Mutagenetix > Incidental Mutation

Incidental Mutation 'R7182:Lrch3'

559077

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

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.115) question?

Stock #

R7182 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

32914100-33015647 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 32993779 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 551 (D551E)

Ref Sequence

ENSEMBL: ENSMUSP00000023491 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023491] [ENSMUST00000135193] [ENSMUST00000165616] [ENSMUST00000165826] [ENSMUST00000170201] [ENSMUST00000170899]

AlphaFold

Q8BVU0

Predicted Effect

probably benign
Transcript: ENSMUST00000023491
AA Change: D551E

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: D551E

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 benign
Transcript: ENSMUST00000135193
AA Change: D551E

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

SMART Domains

Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: D551E

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

SMART Domains

Protein: ENSMUSP00000117302
Gene: ENSMUSG00000022801
AA Change: D99E

Domain	Start	End	E-Value	Type
low complexity region	31	42	N/A	INTRINSIC
low complexity region	88	103	N/A	INTRINSIC
SCOP:d1h67a_	201	253	1e-11	SMART
Blast:CH	205	253	6e-27	BLAST

Predicted Effect

SMART Domains

Protein: ENSMUSP00000133034
Gene: ENSMUSG00000022801
AA Change: D133E

Domain	Start	End	E-Value	Type
low complexity region	122	137	N/A	INTRINSIC
SCOP:d1h67a_	230	265	9e-5	SMART
Blast:CH	234	265	7e-14	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000165616
AA Change: D397E

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

SMART Domains

Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: D397E

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 benign
Transcript: ENSMUST00000165826
AA Change: D174E

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

SMART Domains

Protein: ENSMUSP00000126308
Gene: ENSMUSG00000022801
AA Change: D174E

Domain	Start	End	E-Value	Type
low complexity region	105	116	N/A	INTRINSIC
low complexity region	162	177	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000170201
AA Change: D551E

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

SMART Domains

Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: D551E

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 benign
Transcript: ENSMUST00000170899
AA Change: D501E

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

SMART Domains

Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
AA Change: D501E

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

96% (70/73)

