00
R6519:Lrch3	UTSW	16	32994997	critical splice donor site	probably benign
R6731:Lrch3	UTSW	16	32950420	missense	probably damaging	1.00
R7182:Lrch3	UTSW	16	32993779	missense	probably benign	0.05
R7197:Lrch3	UTSW	16	32990295	missense	probably damaging	1.00
R7319:Lrch3	UTSW	16	32994993	missense	probably benign	0.19
R7392:Lrch3	UTSW	16	32986755	nonsense	probably null
R7408:Lrch3	UTSW	16	32986743	nonsense	probably null
R7414:Lrch3	UTSW	16	32998513	missense	probably damaging	1.00
R7425:Lrch3	UTSW	16	33005707	missense	probably damaging	1.00
R7909:Lrch3	UTSW	16	33009293	missense	probably benign	0.00
R7956:Lrch3	UTSW	16	32986007	missense	probably null
R8009:Lrch3	UTSW	16	33005713	missense	possibly damaging	0.72
R8247:Lrch3	UTSW	16	33009343	nonsense	probably null
R8408:Lrch3	UTSW	16	32955380	missense	probably damaging	1.00
R8686:Lrch3	UTSW	16	32981853	missense	possibly damaging	0.52
R8756:Lrch3	UTSW	16	32988440	missense	probably benign	0.33
R8947:Lrch3	UTSW	16	32981829	missense	possibly damaging	0.66
R9459:Lrch3	UTSW	16	32979405	missense	probably damaging	0.99
R9710:Lrch3	UTSW	16	32975738	nonsense	probably null
Z1176:Lrch3	UTSW	16	32914316	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- CTGGAAAACCTGCTTGTGGG -3'
(R):5'- TGCCGAGATTTCTGAGAGCG -3'

Sequencing Primer
(F):5'- AGTACTCTGGCCCTGTGG -3'
(R):5'- CCGAGATTTCTGAGAGCGATTCAAG -3'

Posted On

2016-07-22