Incidental Mutation 'R9372:Lrch4'
ID 709370
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
Accession Numbers
Essential gene? Probably non essential (E-score: 0.173) question?
Stock # R9372 (G1)
Quality Score 225.009
Status Not validated
Chromosome 5
Chromosomal Location 137627385-137639361 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 137631953 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 114 (T114A)
Ref Sequence ENSEMBL: ENSMUSP00000031734 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031734] [ENSMUST00000111002] [ENSMUST00000136028] [ENSMUST00000175968] [ENSMUST00000176011] [ENSMUST00000176667] [ENSMUST00000177477] [ENSMUST00000177545]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000031734
AA Change: T114A

PolyPhen 2 Score 0.702 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: T114A

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: ENSMUST00000111002
SMART Domains Protein: ENSMUSP00000106630
Gene: ENSMUSG00000089984

DomainStartEndE-ValueType
Pfam:RCC1 247 293 4.2e-11 PFAM
low complexity region 303 316 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000136028
Predicted Effect possibly damaging
Transcript: ENSMUST00000175968
AA Change: T60A

PolyPhen 2 Score 0.842 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: T60A

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 possibly damaging
Transcript: ENSMUST00000176667
AA Change: T114A

PolyPhen 2 Score 0.584 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: T114A

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: ENSMUST00000176871
Predicted Effect probably benign
Transcript: ENSMUST00000177477
SMART Domains Protein: ENSMUSP00000135724
Gene: ENSMUSG00000093445

DomainStartEndE-ValueType
low complexity region 2 22 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000177545
AA Change: T114A

PolyPhen 2 Score 0.702 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: T114A

