Incidental Mutation 'R5430:Lrch4'
ID 427122
Institutional Source Beutler Lab
Gene Symbol Lrch4
Ensembl Gene ENSMUSG00000093445
Gene Name leucine-rich repeats and calponin homology (CH) domain containing 4
Synonyms LRRN4, LRN, 2810008P14Rik, 2900069C24Rik
MMRRC Submission 042996-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.179) question?
Stock # R5430 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 137627385-137639361 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 137636795 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 433 (S433P)
Ref Sequence ENSEMBL: ENSMUSP00000134767 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031734] [ENSMUST00000057314] [ENSMUST00000166099] [ENSMUST00000175968] [ENSMUST00000176011] [ENSMUST00000176667] [ENSMUST00000177545] [ENSMUST00000177477] [ENSMUST00000196511] [ENSMUST00000177466]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000031734
AA Change: S487P

PolyPhen 2 Score 0.403 (Sensitivity: 0.89; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: S487P

DomainStartEndE-ValueType
low complexity region 2 22 N/A INTRINSIC
LRR 90 112 4.84e1 SMART
LRR_TYP 113 136 4.61e-5 SMART
LRR 158 180 2.63e0 SMART
LRR_TYP 181 204 1.1e-2 SMART
LRR 226 249 3.98e1 SMART
low complexity region 389 405 N/A INTRINSIC
low complexity region 440 453 N/A INTRINSIC
low complexity region 474 479 N/A INTRINSIC
low complexity region 510 530 N/A INTRINSIC
CH 533 642 9.24e-15 SMART
transmembrane domain 656 678 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000057314
SMART Domains Protein: ENSMUSP00000060844
Gene: ENSMUSG00000047182

DomainStartEndE-ValueType
PH 33 135 4.46e-11 SMART
IRS 159 272 1.18e-30 SMART
PTBI 159 272 7.23e-55 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000166099
SMART Domains Protein: ENSMUSP00000127076
Gene: ENSMUSG00000079165

DomainStartEndE-ValueType
Pfam:SAP25 76 261 1.8e-77 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000175968
AA Change: S433P

PolyPhen 2 Score 0.462 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: S433P

DomainStartEndE-ValueType
low complexity region 3 14 N/A INTRINSIC
LRR 36 58 4.84e1 SMART
LRR_TYP 59 82 4.61e-5 SMART
LRR 104 126 2.63e0 SMART
LRR_TYP 127 150 1.1e-2 SMART
LRR 172 195 3.98e1 SMART
low complexity region 335 351 N/A INTRINSIC
low complexity region 386 399 N/A INTRINSIC
low complexity region 420 425 N/A INTRINSIC
low complexity region 456 476 N/A INTRINSIC
CH 479 588 9.24e-15 SMART
transmembrane domain 602 624 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000176011
SMART Domains Protein: ENSMUSP00000135133
Gene: ENSMUSG00000093445

DomainStartEndE-ValueType
low complexity region 2 22 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176075
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176256
Predicted Effect unknown
Transcript: ENSMUST00000176871
AA Change: S46P
Predicted Effect probably benign
Transcript: ENSMUST00000176667
AA Change: S487P

PolyPhen 2 Score 0.335 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: S487P

DomainStartEndE-ValueType
low complexity region 2 22 N/A INTRINSIC
LRR 90 112 4.84e1 SMART
LRR_TYP 113 136 4.61e-5 SMART
LRR 158 180 2.63e0 SMART
LRR_TYP 181 204 1.1e-2 SMART
LRR 226 249 3.98e1 SMART
low complexity region 389 405 N/A INTRINSIC
low complexity region 440 453 N/A INTRINSIC
low complexity region 474 479 N/A INTRINSIC
low complexity region 510 530 N/A INTRINSIC
CH 533 648 4.73e-12 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000177545
AA Change: S487P

PolyPhen 2 Score 0.403 (Sensitivity: 0.89; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: S487P

DomainStartEndE-ValueType
low complexity region 2 22 N/A INTRINSIC
LRR 90 112 4.84e1 SMART
LRR_TYP 113 136 4.61e-5 SMART
LRR 158 180 2.63e0 SMART
LRR_TYP 181 204 1.1e-2 SMART
LRR 226 249 3.98e1 SMART
low complexity region 389 405 N/A INTRINSIC
low complexity region 440 453 N/A INTRINSIC
low complexity region 474 479 N/A INTRINSIC
low complexity region 510 530 N/A INTRINSIC
CH 533 642 9.24e-15 SMART
transmembrane domain 656 678 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000177354
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176988
Predicted Effect noncoding transcript
Transcript: ENSMUST00000177038
Predicted Effect probably benign
Transcript: ENSMUST00000177477
SMART Domains Protein: ENSMUSP00000135724
Gene: ENSMUSG00000093445

