Mutagenetix > Incidental Mutation

Incidental Mutation 'R4352:Lrch1'

327363

Institutional Source

Beutler Lab

Gene Symbol

Lrch1

Ensembl Gene

ENSMUSG00000068015

Gene Name

leucine-rich repeats and calponin homology (CH) domain containing 1

Synonyms

4832412D13Rik, Chdc1

MMRRC Submission

041668-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4352 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

74992115-75185316 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 75056018 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 278 (S278R)

Ref Sequence

ENSEMBL: ENSMUSP00000154004 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000088970] [ENSMUST00000228252]

AlphaFold

P62046

Predicted Effect

probably damaging
Transcript: ENSMUST00000088970
AA Change: S278R

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

SMART Domains

Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: S278R

Domain	Start	End	E-Value	Type
low complexity region	25	44	N/A	INTRINSIC
LRR	109	131	1.86e1	SMART
LRR_TYP	132	155	3.39e-3	SMART
LRR	177	199	1.41e1	SMART
LRR	200	223	4.34e-1	SMART
LRR	245	268	1.66e1	SMART
low complexity region	306	322	N/A	INTRINSIC
CH	591	698	1.71e-18	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227433

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228134

Predicted Effect

probably damaging
Transcript: ENSMUST00000228252
AA Change: S278R

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

Meta Mutation Damage Score

0.1878

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.6%

Validation Efficiency

96% (79/82)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with a leucine-rich repeat and a calponin homology domain. Polymorphism in this gene may be associated with susceptibililty to knee osteoarthritis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2010]
PHENOTYPE: Homozygous knockout leads to increased susceptibility to experimental autoimmune encephalomyelitis as a result of increased migration of T cells into the central nervous system. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	C	T	6: 128,557,349 (GRCm39)	A115T	probably benign	Het
Abtb2	T	A	2: 103,513,738 (GRCm39)	D382E	possibly damaging	Het
Adamts1	T	A	16: 85,599,234 (GRCm39)	D122V	probably benign	Het
Ankrd54	A	T	15: 78,939,662 (GRCm39)	F176I	probably benign	Het
Ano3	T	A	2: 110,576,239 (GRCm39)	E94V	possibly damaging	Het
Arid1b	A	T	17: 5,147,859 (GRCm39)	Q587L	possibly damaging	Het
Atg2a	G	A	19: 6,307,487 (GRCm39)	V1474M	probably benign	Het
Bcl2a1d	A	G	9: 88,613,552 (GRCm39)	V74A	probably damaging	Het
Bmper	A	G	9: 23,395,248 (GRCm39)	I660V	probably benign	Het
Cdh20	A	G	1: 104,906,814 (GRCm39)	D547G	probably damaging	Het
Cds2	T	A	2: 132,105,365 (GRCm39)	M1K	probably null	Het
Ctr9	T	A	7: 110,648,525 (GRCm39)	Y722N	probably damaging	Het
Ddx47	C	T	6: 134,995,018 (GRCm39)	T161I	probably benign	Het
Dvl3	T	C	16: 20,344,394 (GRCm39)	Y257H	possibly damaging	Het
Dzip1	T	C	14: 119,120,938 (GRCm39)	D673G	probably benign	Het
Efcab3	T	A	11: 104,630,140 (GRCm39)	L957Q	probably null	Het
Emilin2	T	C	17: 71,587,726 (GRCm39)	M129V	probably benign	Het
Eml1	A	T	12: 108,501,096 (GRCm39)		probably benign	Het
