Mutagenetix > Incidental Mutation

Incidental Mutation 'RF018:Lrch1'

603703

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

RF018 (G1)

Quality Score

217.468

Status

Not validated

Chromosome

Chromosomal Location

74992115-75185316 bp(-) (GRCm39)

Type of Mutation

frame shift

DNA Base Change (assembly)

GCTGGTGGTGT to G at 75184995 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000086363 (fasta)

Gene Model

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

AlphaFold

P62046

Predicted Effect

probably null
Transcript: ENSMUST00000088970

SMART Domains

Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015

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

probably null
Transcript: ENSMUST00000228252

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.3%
20x: 98.6%

Validation Efficiency

100% (54/54)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A030005L19Rik	GTGGCTGCT	GTGGCTGCTTTGGCTGCT	1: 82,891,293 (GRCm39)		probably benign	Het
Abca15	T	A	7: 119,993,683 (GRCm39)	V1301E	possibly damaging	Het
Adcy10	T	A	1: 165,379,678 (GRCm39)	V980E	probably damaging	Het
Aldh1a2	T	C	9: 71,192,552 (GRCm39)	V469A	probably damaging	Het
Alk	T	A	17: 72,256,808 (GRCm39)	T684S	probably benign	Het
Ankhd1	GGCGGC	GGCGGCAGCGGC	18: 36,693,965 (GRCm39)		probably benign	Het
Anks1b	G	A	10: 89,869,087 (GRCm39)	G49D	probably damaging	Het
Blm	CCTCCTCC	CCTCCTCCTCCTACTCCTCC	7: 80,162,674 (GRCm39)		probably null	Het
Btnl10	CAAA	CAAAAAA	11: 58,814,752 (GRCm39)		probably benign	Het
Ccdc81	C	A	7: 89,515,906 (GRCm39)		probably null	Het
Cd209g	A	G	8: 4,187,398 (GRCm39)	Y194C	probably benign	Het
Cenpc1	A	T	5: 86,193,228 (GRCm39)	S220R	possibly damaging	Het
Ddx42	A	T	11: 106,123,630 (GRCm39)		probably null	Het
Dock4	GTGCCGGTGCCCGT	G	12: 40,894,398 (GRCm39)		probably null	Het
Eif5b	A	T	1: 38,060,673 (GRCm39)		probably null	Het
Ell2	C	A	13: 75,911,727 (GRCm39)	H338N	probably damaging	Het
Entpd2	CTT	CTTT	2: 25,290,907 (GRCm39)		probably null	Het
Flywch1	CCACTCCTGGTGT	CCACTCCTGGTGTGGGGAGGCTACGTACTCACGCACTCCTGGTGT	17: 23,981,140 (GRCm39)		probably null	Het
Gm8369	GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	19: 11,489,106 (GRCm39)		probably null	Het
Gnat2	T	C	3: 108,003,645 (GRCm39)	S107P	unknown	Het
Guk1	T	A	11: 59,077,234 (GRCm39)	D70V	probably benign	Het
Itpkb	C	T	1: 180,160,887 (GRCm39)	R338W	probably damaging	Het
Krtap28-10	ACCACAGCCACAGCCACCACAGCCACAGCC	ACCACAGCCACAGCCCCCACAGCCACAGCCACCACAGCCACAGCC	1: 83,019,974 (GRCm39)		probably benign	Het
Lamp3	A	C	16: 19,520,000 (GRCm39)	I61R	probably benign	Het
Lrp1b	C	T	2: 41,000,919 (GRCm39)	E2216K		Het
Lrrc27	A	G	7: 138,806,016 (GRCm39)	D227G	probably benign	Het
Lrrk1	C	T	7: 66,031,250 (GRCm39)	G16E	possibly damaging	Het
Lrrtm1	T	A	6: 77,221,334 (GRCm39)	S264T	possibly damaging	Het
Lypd8	CCAATCACCAACA	CCAATCACCAACAGTTTCCTCGCCTCTGTTACCCCACCAATCACCAACA	11: 58,281,058 (GRCm39)		probably benign	Het
Mamld1	CAG	CAGAAG	X: 70,162,455 (GRCm39)		probably benign	Het
Mpo	G	C	11: 87,688,465 (GRCm39)	A375P	probably damaging	Het
Myo9a	A	G	9: 59,776,869 (GRCm39)	H1089R	probably benign	Het
