Mutagenetix > Incidental Mutation

Incidental Mutation 'LCD18:Lrch1'

478223

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 #

LCD18 (G1)

Quality Score

999

Status

Validated

Chromosome

Chromosomal Location

74992115-75185316 bp(-) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

C to T at 75142461 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000154004 (fasta)

Gene Model

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

AlphaFold

P62046

Predicted Effect

probably benign
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 benign
Transcript: ENSMUST00000228252

Coding Region Coverage

1x: 0.0%
3x: 0.0%
10x: 0.0%
20x: 0.0%

Validation Efficiency

88% (169/191)

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A330008L17Rik	A	G	8: 100,450,057 (GRCm39)		noncoding transcript	Het
Aff2	C	A	X: 68,791,141 (GRCm39)		probably benign	Het
Aldh1a1	C	A	19: 20,604,010 (GRCm39)		probably benign	Het
Anxa7	C	T	14: 20,519,479 (GRCm39)	G113E	probably damaging	Het
Apba2	A	T	7: 64,271,908 (GRCm39)		probably benign	Het
Apc2	G	C	10: 80,135,808 (GRCm39)		probably benign	Het
App	C	G	16: 84,822,300 (GRCm39)		probably benign	Het
Asic2	C	A	11: 80,876,570 (GRCm39)		probably benign	Het
Btk	T	C	X: 133,479,574 (GRCm39)		probably benign	Het
Car12	C	A	9: 66,668,958 (GRCm39)		probably benign	Het
Ccdc121	GAGAAG	GAG	5: 31,644,717 (GRCm39)		probably benign	Het
Ccdc191	G	A	16: 43,742,164 (GRCm39)		probably benign	Het
Ccdc34	N		2: 110,016,318 (GRCm38)		probably benign	Het
Cd164	G	T	10: 41,397,922 (GRCm39)	A59S	probably benign	Het
Cd22	C	T	7: 30,577,507 (GRCm39)	R2H	possibly damaging	Het
Cdv3	C	A	9: 103,242,553 (GRCm39)		probably benign	Het
Cdv3	A	T	9: 103,242,542 (GRCm39)		probably benign	Het
Celf2	N		2: 6,779,076 (GRCm38)		probably benign	Het
Cfap299	G	A	5: 98,855,367 (GRCm39)		probably benign	Het
Clec18a	C	A	8: 111,802,768 (GRCm39)		probably benign	Het
Cnpy3	GGATGGAT	GGATAGATAGATAGATAGATGGAT	17: 47,048,462 (GRCm39)		probably benign	Het
Cntn4	A	G	6: 106,530,901 (GRCm39)		probably benign	Het
Cntnap5c	G	C	17: 58,469,155 (GRCm39)		probably benign	Het
Col2a1	C	A	15: 97,886,862 (GRCm39)		probably null	Het
Cpne3	G	T	4: 19,563,382 (GRCm39)		probably benign	Het
Cracd	GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	5: 76,806,589 (GRCm39)		probably benign	Het
Dab1	T	G	4: 103,903,769 (GRCm39)		probably benign	Het
Dapp1	G	A	3: 137,645,161 (GRCm39)		probably benign	Het
Dcc	G	A	18: 72,430,518 (GRCm39)		probably benign	Het
Dcun1d1	GAAAAAAAAA	GAAAAAAAAAA	3: 35,992,154 (GRCm39)		probably benign	Het
Dennd1b	G	A	1: 139,042,502 (GRCm39)		probably benign	Het
Dhdds	TAA	TA	4: 133,697,674 (GRCm39)		probably benign	Het