DomainStartEndE-ValueType
low complexity region 2 22 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000196511
SMART Domains Protein: ENSMUSP00000142730
Gene: ENSMUSG00000047182

DomainStartEndE-ValueType
PH 33 135 4.46e-11 SMART
IRS 159 272 1.18e-30 SMART
PTBI 159 272 7.23e-55 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000177466
Predicted Effect probably benign
Transcript: ENSMUST00000176768
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.7%
Validation Efficiency 96% (54/56)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that contains leucine-rich repeats (LRR) at its amino terminus and that is known to be involved in ligand binding. The carboxyl terminus may act as a membrane anchor. Identified structural elements suggest that the encoded protein resembles a receptor. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001J11Rik T A 9: 39,963,587 (GRCm39) noncoding transcript Het
Acot11 C T 4: 106,617,327 (GRCm39) G240R probably damaging Het
Ankrd34a G A 3: 96,504,837 (GRCm39) G14R probably damaging Het
Arhgef1 C A 7: 24,611,732 (GRCm39) probably null Het
Brsk1 T C 7: 4,713,435 (GRCm39) F702L probably benign Het
Chrna3 C T 9: 54,920,192 (GRCm39) V470I probably damaging Het
Cpm A G 10: 117,511,986 (GRCm39) Q310R possibly damaging Het
Dennd5a T C 7: 109,533,447 (GRCm39) T108A probably damaging Het
Dvl3 C T 16: 20,342,481 (GRCm39) R145W probably damaging Het
E4f1 G A 17: 24,663,944 (GRCm39) A532V probably damaging Het
Eid1 A G 2: 125,515,550 (GRCm39) T147A probably damaging Het
Eipr1 A T 12: 28,913,015 (GRCm39) N239Y probably damaging Het
Eml5 T C 12: 98,760,417 (GRCm39) I1777M probably damaging Het
Gm11787 A T 4: 3,512,786 (GRCm39) noncoding transcript Het
Gnat2 T C 3: 108,005,716 (GRCm39) L227P probably damaging Het
H2-T15 C T 17: 36,366,967 (GRCm39) V359I probably benign Het
Jag1 T C 2: 136,943,626 (GRCm39) H190R possibly damaging Het
Kdm7a A G 6: 39,126,276 (GRCm39) W570R possibly damaging Het
Lmbrd1 A G 1: 24,732,061 (GRCm39) T93A possibly damaging Het
Lrp1 G A 10: 127,376,930 (GRCm39) R4216W probably damaging Het
Magohb A G 6: 131,266,381 (GRCm39) Y42H probably damaging Het
Melk A G 4: 44,309,033 (GRCm39) H130R probably damaging Het
Mettl24 G T 10: 40,613,780 (GRCm39) R173L probably benign Het
Mup4 A T 4: 59,960,044 (GRCm39) H73Q probably damaging Het
Mylk2 A T 2: 152,759,468 (GRCm39) E386V probably damaging Het
Nppb C T 4: 148,070,838 (GRCm39) P71L probably benign Het
Oca2 T C 7: 55,945,208 (GRCm39) V272A probably damaging Het
Or14j6 T A 17: 38,215,304 (GRCm39) I289N probably damaging Het
Or2t6 C T 14: 14,175,692 (GRCm38) R130H probably benign Het
Or4c10 A T 2: 89,760,257 (GRCm39) I35F probably benign Het
Osbpl6 T C 2: 76,416,482 (GRCm39) S628P probably damaging Het
Papola T C 12: 105,775,843 (GRCm39) V253A probably damaging Het
Pex12 T C 11: 83,188,572 (GRCm39) D141G probably damaging Het
Ppm1k A T 6: 57,501,871 (GRCm39) C97* probably null Het
Ptprh T A 7: 4,554,046 (GRCm39) E807V probably damaging Het
Sema3a A T 5: 13,615,730 (GRCm39) T385S probably damaging Het
Sfn T C 4: 133,328,938 (GRCm39) Y48C probably damaging Het
Slc38a8 A G 8: 120,220,959 (GRCm39) I200T probably benign Het