Nalf2	CGCCGC	CGCCGCTGCCGC	X: 98,864,967 (GRCm39)		probably benign	Het
Ndufc2	T	C	7: 97,056,228 (GRCm39)	*109Q	probably null	Het
Nudt16	A	T	9: 105,008,898 (GRCm39)	Y28N	probably damaging	Het
Nudt4	A	T	10: 95,385,675 (GRCm39)		probably null	Het
Nusap1	AGATACACGTTAGCAGTGAGGAGCAAGCTG	AGATACACGTTAGCAGTGAGGAGCAAGCTGCGATACACGTTAGCAGTGAGGAGCAAGCTG	2: 119,458,059 (GRCm39)		probably benign	Het
Or2ag15	T	A	7: 106,340,692 (GRCm39)	I150F	probably benign	Het
P2ry12	T	A	3: 59,124,833 (GRCm39)	T281S	probably benign	Het
P4ha2	TGTTGG	T	11: 54,001,072 (GRCm39)		probably null	Het
Pcnx2	A	G	8: 126,604,258 (GRCm39)	V666A	probably damaging	Het
Pde6a	T	A	18: 61,364,475 (GRCm39)	I177N	possibly damaging	Het
Pgm1	A	T	4: 99,819,500 (GRCm39)		probably null	Het
Plce1	T	A	19: 38,705,651 (GRCm39)	W1019R	probably damaging	Het
Plch1	C	A	3: 63,628,636 (GRCm39)	K542N	probably damaging	Het
Plekhj1	T	C	10: 80,632,471 (GRCm39)	Q113R	not run	Het
Postn	A	T	3: 54,291,913 (GRCm39)	I705F	probably damaging	Het
Ppp1r15b	G	T	1: 133,059,352 (GRCm39)		probably benign	Het
Prkab1	T	C	5: 116,159,689 (GRCm39)	E59G	probably damaging	Het
Qrfprl	T	A	6: 65,433,174 (GRCm39)	Y331*	probably null	Het
Raph1	GG	GGGGG	1: 60,528,426 (GRCm39)		probably benign	Het
Rassf6	AGCAATGGGGATTC	AGCAATGGGGATTCTGCCTCACTCATGGTCCTGTAGCGCAATGGGGATTC	5: 90,756,788 (GRCm39)		probably benign	Het
Rnf144a	TCTC	TCTCTCTCTCTCTCTCACTC	12: 26,364,013 (GRCm39)		probably benign	Het
Ros1	T	A	10: 52,031,217 (GRCm39)	M484L	probably benign	Het
Rpa1	GCTGCTGCC	GC	11: 75,209,343 (GRCm39)		probably null	Het
Sectm1b	A	G	11: 120,945,756 (GRCm39)	V195A	probably benign	Het
Sirpa	TCATCAG	T	2: 129,451,123 (GRCm39)		probably null	Het
Slc28a1	T	A	7: 80,819,032 (GRCm39)		probably null	Het
Sphk1	G	C	11: 116,425,771 (GRCm39)	S42T	possibly damaging	Het
Spta1	T	C	1: 174,036,885 (GRCm39)	L1132P	probably damaging	Het
Srrt	A	T	5: 137,298,262 (GRCm39)	N303K	probably benign	Het
Ssh2	A	G	11: 77,344,880 (GRCm39)	E955G	probably damaging	Het
Strn	CCAGTC	CCAGTCCGTGCTCCCTTACCCCAGTCCGTGCTCCCTTACCACAGTC	17: 78,984,712 (GRCm39)		probably null	Het
Tchhl1	T	C	3: 93,377,691 (GRCm39)	F132L	probably benign	Het
Tex14	A	G	11: 87,405,572 (GRCm39)	E828G	probably benign	Het
Tfeb	CAG	CAGGAG	17: 48,097,020 (GRCm39)		probably benign	Het
Tmtc1	T	C	6: 148,149,009 (GRCm39)	Y699C	probably damaging	Het
Ubn1	A	G	16: 4,882,256 (GRCm39)	Y239C	probably damaging	Het
Vmn2r23	T	G	6: 123,690,075 (GRCm39)	L317R	probably benign	Het
Vmn2r78	C	T	7: 86,603,639 (GRCm39)	R606*	probably null	Het
Vps72	T	G	3: 95,028,719 (GRCm39)		probably null	Het
Zc3h11a	A	G	1: 133,554,853 (GRCm39)	S376P	possibly damaging	Het
Zfp384	GCCCAGGC	GCCCAGGCCCAGTCCCAGGC	6: 125,013,452 (GRCm39)		probably benign	Het
Zfp598	CAACCAC	CAACCACAACCAC	17: 24,899,745 (GRCm39)		probably benign	Het
Zfp628	TACTCCTCCACCC	T	7: 4,923,948 (GRCm39)		probably benign	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
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
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'- TCTAGTAACACATTCGGGCC -3'
(R):5'- AAACCTTGGCGATCGAACTGC -3'

Sequencing Primer
(F):5'- CTTGTCTCACCTGCCCGAAC -3'
(R):5'- GATCGAACTGCTGCCTCCAC -3'

Posted On

2019-12-04