Incidental Mutation 'R1618:Lrch1'
ID 174464
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 039655-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1618 (G1)
Quality Score 225
Status Validated
Chromosome 14
Chromosomal Location 74992115-75185316 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 75051144 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 331 (D331G)
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: D331G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: D331G

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000228252
AA Change: D331G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Meta Mutation Damage Score 0.3351 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.3%
  • 20x: 89.1%
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930449E01Rik T C 14: 105,736,380 (GRCm39) noncoding transcript Het
Abca8b A T 11: 109,840,714 (GRCm39) probably benign Het
Akp3 G A 1: 87,055,593 (GRCm39) G547R unknown Het
Anln A G 9: 22,262,214 (GRCm39) probably null Het
Anpep T G 7: 79,485,165 (GRCm39) Q607P probably benign Het
Arl13b A C 16: 62,633,640 (GRCm39) probably null Het
Asxl3 T C 18: 22,650,044 (GRCm39) S678P probably damaging Het
Atf6b C T 17: 34,866,702 (GRCm39) Q58* probably null Het
Camsap3 A G 8: 3,648,740 (GRCm39) T20A probably benign Het
Cfap46 T A 7: 139,232,726 (GRCm39) M782L probably benign Het
Cngb3 T C 4: 19,364,260 (GRCm39) S155P probably benign Het
Coro1a T C 7: 126,300,719 (GRCm39) I162V probably benign Het
Cry1 T A 10: 84,982,318 (GRCm39) I343F probably damaging Het
Csnk1e A T 15: 79,309,050 (GRCm39) M292K probably benign Het
Cul7 T A 17: 46,974,116 (GRCm39) L1467H probably damaging Het
Cul9 A T 17: 46,836,818 (GRCm39) M1069K probably benign Het
Cyp2c67 C A 19: 39,631,708 (GRCm39) probably benign Het
Dnah11 T C 12: 117,979,200 (GRCm39) I2633V probably damaging Het
Eif4g3 C A 4: 137,933,369 (GRCm39) D1731E probably damaging Het
Epb41l4b T C 4: 57,032,204 (GRCm39) T592A probably benign Het
Evi5 T C 5: 107,946,984 (GRCm39) probably benign Het
Exo1 T A 1: 175,728,952 (GRCm39) M672K probably benign Het
Fcho1 T C 8: 72,163,047 (GRCm39) S661G probably damaging Het
Fnip2 A G 3: 79,415,475 (GRCm39) Y188H possibly damaging Het
Foxb1 T C 9: 69,667,293 (GRCm39) D79G probably damaging Het
Fyco1 T C 9: 123,658,346 (GRCm39) Y610C probably damaging Het
Gm3095 T A 14: 15,170,441 (GRCm39) Y97N probably damaging Het
Gm3095 C A 14: 15,170,440 (GRCm39) N96K probably damaging Het
Gmfb A T 14: 47,049,237 (GRCm39) L128* probably null Het
Gprc5c T A 11: 114,755,220 (GRCm39) V299D possibly damaging Het
Hsfy2 C T 1: 56,676,388 (GRCm39) V50I probably benign Het
Hspa12b A C 2: 130,982,849 (GRCm39) K236Q probably benign Het
Impg2 A G 16: 56,080,221 (GRCm39) Y566C probably damaging Het
Itpr3 A C 17: 27,335,581 (GRCm39) probably null Het
Kprp G A 3: 92,732,783 (GRCm39) T89I probably damaging Het
Lcmt2 T C 2: 120,969,133 (GRCm39) E650G probably damaging Het
Mroh9 T A 1: 162,852,110 (GRCm39) I860F probably benign Het
Mylk G C 16: 34,699,845 (GRCm39) E403Q possibly damaging Het
Myt1l A G 12: 29,877,396 (GRCm39) D349G unknown Het
Ndufs2 T C 1: 171,073,690 (GRCm39) T31A probably benign Het
Ndufs3 A T 2: 90,729,016 (GRCm39) S157T probably benign Het
Nfix G A 8: 85,453,155 (GRCm39) R300C probably damaging Het
Noct T A 3: 51,155,251 (GRCm39) S6R probably damaging Het
Npas2 T A 1: 39,339,808 (GRCm39) H119Q probably damaging Het
Oprl1 A T 2: 181,360,646 (GRCm39) Y207F probably benign Het
Or2n1e G A 17: 38,586,557 (GRCm39) probably null Het
Or4c11 A G 2: 88,695,871 (GRCm39) probably null Het
Or8k30 T G 2: 86,339,193 (GRCm39) L130R probably damaging Het
Palm3 G T 8: 84,756,291 (GRCm39) S601I possibly damaging Het
Plscr1 T A 9: 92,148,548 (GRCm39) C163S probably damaging Het
Ptprk A T 10: 28,369,166 (GRCm39) M713L probably benign Het
Rdm1 A G 11: 101,519,217 (GRCm39) D72G possibly damaging Het
Reln T C 5: 22,265,366 (GRCm39) D442G probably benign Het
Rims4 C T 2: 163,705,849 (GRCm39) V262M possibly damaging Het
Sbno1 T C 5: 124,542,279 (GRCm39) Y338C probably damaging Het
Seh1l T G 18: 67,921,806 (GRCm39) V222G probably damaging Het
Septin12 T C 16: 4,814,340 (GRCm39) K43R probably damaging Het
Slc25a18 A C 6: 120,763,303 (GRCm39) probably benign Het
Slc33a1 T C 3: 63,855,650 (GRCm39) T332A possibly damaging Het
Slc35d3 A G 10: 19,724,909 (GRCm39) S316P probably benign Het
Spmip7 A G 11: 11,438,641 (GRCm39) probably benign Het
Srrm2 T A 17: 24,037,906 (GRCm39) probably benign Het
Srsf12 C T 4: 33,230,974 (GRCm39) S156L probably damaging Het
Syce3 A G 15: 89,274,606 (GRCm39) M49T probably benign Het
Tjp3 T C 10: 81,112,094 (GRCm39) probably benign Het
Tnks G T 8: 35,342,430 (GRCm39) N373K probably damaging Het
Togaram1 A G 12: 65,013,847 (GRCm39) N366S possibly damaging Het
Trpm1 G A 7: 63,890,283 (GRCm39) R962H probably damaging Het
Trpm6 A T 19: 18,854,995 (GRCm39) M1885L possibly damaging Het
Tshz3 A G 7: 36,471,221 (GRCm39) D1070G probably damaging Het
Ush2a T C 1: 188,546,421 (GRCm39) M3399T probably benign Het
Utp15 G A 13: 98,393,695 (GRCm39) T196I probably benign Het
Vmn1r168 T C 7: 23,240,725 (GRCm39) I194T probably benign Het
Vmn2r73 C T 7: 85,525,120 (GRCm39) W9* probably null Het
Wdr17 T C 8: 55,092,930 (GRCm39) Y1076C probably damaging Het
Zan T C 5: 137,382,092 (GRCm39) T5152A unknown Het
Zbtb46 A T 2: 181,066,042 (GRCm39) V36E possibly damaging Het
Zfp558 T C 9: 18,380,579 (GRCm39) I9M possibly damaging Het
Zscan2 T A 7: 80,525,534 (GRCm39) Y418* probably null Het
Other mutations in Lrch1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- AAATGTCTGAGCCTTGGTTTCCCC -3'
(R):5'- GTGCAGCGTAAGCACTGTAAATCTG -3'

Sequencing Primer
(F):5'- GAGTAACTGATCATCTGCACCTC -3'
(R):5'- TGTAAATCTGTACTCACAGCCG -3'
Posted On 2014-04-24