Mutagenetix > Incidental Mutation

Incidental Mutation 'R7319:Lrch3'

568089

Institutional Source

Beutler Lab

Gene Symbol

Lrch3

Ensembl Gene

ENSMUSG00000022801

Gene Name

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

Synonyms

LOC385628, 2210409B11Rik

MMRRC Submission

045415-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.100) question?

Stock #

R7319 (G1)

Quality Score

214.009

Status

Validated

Chromosome

Chromosomal Location

32734470-32836017 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 32815363 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 585 (T585A)

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: T585A

PolyPhen 2 Score 0.190 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: T585A

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: T585A

PolyPhen 2 Score 0.198 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: T585A

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: T133A

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: T167A

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: T431A

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: T431A

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: T208A

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000126308
Gene: ENSMUSG00000022801
AA Change: T208A

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: T585A

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: T585A

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: T535A

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
AA Change: T535A

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

Meta Mutation Damage Score

0.0669

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

96% (79/82)

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9930012K11Rik	A	T	14: 70,393,635 (GRCm39)	I287N	probably benign	Het
Aco2	G	T	15: 81,787,820 (GRCm39)	E223D	probably damaging	Het
Acsf3	T	A	8: 123,539,770 (GRCm39)	I466N	probably damaging	Het
Albfm1	G	A	5: 90,719,625 (GRCm39)		probably null	Het
Aox3	T	A	1: 58,191,761 (GRCm39)	F438I	probably benign	Het
Arhgap33	T	C	7: 30,225,794 (GRCm39)	T591A	probably benign	Het
Ash1l	C	T	3: 88,888,694 (GRCm39)	A191V	probably benign	Het
Btg2	T	C	1: 134,006,779 (GRCm39)	K5E	probably benign	Het
C1galt1	T	A	6: 7,871,150 (GRCm39)	Y329N	probably damaging	Het
Cacna1h	A	G	17: 25,608,435 (GRCm39)	I824T	possibly damaging	Het
Carmil3	A	G	14: 55,731,817 (GRCm39)	I182V	probably benign	Het
Ccdc150	T	A	1: 54,302,496 (GRCm39)		probably null	Het
Chek1	T	A	9: 36,633,939 (GRCm39)	R129W	probably damaging	Het
Chrna6	A	G	8: 27,896,815 (GRCm39)	M354T	possibly damaging	Het
Cpq	A	G	15: 33,250,185 (GRCm39)	T181A	probably benign	Het
Csmd2	A	T	4: 128,287,472 (GRCm39)	Y1069F		Het
Defb28	T	A	2: 152,361,974 (GRCm39)	C45S	possibly damaging	Het
Dnah1	A	G	14: 31,018,551 (GRCm39)	Y1360H	probably benign	Het
Dnah7c	T	C	1: 46,823,608 (GRCm39)	V3749A	possibly damaging	Het
Dnah7c	T	A	1: 46,819,935 (GRCm39)	D3728E	probably benign	Het
Dym	G	A	18: 75,196,245 (GRCm39)		probably null	Het
Dync2i2	G	A	2: 29,928,341 (GRCm39)	P95L	probably benign	Het
Dzip3	A	G	16: 48,747,903 (GRCm39)		probably null	Het
Eef1akmt4	A	G	16: 20,436,666 (GRCm39)	K163E	probably benign	Het
Fbrs	A	G	7: 127,081,985 (GRCm39)	T242A	possibly damaging	Het
Fgfr3	G	A	5: 33,885,146 (GRCm39)	V87M	possibly damaging	Het