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930562C15Rik	T	C	16: 4,849,714	V323A	unknown	Het
AC117241.1	A	G	17: 7,352,688	V158A	unknown	Het
Acadm	A	G	3: 153,941,881		probably null	Het
Adcy10	T	G	1: 165,543,470		probably null	Het
Aldh6a1	C	T	12: 84,441,831	A94T	probably benign	Het
Ano2	T	A	6: 125,790,293	L229Q	probably damaging	Het
Cacna1h	C	T	17: 25,377,655	R1828H	probably damaging	Het
Ccdc33	A	T	9: 58,034,173		probably null	Het
Cep112	A	C	11: 108,682,844	D6A	probably benign	Het
Chd9	T	C	8: 91,006,622	F1373S	unknown	Het
Cog5	T	C	12: 31,685,708	L158P	probably damaging	Het
Col6a3	G	A	1: 90,803,678	Q1618*	probably null	Het
Dlg5	A	G	14: 24,244,856	V3A		Het
Dnah7a	T	A	1: 53,620,461		probably null	Het
Dpp10	A	T	1: 123,341,151	H716Q	probably benign	Het
Epor	A	G	9: 21,963,329	F35L	probably benign	Het
Ergic1	A	T	17: 26,654,882	Y92F		Het
Fam71a	C	T	1: 191,163,351	R365H	probably damaging	Het
Fam98a	G	A	17: 75,539,018	Q273*	probably null	Het
Fhdc1	G	A	3: 84,448,850	T429I	probably damaging	Het
Fmnl2	T	A	2: 53,107,441	L468Q	unknown	Het
Fmnl3	C	T	15: 99,321,782	R695Q	probably damaging	Het
Gabrg2	T	C	11: 41,920,506	M271V	probably damaging	Het
Gk5	G	T	9: 96,119,526	V26L	possibly damaging	Het
Gm14412	A	C	2: 177,315,615	N162K	probably benign	Het
Gm3604	T	C	13: 62,371,875	D22G	probably damaging	Het
Gm5565	G	T	5: 146,158,055	H294N	probably benign	Het
Hsf2	T	A	10: 57,505,176	D287E	possibly damaging	Het
Impdh2	G	A	9: 108,563,208	R231H	possibly damaging	Het
Irak3	T	C	10: 120,166,511	H234R	probably damaging	Het
Lrba	GTTCCCTTC	GTTC	3: 86,741,458		probably null	Het
Manba	A	T	3: 135,567,513	N736I	probably benign	Het
Map2	A	G	1: 66,412,653	D234G	possibly damaging	Het
Mdk	C	A	2: 91,930,852	K121N	unknown	Het
Mfn1	T	A	3: 32,564,220	L526Q	probably damaging	Het
Mfsd2b	A	G	12: 4,866,157		probably null	Het
Mnat1	G	T	12: 73,230,678	E233*	probably null	Het
Mtmr4	T	C	11: 87,604,605		probably null	Het
Mtrf1	A	G	14: 79,423,464	E432G	possibly damaging	Het
Muc5b	C	T	7: 141,842,645	R165C	unknown	Het
Naip6	T	A	13: 100,316,149	I135F	probably benign	Het
Nod2	A	G	8: 88,663,832	T256A	probably benign	Het
Notch4	T	A	17: 34,583,499	V1298E	probably damaging	Het
Nudc	G	T	4: 133,534,465	D169E	possibly damaging	Het
Obscn	A	T	11: 59,035,101	I5602N	probably damaging	Het
Olfr1468-ps1	G	A	19: 13,375,844	G294E	unknown	Het
Osbpl10	G	A	9: 115,067,251	D18N	probably damaging	Het
Pigk	G	A	3: 152,722,551	V72I	possibly damaging	Het
Prl8a6	C	T	13: 27,437,170	E26K	probably damaging	Het
Prpf8	A	G	11: 75,490,727	Y318C	possibly damaging	Het
Rab13	A	G	3: 90,224,763	D159G	possibly damaging	Het
Rgl2	T	C	17: 33,934,990	F457L	possibly damaging	Het
Ryr2	T	C	13: 11,759,757	H1171R	probably benign	Het
Scn4a	T	A	11: 106,330,308	I842F	probably benign	Het
Scnm1	A	T	3: 95,133,854	N14K	possibly damaging	Het
Serinc1	A	T	10: 57,524,361	I137N	probably benign	Het
Slc30a3	T	C	5: 31,086,825	Q371R	probably benign	Het
Slc30a3	A	C	5: 31,089,670	M103R	probably damaging	Het
Slco1a1	A	T	6: 141,911,839	C589S	probably damaging	Het
Slco1b2	A	G	6: 141,656,930	Y203C	probably damaging	Het
Spty2d1	A	T	7: 46,998,523	D219E	probably benign	Het
Svep1	A	T	4: 58,043,991	S3552T	probably benign	Het
Tmem62	A	G	2: 121,004,743	I516M	probably benign	Het
Trim61	A	T	8: 65,013,614	S332T	probably damaging	Het
Trmt10b	A	C	4: 45,308,520	T227P	probably benign	Het
Trpc3	T	C	3: 36,655,109	Q406R	probably benign	Het
Ttc30b	A	T	2: 75,937,949	Y153*	probably null	Het
Ush2a	A	T	1: 188,753,543	Y2950F	probably benign	Het
Usp32	C	T	11: 85,040,170	G478D	probably benign	Het
Wdfy3	A	G	5: 101,943,892	L527P	possibly damaging	Het
Wdr73	A	G	7: 80,893,678	V163A	possibly damaging	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
R5223:Lrch3	UTSW	16	32914397	missense	probably damaging	0.99
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
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'- AGTTTGTTGATGACCCTCCC -3'
(R):5'- ATTCGCTATGCATGGAGGGG -3'

Sequencing Primer
(F):5'- GTTGATGACCCTCCCTCTGC -3'
(R):5'- ACACACACTTCCATGACTTTAGGTG -3'

Posted On

2019-06-26