Incidental Mutation 'R7051:Lrch1'
ID 547617
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 045148-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7051 (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 G at 75022962 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 637 (V637A)
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: V637A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: V637A

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 damaging
Transcript: ENSMUST00000228252
AA Change: V610A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Meta Mutation Damage Score 0.9489 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 95% (80/84)
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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5930422O12Rik C T 8: 33,919,201 (GRCm39) S7L unknown Het
Aggf1 T C 13: 95,488,125 (GRCm39) K674R possibly damaging Het
Ampd1 T C 3: 102,997,389 (GRCm39) F264L probably damaging Het
Ankle1 A T 8: 71,860,387 (GRCm39) S302C probably damaging Het
Ankrd17 G A 5: 90,514,310 (GRCm39) probably benign Het
Arhgap18 T A 10: 26,725,917 (GRCm39) N47K possibly damaging Het
Atp5pb T C 3: 105,851,083 (GRCm39) N205D probably benign Het
Atp8b3 C T 10: 80,355,858 (GRCm39) E1285K probably benign Het
Atp8b3 C A 10: 80,365,552 (GRCm39) V401L probably damaging Het
Cacna1a G A 8: 85,356,544 (GRCm39) R1929Q possibly damaging Het
Cadm2 C T 16: 66,679,767 (GRCm39) S22N possibly damaging Het
Ccdc177 C T 12: 80,805,927 (GRCm39) V116M probably damaging Het
Cdhr18 A G 14: 13,828,486 (GRCm38) V758A Het
Cdkl2 A T 5: 92,181,084 (GRCm39) I185N probably damaging Het
Cfhr2 T A 1: 139,738,716 (GRCm39) I282L probably benign Het
Clns1a T A 7: 97,361,824 (GRCm39) probably null Het
Commd2 A T 3: 57,554,107 (GRCm39) I198N probably damaging Het
Creb3l2 C T 6: 37,313,200 (GRCm39) V365I possibly damaging Het
Dcaf6 A T 1: 165,251,886 (GRCm39) N79K possibly damaging Het
Dlg5 T C 14: 24,196,263 (GRCm39) N1622D possibly damaging Het
Dock7 C T 4: 98,834,969 (GRCm39) R1802H probably damaging Het
Dpy19l2 T C 9: 24,495,789 (GRCm39) K643R probably benign Het
Dscam G A 16: 96,620,986 (GRCm39) T574M probably benign Het
Fam209 A G 2: 172,315,969 (GRCm39) T115A probably damaging Het
Fastkd5 C T 2: 130,456,337 (GRCm39) C751Y probably damaging Het
Fat3 C A 9: 16,289,123 (GRCm39) L133F probably damaging Het
Fcsk A T 8: 111,616,971 (GRCm39) I393N probably damaging Het
Frmd6 T C 12: 70,944,170 (GRCm39) V516A possibly damaging Het
Fry G A 5: 150,318,634 (GRCm39) D955N possibly damaging Het
Gm7298 T C 6: 121,751,993 (GRCm39) probably null Het
Golga7b T A 19: 42,256,899 (GRCm39) *168R probably null Het
Golim4 T A 3: 75,800,309 (GRCm39) Q395L probably benign Het
Gxylt2 T A 6: 100,781,537 (GRCm39) L404* probably null Het
H1f4 A G 13: 23,806,422 (GRCm39) V20A probably benign Het
Ighmbp2 G T 19: 3,311,462 (GRCm39) S984R probably damaging Het
Irf8 C T 8: 121,466,581 (GRCm39) R9W probably damaging Het
