Incidental Mutation 'R8943:Lrch1'
ID 681119
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 068782-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8943 (G1)
Quality Score 225.009
Status Validated
Chromosome 14
Chromosomal Location 74992115-75185316 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 75032808 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Lysine at position 514 (I514K)
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: I514K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: I514K

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 probably benign
Transcript: ENSMUST00000228252
AA Change: I514K

PolyPhen 2 Score 0.056 (Sensitivity: 0.94; Specificity: 0.84)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.5%
Validation Efficiency 98% (50/51)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610021A01Rik T C 7: 41,275,667 (GRCm39) S457P probably damaging Het
Aak1 A G 6: 86,964,234 (GRCm39) N945S unknown Het
Actr1a C A 19: 46,369,438 (GRCm39) R192L possibly damaging Het
Adgrl2 T A 3: 148,534,119 (GRCm39) N1036I probably damaging Het
Ak5 A G 3: 152,361,511 (GRCm39) V137A probably damaging Het
Aldh1a2 T C 9: 71,169,055 (GRCm39) V179A probably damaging Het
Ap2b1 A T 11: 83,237,579 (GRCm39) I548F probably damaging Het
Arhgef10l A G 4: 140,292,550 (GRCm39) Y352H probably damaging Het
Atad5 C T 11: 79,986,524 (GRCm39) T537M possibly damaging Het
Atoh7 A G 10: 62,935,938 (GRCm39) K2E possibly damaging Het
BC061237 A G 14: 44,741,658 (GRCm39) I134V probably benign Het
Cadm1 T C 9: 47,701,136 (GRCm39) I141T probably damaging Het
Capn10 T C 1: 92,871,454 (GRCm39) S351P probably damaging Het
Cct6b T C 11: 82,654,959 (GRCm39) probably benign Het
Cd19 T C 7: 126,011,330 (GRCm39) T284A probably benign Het
Cfap53 A G 18: 74,432,253 (GRCm39) Y47C probably damaging Het
Cldn18 T C 9: 99,578,162 (GRCm39) M194V probably benign Het
Dgkb T A 12: 38,652,777 (GRCm39) Y721N probably damaging Het
Dmbt1 A G 7: 130,721,372 (GRCm39) Q1880R possibly damaging Het
Dock2 T C 11: 34,599,646 (GRCm39) N311S possibly damaging Het
Dpysl5 G T 5: 30,935,375 (GRCm39) M159I probably benign Het
Eif2b3 G A 4: 116,901,778 (GRCm39) G147E probably damaging Het
Fam193a A G 5: 34,597,796 (GRCm39) D531G probably benign Het
Fndc3b T C 3: 27,555,329 (GRCm39) probably benign Het
Foxe3 C A 4: 114,782,523 (GRCm39) A230S unknown Het
Gm5591 A T 7: 38,219,727 (GRCm39) V382E probably benign Het
Gm7995 A T 14: 42,132,228 (GRCm39) N21I probably damaging Het
Ipo8 G A 6: 148,676,547 (GRCm39) P981S probably benign Het
Kcnh8 A G 17: 53,104,486 (GRCm39) D161G probably benign Het
Krt71 A G 15: 101,645,180 (GRCm39) I377T possibly damaging Het
Krt75 A T 15: 101,476,767 (GRCm39) M374K probably benign Het
Krt9 TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC 11: 100,079,903 (GRCm39) probably benign Het
Lpcat1 A G 13: 73,662,029 (GRCm39) T409A probably benign Het
Mc4r A C 18: 66,993,110 (GRCm39) M1R probably null Het
Mthfd1l A T 10: 3,978,466 (GRCm39) H442L probably damaging Het
Or5d38 T A 2: 87,954,718 (GRCm39) I204F probably damaging Het
Pdcd1lg2 T C 19: 29,423,553 (GRCm39) M199T probably benign Het
Pigg G A 5: 108,484,066 (GRCm39) V438M probably damaging Het
Pira12 T C 7: 3,898,365 (GRCm39) E319G probably benign Het
Ppfibp1 T A 6: 146,920,681 (GRCm39) probably null Het
Rbm15 T A 3: 107,239,372 (GRCm39) Y342F possibly damaging Het
Rhbdl1 A T 17: 26,054,116 (GRCm39) V278E probably damaging Het
Ryr3 T C 2: 112,465,669 (GRCm39) N4781S probably damaging Het
Scn7a A T 2: 66,525,206 (GRCm39) silent Het
Sfswap A G 5: 129,581,168 (GRCm39) R114G probably damaging Het
Sohlh2 C A 3: 55,104,282 (GRCm39) A258D possibly damaging Het
Sstr4 T A 2: 148,237,782 (GRCm39) V131D possibly damaging Het
Tenm2 T C 11: 36,834,861 (GRCm39) T45A probably damaging Het
Tmem131l A T 3: 83,831,479 (GRCm39) F818I probably damaging Het
Trappc6b A G 12: 59,097,149 (GRCm39) F58L probably damaging Het
Vmn1r229 A T 17: 21,035,418 (GRCm39) H221L possibly damaging Het
Vmn1r33 T A 6: 66,588,783 (GRCm39) Y257F probably damaging Het
Wdfy3 T C 5: 101,993,231 (GRCm39) probably benign Het
Zfp446 C T 7: 12,713,564 (GRCm39) Q177* probably null Het
Zup1 A G 10: 33,795,301 (GRCm39) *552Q 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
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
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'- CCGACTAGAACTGGCAAAGC -3'
(R):5'- GGCTTTGTGTCACTGCAAGATG -3'

Sequencing Primer
(F):5'- TGGCAAAGCTCATATTACTCACG -3'
(R):5'- CACTGCAAGATGATTTTGTAGTGAGC -3'
Posted On 2021-08-31