Mutagenetix > Incidental Mutation

Incidental Mutation 'R6740:Lrch1'

527441

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 #

R6740 (G1) of strain 613

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

74992115-75185316 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75049063 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 395 (S395P)

Ref Sequence

ENSEMBL: ENSMUSP00000154004 (fasta)

Gene Model

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

AlphaFold

P62046

Predicted Effect

probably benign
Transcript: ENSMUST00000088970
AA Change: S395P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: S395P

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: ENSMUST00000228134

Predicted Effect

probably benign
Transcript: ENSMUST00000228252
AA Change: S395P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Meta Mutation Damage Score

0.0972

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.8%

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: 8 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Cyp2e1	C	T	7: 140,343,693 (GRCm39)		probably benign	Het
Eea1	C	G	10: 95,859,855 (GRCm39)	H714D	probably benign	Het
Efcab8	A	G	2: 153,646,814 (GRCm39)	H381R	probably damaging	Het
Fer1l4	A	G	2: 155,873,142 (GRCm39)	S1313P	probably damaging	Het
Itih3	T	C	14: 30,634,644 (GRCm39)	N121S	probably benign	Het
Lgr6	C	T	1: 134,921,748 (GRCm39)	A199T	probably damaging	Het
Rnf180	G	A	13: 105,318,014 (GRCm39)	A466V	possibly damaging	Het
Zfp1006	A	C	8: 129,960,881 (GRCm39)		probably null	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
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'- GCCTCAAGCTTAGAGAGGAG -3'
(R):5'- CCCCTTTACATTCTGCAGAGG -3'

Sequencing Primer
(F):5'- CCTCAAGCTTAGAGAGGAGATGCTG -3'
(R):5'- GGCAATAAATCATGGGTTGCTC -3'

Posted On

2018-07-23