Fst	A	T	13: 114,595,068 (GRCm39)	C19S	probably benign	Het
Gm7276	G	A	18: 77,273,216 (GRCm39)	R173W	unknown	Het
Gm9195	G	A	14: 72,697,929 (GRCm39)	H1284Y	probably benign	Het
Herc6	C	A	6: 57,581,074 (GRCm39)	T258K	probably damaging	Het
Hip1r	A	G	5: 124,137,174 (GRCm39)	Y678C	probably damaging	Het
Ifne	A	T	4: 88,798,243 (GRCm39)	N58K	probably damaging	Het
Ighv1-26	A	T	12: 114,752,163 (GRCm39)	H60Q	possibly damaging	Het
Ints1	A	G	5: 139,746,520 (GRCm39)	F1276L	probably damaging	Het
Itprid2	A	T	2: 79,466,416 (GRCm39)	D82V	probably damaging	Het
Kcnc4	T	A	3: 107,366,100 (GRCm39)	E36V	probably benign	Het
Kcnq2	C	T	2: 180,750,895 (GRCm39)	G315S	probably damaging	Het
Kdm4c	G	A	4: 74,255,200 (GRCm39)	V585M	probably damaging	Het
Klhl26	C	T	8: 70,905,592 (GRCm39)	R106H	probably damaging	Het
Kmo	T	C	1: 175,481,221 (GRCm39)	F313S	probably damaging	Het
Lmtk3	T	A	7: 45,443,740 (GRCm39)	S808T	unknown	Het
Lrch4	T	A	5: 137,637,977 (GRCm39)	H86Q		Het
Map3k20	A	G	2: 72,195,062 (GRCm39)	D113G	probably damaging	Het
Mbd3l1	T	C	9: 18,396,417 (GRCm39)	S181P	probably benign	Het
Mccc2	T	C	13: 100,104,241 (GRCm39)	T303A	probably benign	Het
Med27	A	G	2: 29,303,490 (GRCm39)	R147G	possibly damaging	Het
Mrps5	T	A	2: 127,437,762 (GRCm39)	S196R	possibly damaging	Het
Muc21	GGGGTGGGCATAGATCCTGAGGCAGAGCTGGATGCAGTGGTGGTCAGGGTGGG	GGGGTGGG	17: 35,932,935 (GRCm39)		probably benign	Het
Myo16	A	T	8: 10,526,185 (GRCm39)		probably null	Het
Nudt2	A	T	4: 41,477,575 (GRCm39)	M19L	probably benign	Het
Pcdha11	C	T	18: 37,146,245 (GRCm39)	P779S	probably benign	Het
Phykpl	A	G	11: 51,489,530 (GRCm39)	T379A	probably benign	Het
Plekha8	A	C	6: 54,601,206 (GRCm39)	M270L	probably benign	Het
Plekhg5	A	G	4: 152,192,885 (GRCm39)	H593R	probably benign	Het
Polr2a	T	C	11: 69,637,196 (GRCm39)	N293S	possibly damaging	Het
Pramel32	G	A	4: 88,548,184 (GRCm39)	P74S	probably benign	Het
Prex2	T	A	1: 11,232,532 (GRCm39)	N866K	probably benign	Het
Psme4	A	T	11: 30,757,790 (GRCm39)	I308L	probably benign	Het
Ptprb	T	C	10: 116,177,309 (GRCm39)	V1003A	probably benign	Het
Rbbp8	T	A	18: 11,865,269 (GRCm39)	D719E	probably damaging	Het
Rnaset2b	A	T	17: 7,259,166 (GRCm39)	D144V	probably benign	Het
Senp6	T	G	9: 80,033,481 (GRCm39)	D662E	probably damaging	Het
Serpinb3c	T	C	1: 107,200,817 (GRCm39)	N200S	possibly damaging	Het
Serpinb9g	C	G	13: 33,672,543 (GRCm39)	Y113*	probably null	Het
Sgf29	T	C	7: 126,270,821 (GRCm39)	I134T	probably benign	Het
Sh3bp4	T	G	1: 89,080,824 (GRCm39)		probably null	Het
Stab1	G	A	14: 30,862,783 (GRCm39)	L2243F	probably damaging	Het
Sympk	T	C	7: 18,769,770 (GRCm39)	V149A	probably benign	Het
Syt3	C	T	7: 44,041,953 (GRCm39)	Q271*	probably null	Het
Tas2r109	A	G	6: 132,957,663 (GRCm39)	I89T	probably benign	Het
Tgif1	A	G	17: 71,151,847 (GRCm39)	S255P	probably damaging	Het
Tm9sf1	G	A	14: 55,875,432 (GRCm39)		probably benign	Het
Tnf	A	G	17: 35,419,347 (GRCm39)	F161S	possibly damaging	Het
Topaz1	T	A	9: 122,579,428 (GRCm39)	S779R	possibly damaging	Het
Topors	A	G	4: 40,260,540 (GRCm39)	S915P	unknown	Het
Tpm4	C	T	8: 72,900,321 (GRCm39)	L161F	probably damaging	Het
Trim38	C	T	13: 23,975,384 (GRCm39)	T441I	probably damaging	Het
Trpv1	A	G	11: 73,141,620 (GRCm39)	M548V	probably benign	Het
Vmn2r68	T	A	7: 84,883,042 (GRCm39)	T237S	probably benign	Het
Zc3hav1	A	G	6: 38,309,209 (GRCm39)	S538P	probably benign	Het
Zfp541	C	T	7: 15,813,294 (GRCm39)	T649I	probably benign	Het