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
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 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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2200002D01Rik CCTTCTCCTTCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC CCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC 7: 28,947,048 (GRCm39) probably benign Het
Aass T C 6: 23,078,856 (GRCm39) T719A probably damaging Het
Abcb8 A G 5: 24,605,114 (GRCm39) E100G probably benign Het
Actr1b C T 1: 36,741,561 (GRCm39) E104K probably damaging Het
Atad5 T A 11: 79,985,094 (GRCm39) S60R possibly damaging Het
Bcan G T 3: 87,895,610 (GRCm39) A842D probably benign Het
Cacna2d2 G A 9: 107,394,802 (GRCm39) E623K probably benign Het
Cdk15 T C 1: 59,370,142 (GRCm39) Y393H probably benign Het
Ceacam12 C T 7: 17,803,229 (GRCm39) R212C probably benign Het
Ceacam5 T C 7: 17,481,267 (GRCm39) I338T possibly damaging Het
Crcp A G 5: 130,088,664 (GRCm39) D139G possibly damaging Het
Crls1 T A 2: 132,707,802 (GRCm39) Y290* probably null Het
Dcun1d5 A G 9: 7,206,780 (GRCm39) N206D probably damaging Het
Dmtf1 A T 5: 9,190,399 (GRCm39) V105E possibly damaging Het
Dnah7a T C 1: 53,543,474 (GRCm39) Y2232C probably benign Het
Dnajc25 T A 4: 59,003,394 (GRCm39) V55E probably damaging Het
Dpy19l4 T C 4: 11,303,343 (GRCm39) M193V possibly damaging Het
Dsc1 A T 18: 20,221,489 (GRCm39) V662E probably damaging Het
Enpp6 G A 8: 47,506,627 (GRCm39) V144I possibly damaging Het
Fip1l1 A G 5: 74,707,463 (GRCm39) T204A possibly damaging Het
Flvcr2 T C 12: 85,793,795 (GRCm39) V57A probably benign Het
Fsip2 T G 2: 82,822,756 (GRCm39) I6163S possibly damaging Het
Gipr T A 7: 18,896,863 (GRCm39) M136L probably benign Het
Gm7298 A G 6: 121,748,746 (GRCm39) I674V probably benign Het
Gtf2a1 C T 12: 91,534,592 (GRCm39) V221I probably damaging Het
Haus3 A T 5: 34,321,002 (GRCm39) D481E probably benign Het
Hinfp A C 9: 44,209,083 (GRCm39) V345G probably damaging Het
Hs3st5 A T 10: 36,708,698 (GRCm39) K78* probably null Het
Ighv1-31 T C 12: 114,792,894 (GRCm39) Y114C probably damaging Het
Ighv5-15 T A 12: 113,790,357 (GRCm39) T88S probably damaging Het
Ildr1 G A 16: 36,542,721 (GRCm39) D418N probably damaging Het
Ints10 C T 8: 69,271,967 (GRCm39) T556I probably damaging Het
Isoc1 G T 18: 58,792,757 (GRCm39) R65L possibly damaging Het
Itm2c C T 1: 85,833,055 (GRCm39) R130C probably damaging Het
Jup C T 11: 100,270,391 (GRCm39) C372Y probably damaging Het
Kif11 T C 19: 37,399,892 (GRCm39) V793A probably benign Het
Klrg1 A C 6: 122,256,699 (GRCm39) V29G probably benign Het
Map3k3 C T 11: 106,033,335 (GRCm39) T196M probably damaging Het
Marchf1 C A 8: 66,921,145 (GRCm39) T274N probably benign Het
Nxpe5 A T 5: 138,249,445 (GRCm39) T412S probably benign Het
Or10q1 C T 19: 13,727,069 (GRCm39) H200Y probably benign Het
Pcnt A G 10: 76,258,960 (GRCm39) W502R probably damaging Het
Pfdn5 T C 15: 102,235,286 (GRCm39) probably null Het
Pkn2 A T 3: 142,535,018 (GRCm39) V232E probably damaging Het
Ppfibp1 T C 6: 146,898,307 (GRCm39) S88P probably damaging Het
Prr23a4 A G 9: 98,785,478 (GRCm39) I48V probably benign Het
Ptprz1 G A 6: 23,045,706 (GRCm39) E2159K probably damaging Het
Smyd3 T C 1: 178,871,470 (GRCm39) E303G possibly damaging Het
Snx13 T A 12: 35,151,048 (GRCm39) N336K possibly damaging Het
Src A G 2: 157,311,808 (GRCm39) E512G possibly damaging Het
Stard9 T A 2: 120,495,420 (GRCm39) C98* probably null Het
Tapbpl A G 6: 125,203,672 (GRCm39) V336A probably benign Het
Tbrg1 G A 9: 37,563,945 (GRCm39) T230I probably damaging Het
Tm7sf3 C T 6: 146,525,179 (GRCm39) D89N possibly damaging Het
Tmem132c G A 5: 127,640,145 (GRCm39) G772D probably damaging Het
Tmem219 C T 7: 126,496,017 (GRCm39) G119S possibly damaging Het
Ttbk2 T A 2: 120,603,766 (GRCm39) S325C probably benign Het
Ttc28 A T 5: 111,331,073 (GRCm39) Y431F probably benign Het
Vmn1r27 A T 6: 58,192,746 (GRCm39) M86K possibly damaging Het
Vmn2r15 G A 5: 109,441,953 (GRCm39) P160L possibly damaging Het
Zfc3h1 A T 10: 115,221,223 (GRCm39) S41C unknown Het
Zfp260 C A 7: 29,804,232 (GRCm39) T44K probably benign Het
Zfp7 TGCGGGAAAGGTTTCCACCTGAGCG TGCG 15: 76,774,800 (GRCm39) probably benign Het
Zfp760 A G 17: 21,941,035 (GRCm39) N70S probably benign Het
Zfp788 T A 7: 41,299,708 (GRCm39) Y781* probably null Het
Zfp800 A T 6: 28,256,433 (GRCm39) S52T possibly damaging 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
R5430:Lrch4 UTSW 5 137,636,795 (GRCm39) missense possibly damaging 0.46
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
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'- CTCAGTCCCCATTGTGTGAG -3'
(R):5'- TGATAAGCACTCGAAGGGGC -3'

Sequencing Primer
(F):5'- ATTGTGTGAGGCCGAACC -3'
(R):5'- TGGCAACGACGACAGCTG -3'
Posted On 2022-04-18