Dnah12	G	T	14: 26,571,342 (GRCm39)	G2817V	probably damaging	Het
Dnm3	CATATATATATATATATATATATA	CATATATATATATATATATATA	1: 162,234,130 (GRCm39)		probably benign	Het
Dock10	N		1: 80,716,623 (GRCm38)		probably benign	Het
Dusp10	G	T	1: 183,769,253 (GRCm39)	C73F	probably damaging	Het
Fgf20	A	C	8: 40,745,359 (GRCm39)		probably benign	Het
Ftsj3	G	T	11: 106,140,885 (GRCm39)		probably benign	Het
Gls	T	G	1: 52,222,526 (GRCm39)		probably benign	Het
Gm12130	T	C	11: 38,397,750 (GRCm39)		noncoding transcript	Het
Gm14936	G	A	X: 111,908,447 (GRCm39)		noncoding transcript	Het
Gm16630	C	T	6: 48,118,203 (GRCm39)		noncoding transcript	Het
Gm22194	AGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	10: 11,816,707 (GRCm39)		noncoding transcript	Het
Gm26917	C	G	17: 40,154,862 (GRCm39)		noncoding transcript	Het
Gm35048	GACACACACACACACACACACACACACACACACACACAC	GACACACACACACACACACACACACACACACACACAC	1: 90,449,248 (GRCm39)		noncoding transcript	Het
Gm37311	G	A	16: 77,415,169 (GRCm39)		noncoding transcript	Het
Gm37928	AACACACACACACACACACACACACACACACACA	AACACACACACACACACACACACACACACACACACA	3: 118,328,206 (GRCm39)		noncoding transcript	Het
Gm4302	T	C	10: 100,177,306 (GRCm39)	W197R	probably benign	Het
H2-Q4	G	A	17: 35,599,381 (GRCm39)	D155N	probably damaging	Het
H2-T23	T	C	17: 36,342,108 (GRCm39)		probably benign	Het
Hgs	CTTTTTTT	CTTTTTT	11: 120,360,404 (GRCm39)		probably benign	Het
Ighv5-9	C	T	12: 113,625,497 (GRCm39)	S82N	probably benign	Het
Il1rap	C	A	16: 26,450,343 (GRCm39)		probably benign	Het
Inhbc	N		10: 127,367,140 (GRCm38)		probably benign	Het
Inpp4b	C	T	8: 82,419,639 (GRCm39)		probably benign	Het
Kars1	N		8: 111,993,708 (GRCm38)		probably benign	Het
Kcng4	G	T	8: 120,360,258 (GRCm39)	Y39*	probably null	Het
Kcnh7	A	G	2: 62,880,143 (GRCm39)		probably benign	Het
Klhl1	G	C	14: 96,555,166 (GRCm39)		probably benign	Het
Lrp1b	G	C	2: 42,127,574 (GRCm39)		probably benign	Het
Lsm8	G	A	6: 18,844,315 (GRCm39)		probably benign	Het
Lsm8	G	A	6: 18,854,320 (GRCm39)		probably benign	Het
Magi2	T	C	5: 20,159,509 (GRCm39)		probably benign	Het
Matcap2	N		9: 22,442,083 (GRCm38)		probably benign	Het
Mef2c	G	A	13: 83,753,942 (GRCm39)		probably benign	Het
Mei4	A	G	9: 82,069,012 (GRCm39)		probably benign	Het
Mid1	T	A	X: 168,788,560 (GRCm39)		probably benign	Het
Mndal	G	C	1: 173,707,784 (GRCm39)		probably benign	Het
Mpped2	C	A	2: 106,551,773 (GRCm39)		probably benign	Het
Mtarc2	TAGGCAGCCAATCAGAGCACTGCCTCTCAGCGCCAGGCAGCCAATCAGAGCACTGCCTCTCAGCGCCAGGCA	TAGGCAGCCAATCAGAGCACTGCCTCTCAGCGCCAGGCA	1: 184,554,985 (GRCm39)		probably benign	Het
Mtf1	A	G	4: 124,723,109 (GRCm39)		probably benign	Het
Mxd1	T	C	6: 86,644,388 (GRCm39)		probably benign	Het
Nbea	G	T	3: 55,608,948 (GRCm39)		probably benign	Het