Other mutations in Lrch3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01129:Lrch3	APN	16	32,815,335 (GRCm39)	missense	probably benign	0.10
IGL01400:Lrch3	APN	16	32,799,911 (GRCm39)	missense	probably damaging	1.00
IGL02565:Lrch3	APN	16	32,826,084 (GRCm39)	missense	probably benign	0.00
IGL03076:Lrch3	APN	16	32,802,223 (GRCm39)	missense	possibly damaging	0.52
IGL03103:Lrch3	APN	16	32,772,507 (GRCm39)	missense	probably damaging	1.00
IGL03125:Lrch3	APN	16	32,734,647 (GRCm39)	missense	possibly damaging	0.83
IGL03349:Lrch3	APN	16	32,775,694 (GRCm39)	missense	probably damaging	1.00
eluted	UTSW	16	32,806,377 (GRCm39)	missense	probably null
leached	UTSW	16	32,779,833 (GRCm39)	missense	probably damaging	1.00
R0054:Lrch3	UTSW	16	32,816,222 (GRCm39)	intron	probably benign
R0123:Lrch3	UTSW	16	32,782,124 (GRCm39)	splice site	probably benign
R0225:Lrch3	UTSW	16	32,782,124 (GRCm39)	splice site	probably benign
R0326:Lrch3	UTSW	16	32,799,870 (GRCm39)	missense	probably damaging	1.00
R0455:Lrch3	UTSW	16	32,807,250 (GRCm39)	missense	probably damaging	0.99
R0734:Lrch3	UTSW	16	32,817,853 (GRCm39)	nonsense	probably null
R1204:Lrch3	UTSW	16	32,829,584 (GRCm39)	missense	probably damaging	1.00
R1470:Lrch3	UTSW	16	32,808,865 (GRCm39)	splice site	probably benign
R1526:Lrch3	UTSW	16	32,770,746 (GRCm39)	missense	probably damaging	1.00
R1597:Lrch3	UTSW	16	32,770,781 (GRCm39)	nonsense	probably null
R1850:Lrch3	UTSW	16	32,807,163 (GRCm39)	missense	probably benign	0.01
R1966:Lrch3	UTSW	16	32,734,755 (GRCm39)	missense	possibly damaging	0.94
R2241:Lrch3	UTSW	16	32,816,211 (GRCm39)	missense	probably damaging	0.99
R2313:Lrch3	UTSW	16	32,782,045 (GRCm39)	missense	probably damaging	1.00
R2902:Lrch3	UTSW	16	32,770,766 (GRCm39)	missense	probably damaging	1.00
R4723:Lrch3	UTSW	16	32,808,854 (GRCm39)	splice site	probably null
R4795:Lrch3	UTSW	16	32,826,074 (GRCm39)	missense	probably damaging	1.00
R4970:Lrch3	UTSW	16	32,818,883 (GRCm39)	missense	probably damaging	1.00
R5223:Lrch3	UTSW	16	32,734,767 (GRCm39)	missense	probably damaging	0.99
R5292:Lrch3	UTSW	16	32,796,177 (GRCm39)	missense	probably damaging	1.00
R5414:Lrch3	UTSW	16	32,806,335 (GRCm39)	splice site	probably null
R5470:Lrch3	UTSW	16	32,818,960 (GRCm39)	missense	probably damaging	1.00
R5594:Lrch3	UTSW	16	32,734,554 (GRCm39)	missense	probably damaging	0.99
R5843:Lrch3	UTSW	16	32,818,896 (GRCm39)	missense	probably damaging	1.00
R5862:Lrch3	UTSW	16	32,816,179 (GRCm39)	missense	probably damaging	1.00
R5911:Lrch3	UTSW	16	32,779,833 (GRCm39)	missense	probably damaging	1.00
R5932:Lrch3	UTSW	16	32,796,106 (GRCm39)	missense	probably damaging	1.00
R6519:Lrch3	UTSW	16	32,815,367 (GRCm39)	critical splice donor site	probably benign
R6731:Lrch3	UTSW	16	32,770,790 (GRCm39)	missense	probably damaging	1.00
R7182:Lrch3	UTSW	16	32,814,149 (GRCm39)	missense	probably benign	0.05
R7197:Lrch3	UTSW	16	32,810,665 (GRCm39)	missense	probably damaging	1.00
R7392:Lrch3	UTSW	16	32,807,125 (GRCm39)	nonsense	probably null
R7408:Lrch3	UTSW	16	32,807,113 (GRCm39)	nonsense	probably null
R7414:Lrch3	UTSW	16	32,818,883 (GRCm39)	missense	probably damaging	1.00
R7425:Lrch3	UTSW	16	32,826,077 (GRCm39)	missense	probably damaging	1.00
R7909:Lrch3	UTSW	16	32,829,663 (GRCm39)	missense	probably benign	0.00
R7956:Lrch3	UTSW	16	32,806,377 (GRCm39)	missense	probably null
R8009:Lrch3	UTSW	16	32,826,083 (GRCm39)	missense	possibly damaging	0.72
R8247:Lrch3	UTSW	16	32,829,713 (GRCm39)	nonsense	probably null
R8408:Lrch3	UTSW	16	32,775,750 (GRCm39)	missense	probably damaging	1.00
R8686:Lrch3	UTSW	16	32,802,223 (GRCm39)	missense	possibly damaging	0.52
R8756:Lrch3	UTSW	16	32,808,810 (GRCm39)	missense	probably benign	0.33
R8947:Lrch3	UTSW	16	32,802,199 (GRCm39)	missense	possibly damaging	0.66
R9459:Lrch3	UTSW	16	32,799,775 (GRCm39)	missense	probably damaging	0.99
R9710:Lrch3	UTSW	16	32,796,108 (GRCm39)	nonsense	probably null
Z1176:Lrch3	UTSW	16	32,734,686 (GRCm39)	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- TGGAGAGACTAGTTAGATCTTTAAAGA -3'
(R):5'- TGGCCAACTAGTAAAACCAGAAA -3'

Sequencing Primer
(F):5'- GAAGGCAAATTGCATGGC -3'
(R):5'- AACTGTGCTAAGCCTGGTGAC -3'

Posted On

2019-06-26