Espnl	A	T	1: 91,262,443 (GRCm39)	D296V	probably damaging	Het
Fam161a	T	G	11: 22,970,798 (GRCm39)	S109R	possibly damaging	Het
Fat3	T	G	9: 16,158,074 (GRCm39)	T1179P	possibly damaging	Het
Gfra1	A	T	19: 58,255,456 (GRCm39)	N330K	probably benign	Het
Gfy	T	C	7: 44,827,040 (GRCm39)	E352G	probably benign	Het
Gm20775	A	T	Y: 10,641,648 (GRCm39)		noncoding transcript	Het
Gm5885	T	A	6: 133,508,152 (GRCm39)		noncoding transcript	Het
Gpatch11	T	C	17: 79,148,446 (GRCm39)	L128P	probably damaging	Het
H2-Q1	A	G	17: 35,539,919 (GRCm39)	N63D	possibly damaging	Het
Itgb2	A	T	10: 77,392,001 (GRCm39)	N358I	probably benign	Het
Jmjd1c	A	G	10: 67,080,588 (GRCm39)	T2247A	probably damaging	Het
Kcnma1	T	A	14: 23,361,720 (GRCm39)	K1036I	probably damaging	Het
Llgl1	C	T	11: 60,600,394 (GRCm39)	P581L	probably benign	Het
Lrp2	C	A	2: 69,262,526 (GRCm39)		probably null	Het
Lyn	G	A	4: 3,789,796 (GRCm39)	R443H	probably damaging	Het
Mecom	C	A	3: 30,020,887 (GRCm39)	V452L	possibly damaging	Het
Mpzl1	G	A	1: 165,433,376 (GRCm39)	Q36*	probably null	Het
Msantd5	A	G	11: 51,125,646 (GRCm39)	N190D	possibly damaging	Het
Npr2	T	C	4: 43,646,592 (GRCm39)	S647P	probably damaging	Het
Nrp2	A	G	1: 62,777,576 (GRCm39)	D127G	probably damaging	Het
Otogl	A	T	10: 107,705,396 (GRCm39)	C644S	probably damaging	Het
Pabpc4	C	T	4: 123,184,060 (GRCm39)	T191I	probably damaging	Het
Paqr3	T	C	5: 97,247,455 (GRCm39)	T218A	probably benign	Het
Pcdh7	C	T	5: 57,879,361 (GRCm39)	S972L	possibly damaging	Het
Pcnx2	T	C	8: 126,489,590 (GRCm39)	H1668R	probably damaging	Het
Prb1b	T	G	6: 132,290,624 (GRCm39)	Y25S	unknown	Het
Ralb	A	G	1: 119,411,282 (GRCm39)	M19T	probably benign	Het
Rcan1	A	G	16: 92,190,384 (GRCm39)	I185T	probably benign	Het
Rnf38	A	T	4: 44,149,100 (GRCm39)	N82K	possibly damaging	Het
Rock1	T	A	18: 10,079,237 (GRCm39)	Q1077L	probably damaging	Het
Sesn3	C	T	9: 14,231,669 (GRCm39)	A200V	probably damaging	Het
Shh	T	C	5: 28,663,187 (GRCm39)	E327G	probably benign	Het
Shmt2	G	A	10: 127,354,686 (GRCm39)	A333V	probably damaging	Het
Slc15a2	T	A	16: 36,592,390 (GRCm39)	I256F	probably benign	Het
Sptbn5	T	C	2: 119,913,680 (GRCm39)		noncoding transcript	Het
Sst	A	G	16: 23,708,565 (GRCm39)	S89P	probably damaging	Het
Taf10	A	G	7: 105,392,614 (GRCm39)		probably benign	Het
Tas2r139	T	A	6: 42,118,689 (GRCm39)	W274R	probably damaging	Het
Tbc1d20	T	A	2: 152,150,114 (GRCm39)		probably benign	Het
Tbc1d5	A	G	17: 51,089,429 (GRCm39)	S584P	probably damaging	Het
Tcstv1a	T	C	13: 120,355,407 (GRCm39)	D75G	probably damaging	Het
Tex10	T	G	4: 48,452,039 (GRCm39)	T696P	possibly damaging	Het
Tgfbr1	T	C	4: 47,402,863 (GRCm39)	F206S	probably damaging	Het
Tmem241	A	T	18: 12,246,496 (GRCm39)	H51Q	probably benign	Het
Trim5	A	T	7: 103,926,015 (GRCm39)	V182D	probably damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Txnl1	A	G	18: 63,804,750 (GRCm39)	V248A	possibly damaging	Het
Ubr5	A	G	15: 38,041,817 (GRCm39)	V204A	probably benign	Het
Ugp2	C	T	11: 21,279,026 (GRCm39)	V387I	probably damaging	Het
Unc45b	G	A	11: 82,804,035 (GRCm39)	D71N	probably damaging	Het
Usp34	A	T	11: 23,270,727 (GRCm39)	Y37F	possibly damaging	Het
Zfp943	A	T	17: 22,212,104 (GRCm39)	I397F	probably damaging	Het

