Mutagenetix > Incidental Mutation

Incidental Mutation 'R2116:Lrch1'

233193

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

040120-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2116 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

74992115-75185316 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 75022971 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 634 (P634L)

Ref Sequence

ENSEMBL: ENSMUSP00000086363 (fasta)

Gene Model

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

AlphaFold

P62046

Predicted Effect

probably damaging
Transcript: ENSMUST00000088970
AA Change: P634L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: P634L

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: ENSMUST00000226799

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228134

Predicted Effect

probably damaging
Transcript: ENSMUST00000228252
AA Change: P607L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229311

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230218

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230381

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.5%
20x: 95.9%

Validation Efficiency

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: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts20	A	G	15: 94,253,243 (GRCm39)	C377R	probably damaging	Het
Adgrv1	T	C	13: 81,677,132 (GRCm39)	K1180E	probably benign	Het
Ankle1	A	G	8: 71,860,562 (GRCm39)	T340A	probably benign	Het
Armc2	A	T	10: 41,839,663 (GRCm39)	L434Q	probably damaging	Het
Ash1l	C	T	3: 88,890,571 (GRCm39)	L817F	probably benign	Het
Atm	C	T	9: 53,412,269 (GRCm39)	E960K	probably benign	Het
Bend5	G	T	4: 111,272,436 (GRCm39)	R22L	probably benign	Het
Cacng6	C	T	7: 3,479,020 (GRCm39)	T133I	probably damaging	Het
Cep120	G	A	18: 53,873,208 (GRCm39)	T41I	probably damaging	Het
Ciz1	T	C	2: 32,257,477 (GRCm39)	L174P	probably damaging	Het
Cmah	G	A	13: 24,612,880 (GRCm39)	D26N	probably benign	Het
Cnot1	A	C	8: 96,452,781 (GRCm39)	D2098E	probably damaging	Het
Cnot10	A	C	9: 114,455,504 (GRCm39)	S207R	probably damaging	Het
Col14a1	A	G	15: 55,271,160 (GRCm39)	T638A	unknown	Het
Coro1a	T	C	7: 126,301,194 (GRCm39)	E102G	probably damaging	Het
Ddx27	A	C	2: 166,869,684 (GRCm39)	D373A	probably benign	Het
Defb38	A	T	8: 19,073,483 (GRCm39)	Y63*	probably null	Het
Dhx37	A	G	5: 125,498,166 (GRCm39)	V681A	probably damaging	Het
Dmxl1	T	A	18: 50,011,884 (GRCm39)	L1347H	probably damaging	Het
Dnmt3l	C	A	10: 77,899,130 (GRCm39)	L110I	probably damaging	Het
Gcn1	A	T	5: 115,736,884 (GRCm39)	M1276L	probably benign	Het
Gfus	A	G	15: 75,797,991 (GRCm39)	F223S	probably damaging	Het
Gm10277	TC	T	11: 77,676,828 (GRCm39)		probably null	Het
Gm12790	G	A	4: 101,824,848 (GRCm39)	T140I	possibly damaging	Het
Golga3	A	T	5: 110,335,261 (GRCm39)	M192L	probably damaging	Het
H2-T22	A	T	17: 36,349,949 (GRCm39)		probably null	Het
Hectd2	C	A	19: 36,591,824 (GRCm39)	T675K	probably damaging	Het
Hinfp	T	C	9: 44,210,912 (GRCm39)	N116S	probably damaging	Het
Hoatz	A	G	9: 51,012,384 (GRCm39)	S79P	possibly damaging	Het
Hs6st3	T	A	14: 120,106,699 (GRCm39)	L369Q	probably damaging	Het
Ift74	A	G	4: 94,515,496 (GRCm39)	T138A	probably benign	Het
Ipo7	T	A	7: 109,650,325 (GRCm39)	Y792N	probably damaging	Het
Jak1	A	T	4: 101,036,872 (GRCm39)	I256N	probably damaging	Het
Kcnd2	T	A	6: 21,216,431 (GRCm39)	L45Q	probably damaging	Het
Klhl3	A	T	13: 58,166,805 (GRCm39)	V342E	probably damaging	Het
Krt28	A	C	11: 99,255,943 (GRCm39)	S439A	probably benign	Het
L3mbtl1	T	A	2: 162,801,990 (GRCm39)		probably null	Het
Lrp1	C	T	10: 127,412,362 (GRCm39)	W1314*	probably null	Het
Lrwd1	T	A	5: 136,159,332 (GRCm39)	Y431F	probably damaging	Het
Lyst	A	G	13: 13,810,286 (GRCm39)	E652G	probably damaging	Het
Mageb3	A	G	2: 121,785,033 (GRCm39)	V223A	probably damaging	Het