Ncor1	N		11: 62,419,782 (GRCm38)		probably benign	Het
Nox4	A	G	7: 86,892,275 (GRCm39)		probably benign	Het
Ocln	C	T	13: 100,657,075 (GRCm39)		probably benign	Het
Ofcc1	G	A	13: 40,246,443 (GRCm39)		probably benign	Het
Or5af2	T	A	11: 58,708,266 (GRCm39)	V144D	possibly damaging	Het
Paics	N		5: 76,956,744 (GRCm38)		probably null	Het
Paqr8	G	T	1: 20,984,882 (GRCm39)		probably benign	Het
Pate9	T	C	9: 36,444,849 (GRCm39)		probably benign	Het
Pdss1	C	T	2: 22,790,980 (GRCm39)		probably benign	Het
Piezo1	G	A	8: 123,222,308 (GRCm39)	R503W	probably damaging	Het
Pkhd1	G	A	1: 20,681,638 (GRCm39)		probably benign	Het
Ppp1r3f	C	A	X: 7,426,575 (GRCm39)	G562V	probably damaging	Het
Prr16	C	T	18: 51,333,396 (GRCm39)		probably benign	Het
Prss38	T	G	11: 59,266,467 (GRCm39)		probably benign	Het
Prxl2c	G	A	13: 64,435,099 (GRCm39)		probably benign	Het
Ptprk	T	C	10: 28,450,983 (GRCm39)		probably benign	Het
Pum1	N		4: 130,730,549 (GRCm38)		probably benign	Het
Rabgef1	N		5: 130,187,586 (GRCm38)		probably null	Het
Rgs16	G	A	1: 153,619,976 (GRCm39)		probably benign	Het
Riok3	G	T	18: 12,263,039 (GRCm39)		probably benign	Het
Rn18s-rs5	T	C	17: 40,159,446 (GRCm39)		noncoding transcript	Het
Robo2	N		16: 74,055,954 (GRCm38)		probably benign	Het
Rps6ka3	A	G	X: 158,062,211 (GRCm39)		probably benign	Het
Rptn	T	A	3: 93,304,848 (GRCm39)	L727Q	probably benign	Het
Slc25a46	C	A	18: 31,730,366 (GRCm39)		probably benign	Het
Spata31f1e	T	C	4: 42,792,885 (GRCm39)	T416A	probably benign	Het
Spsb1	C	T	4: 150,036,943 (GRCm39)		probably benign	Het
Tbc1d19	A	C	5: 53,974,051 (GRCm39)		probably benign	Het
Trav7-4	C	T	14: 53,698,975 (GRCm39)	L41F	probably benign	Het
Trip12	N		1: 84,754,482 (GRCm38)		probably benign	Het
Ttc13	G	A	8: 125,402,605 (GRCm39)		probably benign	Het
Ttll6	C	T	11: 96,046,084 (GRCm39)		probably benign	Het
Unc5b	C	G	10: 60,621,950 (GRCm39)		probably benign	Het
Vmn2r87	C	T	10: 130,314,583 (GRCm39)	M334I	probably benign	Het
Vps13b	G	T	15: 35,847,103 (GRCm39)	A2629S	probably damaging	Het
Wars2	N		3: 99,214,774 (GRCm38)		probably null	Het
Zdhhc3	AACACACACACACACACACACACACACACACAC	AACACACACACACACACACACACACACACACACAC	9: 122,912,087 (GRCm39)		probably benign	Het
Zfp26	C	A	9: 20,349,842 (GRCm39)	A241S	probably benign	Het
Zfp442	C	T	2: 150,261,768 (GRCm39)		probably benign	Het
Zfp808	C	T	13: 62,314,465 (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
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
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'- AGACCCAGGAACATGGCTAG -3'
(R):5'- CCTATGAACATCTGGGCTTGAG -3'

Sequencing Primer
(F):5'- GCAATCTGAAGTCTGAGGTCATCC -3'
(R):5'- CATCTGGGCTTGAGATGTTTCG -3'

Posted On

2017-05-26