Itga4 T C 2: 79,148,470 (GRCm39) V788A possibly damaging Het
Kifap3 G A 1: 163,621,649 (GRCm39) R99H probably damaging Het
Kiss1r T C 10: 79,754,688 (GRCm39) S61P probably damaging Het
Krtap6-1 A T 16: 88,828,606 (GRCm39) M1L unknown Het
Large2 A T 2: 92,197,367 (GRCm39) M411K probably damaging Het
Lcor A G 19: 41,574,191 (GRCm39) D982G probably benign Het
Lingo1 A G 9: 56,527,467 (GRCm39) V374A probably benign Het
Lyar T C 5: 38,382,024 (GRCm39) V2A probably damaging Het
Nell1 C T 7: 50,098,592 (GRCm39) S298L unknown Het
Ogfod3 T A 11: 121,086,031 (GRCm39) I188F probably damaging Het
Opa3 C A 7: 18,978,961 (GRCm39) A142E possibly damaging Het
Or5b123 T A 19: 13,596,769 (GRCm39) M81K possibly damaging Het
Or5k1 T C 16: 58,617,538 (GRCm39) T224A probably benign Het
Pald1 T C 10: 61,159,125 (GRCm39) R769G probably benign Het
Pappa2 T A 1: 158,784,753 (GRCm39) T86S unknown Het
Papss1 T C 3: 131,307,811 (GRCm39) Y266H probably damaging Het
Pcdhga7 C A 18: 37,849,994 (GRCm39) A667D probably damaging Het
Pcsk5 T A 19: 17,411,095 (GRCm39) T1766S probably benign Het
Pds5b T A 5: 150,717,747 (GRCm39) N1129K possibly damaging Het
Pop7 T C 5: 137,499,952 (GRCm39) N127S probably damaging Het
Ppfibp2 A G 7: 107,316,925 (GRCm39) E300G probably damaging Het
Ppp4r3b A G 11: 29,132,507 (GRCm39) K87E probably damaging Het
Psmd3 T A 11: 98,573,659 (GRCm39) M35K possibly damaging Het
Pus7 A G 5: 23,980,677 (GRCm39) V191A probably damaging Het
Rptor C T 11: 119,765,012 (GRCm39) probably benign Het
Sacs A G 14: 61,446,377 (GRCm39) M2808V probably benign Het
Scube3 G A 17: 28,386,573 (GRCm39) V831I probably benign Het
Sin3a A T 9: 57,011,218 (GRCm39) N492Y probably damaging Het
Slc12a3 A G 8: 95,092,572 (GRCm39) T998A probably damaging Het
Slc4a1 T C 11: 102,247,084 (GRCm39) N501S probably benign Het
Sltm G A 9: 70,466,348 (GRCm39) G94R probably damaging Het
Smc4 T A 3: 68,934,835 (GRCm39) W650R probably damaging Het
Smg7 A G 1: 152,724,601 (GRCm39) S527P probably damaging Het
Tcf20 T C 15: 82,740,279 (GRCm39) N391D probably damaging Het
Tiam2 G A 17: 3,498,758 (GRCm39) V845M probably damaging Het
Tln2 A G 9: 67,253,699 (GRCm39) F793L probably benign Het
Uckl1 T C 2: 181,216,037 (GRCm39) I193V probably damaging Het
Ugt1a5 A G 1: 88,094,077 (GRCm39) M102V probably benign Het
Usp38 G A 8: 81,727,750 (GRCm39) P328S possibly damaging Het
Vmn1r189 A G 13: 22,286,285 (GRCm39) V184A possibly damaging Het
Vps13d C A 4: 144,889,914 (GRCm39) A597S probably benign Het
Wdr47 T A 3: 108,525,840 (GRCm39) L121Q probably damaging Het
Wiz A G 17: 32,580,507 (GRCm39) S315P probably damaging Het
Zc3h13 T C 14: 75,568,597 (GRCm39) S1297P probably damaging Het
Zfp27 AATCCGCTTGTGCA AA 7: 29,594,446 (GRCm39) probably benign 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
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'- AGTGAAAATTCTGCTTCCTTGC -3'
(R):5'- TGTCCCCTCACTGACAAGAG -3'

Sequencing Primer
(F):5'- GTGAAAATTCTGCTTCCTTGCTTTGC -3'
(R):5'- GAGCACTTGGGTTTATACATACTTGC -3'
Posted On 2019-05-13