Map1b	G	T	13: 99,567,152 (GRCm39)	S1856R	unknown	Het
Mecom	T	A	3: 30,019,607 (GRCm39)	Q759L	probably damaging	Het
Mfsd6	T	A	1: 52,700,134 (GRCm39)	R671S	probably benign	Het
Mllt10	A	G	2: 18,167,380 (GRCm39)	N435S	probably benign	Het
Mta2	T	C	19: 8,920,880 (GRCm39)	I27T	probably damaging	Het
Ndufab1	A	G	7: 121,700,987 (GRCm39)	L20P	probably benign	Het
Nfatc2ip	T	A	7: 125,984,280 (GRCm39)	Y371F	probably damaging	Het
Nhlrc1	A	C	13: 47,167,661 (GRCm39)	S199A	probably benign	Het
Nipa1	G	T	7: 55,635,273 (GRCm39)	N113K	possibly damaging	Het
Nlgn1	T	A	3: 26,187,414 (GRCm39)	N157I	probably damaging	Het
Nlrp1a	T	A	11: 71,005,326 (GRCm39)	K630*	probably null	Het
Nmi	T	C	2: 51,838,719 (GRCm39)	T272A	probably benign	Het
Nr1i3	T	A	1: 171,046,163 (GRCm39)	L181Q	probably damaging	Het
Nrxn1	A	T	17: 91,011,705 (GRCm39)	I308K	probably damaging	Het
Nup50l	A	T	6: 96,141,841 (GRCm39)	V401E	probably damaging	Het
Or14a256	T	C	7: 86,265,286 (GRCm39)	D189G	probably benign	Het
Or52z15	T	C	7: 103,332,519 (GRCm39)	I188T	probably damaging	Het
Or5al7	A	T	2: 85,993,073 (GRCm39)	Y73*	probably null	Het
Or8g50	T	A	9: 39,648,600 (GRCm39)	M163K	probably damaging	Het
Osgin2	G	A	4: 16,008,648 (GRCm39)	T51M	probably damaging	Het
Pkd1l2	T	A	8: 117,757,461 (GRCm39)	T1526S	possibly damaging	Het
Pkhd1l1	G	T	15: 44,432,878 (GRCm39)	A3378S	probably damaging	Het
Plg	A	T	17: 12,603,364 (GRCm39)	D90V	probably damaging	Het
Plppr3	A	T	10: 79,701,572 (GRCm39)	D423E	probably benign	Het
Prpf8	T	C	11: 75,378,547 (GRCm39)	V66A	possibly damaging	Het
Psg19	A	T	7: 18,528,180 (GRCm39)	Y188N	probably damaging	Het
Ptgs1	C	A	2: 36,127,708 (GRCm39)	S89*	probably null	Het
Ptx3	T	A	3: 66,132,187 (GRCm39)	I236N	probably damaging	Het
Pygm	A	G	19: 6,436,438 (GRCm39)	N100S	probably damaging	Het
Reps1	A	G	10: 18,000,668 (GRCm39)	E760G	probably damaging	Het
Rgs7	T	A	1: 174,918,639 (GRCm39)	N235I	probably damaging	Het
Rgsl1	T	A	1: 153,693,295 (GRCm39)	M629L	probably benign	Het
Rrh	T	C	3: 129,604,336 (GRCm39)	I288M	probably damaging	Het
Sctr	A	T	1: 119,959,312 (GRCm39)	D70V	probably damaging	Het
Sec11c	A	T	18: 65,933,720 (GRCm39)	T9S	probably benign	Het
Spty2d1	C	T	7: 46,645,933 (GRCm39)	G570D	probably damaging	Het
Stx1b	T	C	7: 127,410,077 (GRCm39)	E153G	probably damaging	Het
Synm	G	A	7: 67,383,343 (GRCm39)	R1440W	probably benign	Het
Tcof1	T	C	18: 60,965,857 (GRCm39)	E415G	possibly damaging	Het
Tgfb1i1	G	A	7: 127,851,977 (GRCm39)	R353H	probably damaging	Het
Thbs3	T	C	3: 89,126,699 (GRCm39)	F271S	probably damaging	Het
Tlr5	T	C	1: 182,803,194 (GRCm39)	W833R	probably damaging	Het
Tmem132b	A	G	5: 125,699,615 (GRCm39)	E92G	probably damaging	Het
Tmem221	T	C	8: 72,010,472 (GRCm39)	Y133C	probably damaging	Het
Tmem229b-ps	A	G	10: 53,351,552 (GRCm39)		noncoding transcript	Het
Tnxb	T	C	17: 34,891,201 (GRCm39)	C515R	probably damaging	Het
Trp53rka	T	A	2: 165,333,415 (GRCm39)	N158I	probably damaging	Het
Usp20	T	A	2: 30,906,317 (GRCm39)	C562S	probably damaging	Het
Usp31	C	T	7: 121,247,919 (GRCm39)	V1175M	probably benign	Het
Veph1	G	T	3: 65,964,610 (GRCm39)	N806K	probably benign	Het
Vmn1r223	G	T	13: 23,433,832 (GRCm39)	C142F	probably damaging	Het
Vmn2r80	A	T	10: 79,030,558 (GRCm39)	S795C	probably benign	Het
Wdr41	A	G	13: 95,151,537 (GRCm39)		probably null	Het
Zfp617	A	T	8: 72,686,009 (GRCm39)	H113L	probably benign	Het
Zfp715	T	A	7: 42,947,370 (GRCm39)	R863S	possibly 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
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
R4352:Lrch1	UTSW	14	75,056,018 (GRCm39)	missense	probably damaging	0.98
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'- AGTGAAAATTCTGCTTCCTTGC -3'
(R):5'- TTGTCCCCTCACTGACAAGAG -3'

Sequencing Primer
(F):5'- GTGAAAATTCTGCTTCCTTGCTTTGC -3'
(R):5'- GAGCACTTGGGTTTATACATACTTGC -3'

Posted On

2014-09-18