Other mutations in Lrch1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01124:Lrch1	APN	14	74,994,503 (GRCm39)	missense	probably benign	0.22
IGL01137:Lrch1	APN	14	74,994,532 (GRCm39)	missense	probably damaging	0.98
IGL01978:Lrch1	APN	14	75,023,782 (GRCm39)	missense	probably damaging	1.00
IGL01988:Lrch1	APN	14	75,032,813 (GRCm39)	splice site	probably benign
IGL02036:Lrch1	APN	14	75,032,733 (GRCm39)	splice site	probably benign
IGL02650:Lrch1	APN	14	75,051,138 (GRCm39)	missense	probably damaging	1.00
IGL03006:Lrch1	APN	14	75,051,060 (GRCm39)	missense	probably damaging	0.99
IGL03106:Lrch1	APN	14	75,073,202 (GRCm39)	missense	possibly damaging	0.84
IGL03353:Lrch1	APN	14	75,095,482 (GRCm39)	missense	probably damaging	1.00
FR4304:Lrch1	UTSW	14	75,057,005 (GRCm39)	missense	possibly damaging	0.81
LCD18:Lrch1	UTSW	14	75,142,461 (GRCm39)	intron	probably benign
R0129:Lrch1	UTSW	14	75,073,186 (GRCm39)	missense	probably benign	0.13
R0312:Lrch1	UTSW	14	75,185,034 (GRCm39)	missense	possibly damaging	0.82
R0441:Lrch1	UTSW	14	75,184,985 (GRCm39)	missense	possibly damaging	0.95
R0622:Lrch1	UTSW	14	75,033,491 (GRCm39)	missense	probably benign	0.00
R1418:Lrch1	UTSW	14	75,041,709 (GRCm39)	splice site	probably benign
R1618:Lrch1	UTSW	14	75,051,144 (GRCm39)	missense	probably damaging	1.00
R2116:Lrch1	UTSW	14	75,022,971 (GRCm39)	missense	probably damaging	1.00
R2428:Lrch1	UTSW	14	75,044,985 (GRCm39)	splice site	probably benign
R3707:Lrch1	UTSW	14	75,095,437 (GRCm39)	missense	probably damaging	0.99
R5689:Lrch1	UTSW	14	75,023,764 (GRCm39)	missense	probably damaging	1.00
R5754:Lrch1	UTSW	14	75,054,558 (GRCm39)	missense	probably damaging	1.00
R6142:Lrch1	UTSW	14	75,184,940 (GRCm39)	missense	probably damaging	1.00
R6469:Lrch1	UTSW	14	75,054,525 (GRCm39)	missense	probably damaging	1.00
R6740:Lrch1	UTSW	14	75,049,063 (GRCm39)	missense	probably benign
R6871:Lrch1	UTSW	14	75,049,063 (GRCm39)	missense	probably benign
R7051:Lrch1	UTSW	14	75,022,962 (GRCm39)	missense	probably damaging	1.00
R7438:Lrch1	UTSW	14	74,994,477 (GRCm39)	missense	possibly damaging	0.88
R7509:Lrch1	UTSW	14	75,185,048 (GRCm39)	missense	probably benign	0.25
R8037:Lrch1	UTSW	14	75,023,794 (GRCm39)	missense	probably damaging	1.00
R8262:Lrch1	UTSW	14	75,055,935 (GRCm39)	missense	probably damaging	0.97
R8302:Lrch1	UTSW	14	75,032,772 (GRCm39)	missense	probably benign	0.01
R8943:Lrch1	UTSW	14	75,032,808 (GRCm39)	missense	probably benign	0.06
R9427:Lrch1	UTSW	14	75,032,787 (GRCm39)	missense	probably benign
RF002:Lrch1	UTSW	14	75,185,014 (GRCm39)	small deletion	probably benign
RF009:Lrch1	UTSW	14	75,185,014 (GRCm39)	small deletion	probably benign
RF018:Lrch1	UTSW	14	75,184,995 (GRCm39)	frame shift	probably null
RF022:Lrch1	UTSW	14	75,185,014 (GRCm39)	small deletion	probably benign
RF023:Lrch1	UTSW	14	75,185,006 (GRCm39)	frame shift	probably null
RF037:Lrch1	UTSW	14	75,184,989 (GRCm39)	small deletion	probably benign
RF039:Lrch1	UTSW	14	75,184,989 (GRCm39)	small deletion	probably benign
RF043:Lrch1	UTSW	14	75,185,015 (GRCm39)	frame shift	probably null
RF061:Lrch1	UTSW	14	75,185,007 (GRCm39)	frame shift	probably null
RF061:Lrch1	UTSW	14	75,184,995 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- CAAAGTGTACGGATGCTGACGTC -3'
(R):5'- TTTCTGCCCAAAGTGGAATGTG -3'

Sequencing Primer
(F):5'- ACGGATGCTGACGTCAGGTTATC -3'
(R):5'- GGAAAGAGTCCTAAGAACTCTTGTG -3'

Posted On

2015-07-07