Smarcal1 T C 1: 72,665,776 (GRCm39) V758A probably damaging Het
Stmn4 A G 14: 66,595,463 (GRCm39) M190V possibly damaging Het
Syt3 T G 7: 44,040,337 (GRCm39) L190R possibly damaging Het
Tbl1xr1 T A 3: 22,246,246 (GRCm39) D255E probably benign Het
Ttbk2 C T 2: 120,608,046 (GRCm39) R191H probably damaging Het
Vmn1r238 G T 18: 3,122,521 (GRCm39) L298M possibly damaging Het
Vmn2r45 A C 7: 8,486,333 (GRCm39) Y318* probably null Het
Vsig8 T C 1: 172,387,196 (GRCm39) I24T probably damaging Het
Wdr3 G A 3: 100,064,643 (GRCm39) T166I possibly damaging Het
Zfp354c A G 11: 50,706,022 (GRCm39) I351T probably benign Het
Zfp52 A G 17: 21,775,329 (GRCm39) T8A probably benign Het
Other mutations in Lrch4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00340:Lrch4 APN 5 137,636,009 (GRCm39) missense possibly damaging 0.49
IGL01862:Lrch4 APN 5 137,635,271 (GRCm39) missense probably damaging 1.00
IGL03289:Lrch4 APN 5 137,631,839 (GRCm39) missense probably damaging 1.00
R0144:Lrch4 UTSW 5 137,636,805 (GRCm39) critical splice donor site probably null
R0724:Lrch4 UTSW 5 137,635,570 (GRCm39) missense probably damaging 1.00
R1330:Lrch4 UTSW 5 137,636,051 (GRCm39) missense probably damaging 0.99
R1557:Lrch4 UTSW 5 137,635,818 (GRCm39) missense probably benign 0.00
R1694:Lrch4 UTSW 5 137,636,723 (GRCm39) missense probably benign 0.00
R2358:Lrch4 UTSW 5 137,636,810 (GRCm39) unclassified probably benign
R3755:Lrch4 UTSW 5 137,635,992 (GRCm39) missense probably damaging 1.00
R3756:Lrch4 UTSW 5 137,635,992 (GRCm39) missense probably damaging 1.00
R4608:Lrch4 UTSW 5 137,637,408 (GRCm39) nonsense probably null
R5056:Lrch4 UTSW 5 137,635,113 (GRCm39) missense probably damaging 1.00
R5114:Lrch4 UTSW 5 137,636,179 (GRCm39) missense probably benign
R5181:Lrch4 UTSW 5 137,627,665 (GRCm39) missense probably damaging 1.00
R5325:Lrch4 UTSW 5 137,636,168 (GRCm39) missense probably damaging 1.00
R5712:Lrch4 UTSW 5 137,636,188 (GRCm39) missense possibly damaging 0.57
R5846:Lrch4 UTSW 5 137,631,919 (GRCm39) missense probably damaging 1.00
R5909:Lrch4 UTSW 5 137,632,127 (GRCm39) missense possibly damaging 0.87
R7319:Lrch4 UTSW 5 137,637,977 (GRCm39) missense
R7525:Lrch4 UTSW 5 137,637,727 (GRCm39) missense probably damaging 1.00
R7761:Lrch4 UTSW 5 137,638,025 (GRCm39) missense
R7848:Lrch4 UTSW 5 137,632,116 (GRCm39) missense probably damaging 1.00
R8209:Lrch4 UTSW 5 137,637,997 (GRCm39) missense
R8226:Lrch4 UTSW 5 137,637,997 (GRCm39) missense
R8713:Lrch4 UTSW 5 137,638,125 (GRCm39) nonsense probably null
R9361:Lrch4 UTSW 5 137,635,076 (GRCm39) missense probably damaging 1.00
R9372:Lrch4 UTSW 5 137,631,953 (GRCm39) missense possibly damaging 0.70
R9440:Lrch4 UTSW 5 137,636,051 (GRCm39) missense probably damaging 0.99
R9752:Lrch4 UTSW 5 137,636,218 (GRCm39) missense probably benign
R9796:Lrch4 UTSW 5 137,635,269 (GRCm39) missense probably damaging 0.99
RF009:Lrch4 UTSW 5 137,635,805 (GRCm39) critical splice acceptor site probably null
Predicted Primers PCR Primer
(F):5'- AGAATTCCAGGCCTGACTGC -3'
(R):5'- TTTGGTCTCTGAATGGAGCCC -3'

Sequencing Primer
(F):5'- GCTTCTCCAGCGTCCTGAAG -3'
(R):5'- TCTGAATGGAGCCCAGGGG -3'
Posted On 2016-09-01