Mutagenetix > Incidental Mutation

Incidental Mutation 'R9459:Lrch3'

714779

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

Essential gene?

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

Stock #

R9459 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

32914100-33015647 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 32979405 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 371 (D371V)

Ref Sequence

ENSEMBL: ENSMUSP00000023491 (fasta)

Gene Model

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

AlphaFold

Q8BVU0

Predicted Effect

probably damaging
Transcript: ENSMUST00000023491
AA Change: D371V

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

SMART Domains

Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: D371V

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

possibly damaging
Transcript: ENSMUST00000135193
AA Change: D371V

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: D371V

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: ENSMUSP00000133034
Gene: ENSMUSG00000022801
AA Change: D3V

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 damaging
Transcript: ENSMUST00000165616
AA Change: D245V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: D245V

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

SMART Domains

Protein: ENSMUSP00000126308
Gene: ENSMUSG00000022801

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 damaging
Transcript: ENSMUST00000170201
AA Change: D371V

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: D371V

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: D371V

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
AA Change: D371V

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: 99.7%
20x: 98.9%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020D05Rik	T	A	19: 5,503,729	H8L	probably benign	Het
Abcb1a	T	A	5: 8,685,414		probably null	Het
Alms1	T	A	6: 85,627,964	C2199S	probably damaging	Het
Aox3	A	G	1: 58,150,309	I390V	probably benign	Het
Ap3b2	T	C	7: 81,473,903	N400S	probably benign	Het
Baalc	A	T	15: 38,934,024	N70I	probably benign	Het
Brca2	T	A	5: 150,540,629	V1286D	probably damaging	Het
Ccdc30	T	C	4: 119,377,273	R81G	possibly damaging	Het
Cd209g	T	C	8: 4,135,610	S15P	probably benign	Het
Chrnb3	G	A	8: 27,393,856	W207*	probably null	Het
Cmpk2	C	T	12: 26,478,023	T413M	probably damaging	Het
Coq4	T	A	2: 29,788,550	Y63N	probably damaging	Het
Depdc5	T	A	5: 32,990,773	S1478T	probably damaging	Het
Etf1	A	G	18: 34,906,081	F378L	probably benign	Het
Exoc6	T	C	19: 37,585,893	V324A	probably benign	Het
Frem2	A	G	3: 53,653,486	L1200P	probably benign	Het
Gadl1	T	C	9: 115,965,611	W285R	probably damaging	Het
Gbp3	A	G	3: 142,564,946		probably null	Het
Gm14295	C	T	2: 176,807,372	T5I	possibly damaging	Het
Hps4	T	C	5: 112,375,009	S578P	probably benign	Het
Kctd13	T	A	7: 126,945,082	D317E	probably damaging	Het
Kdm4b	T	A	17: 56,399,509	D881E	probably benign	Het
Klf10	G	A	15: 38,295,927	P473L	probably damaging	Het
Msh2	T	C	17: 87,678,330	S112P	possibly damaging	Het
Msh3	A	G	13: 92,215,539	V1036A	possibly damaging	Het
Mybl1	A	G	1: 9,676,259	V392A	possibly damaging	Het
Myo7a	T	C	7: 98,073,173	I1182V	possibly damaging	Het
Nectin1	A	C	9: 43,803,793	E442A	probably benign	Het
Obsl1	G	T	1: 75,498,240	H839N	probably benign	Het
Olfr1202	T	C	2: 88,817,623	F151L	probably benign	Het
Olfr1505	T	C	19: 13,919,310	C97R	possibly damaging	Het
Pacs1	C	T	19: 5,145,070		probably null	Het
Pcdh17	G	T	14: 84,448,623	E843D	probably benign	Het
Pcnt	A	G	10: 76,392,738	L1531P	probably damaging	Het
Pdgfra	A	G	5: 75,192,468	D973G	probably damaging	Het
Pkd2	A	G	5: 104,466,934	Y214C	probably damaging	Het
Plcb1	T	C	2: 135,322,638	Y427H	probably benign	Het
Ppm1h	A	G	10: 122,907,577	N402S	possibly damaging	Het
Rassf4	T	A	6: 116,641,788		probably null	Het
Ryr1	G	A	7: 29,068,643	T2856I	probably damaging	Het
Serpinb8	A	T	1: 107,605,790	K192*	probably null	Het
Slfn14	T	G	11: 83,279,372	Q482P	possibly damaging	Het
Spata2	A	G	2: 167,485,285	V64A	probably benign	Het
Tax1bp1	T	G	6: 52,729,329	V105G	probably damaging	Het
Tbc1d22a	T	G	15: 86,235,820	S142A	possibly damaging	Het
Tdrd9	T	C	12: 112,025,573	F594S	probably damaging	Het
Uba3	T	C	6: 97,189,598	I281V	probably benign	Het
Uggt2	T	C	14: 119,049,183	E723G	probably benign	Het
Usp20	C	T	2: 31,011,012	S391F	probably damaging	Het
Usp24	T	A	4: 106,342,358	D166E	probably damaging	Het
Vmn1r1	A	G	1: 182,157,938	V54A	probably benign	Het
Zfp442	T	A	2: 150,408,748	E411D	unknown	Het
Zfp804a	T	C	2: 82,259,409	I1194T	probably 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
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
R9710:Lrch3	UTSW	16	32975738	nonsense	probably null
Z1176:Lrch3	UTSW	16	32914316	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- CAAGGGTGTATACTTCAGTGGC -3'
(R):5'- TACCATCACCAACTGTTCTCAG -3'

Sequencing Primer
(F):5'- CATTACAGATGGTTGTGAGCCACC -3'
(R):5'- TGTTCTCAGTCTAGAAAGGGTAAAAG -3'

Posted On

2022-06-15