Incidental Mutation 'R7699:Lemd3'
ID593872
Institutional Source Beutler Lab
Gene Symbol Lemd3
Ensembl Gene ENSMUSG00000048661
Gene NameLEM domain containing 3
SynonymsMan1
MMRRC Submission
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R7699 (G1)
Quality Score225.009
Status Not validated
Chromosome10
Chromosomal Location120923413-120979332 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 120978090 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Asparagine at position 413 (Y413N)
Ref Sequence ENSEMBL: ENSMUSP00000113103 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000119093] [ENSMUST00000119944]
Predicted Effect probably damaging
Transcript: ENSMUST00000119093
AA Change: Y413N

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: Y413N

DomainStartEndE-ValueType
LEM 8 51 1.01e-20 SMART
low complexity region 66 87 N/A INTRINSIC
low complexity region 106 129 N/A INTRINSIC
low complexity region 150 161 N/A INTRINSIC
low complexity region 169 176 N/A INTRINSIC
low complexity region 195 229 N/A INTRINSIC
low complexity region 258 272 N/A INTRINSIC
low complexity region 346 355 N/A INTRINSIC
low complexity region 366 384 N/A INTRINSIC
low complexity region 418 429 N/A INTRINSIC
low complexity region 451 462 N/A INTRINSIC
transmembrane domain 480 502 N/A INTRINSIC
Pfam:MSC 526 779 8.9e-25 PFAM
PDB:4OZ1|B 812 919 2e-23 PDB
SCOP:d1jmta_ 813 894 6e-7 SMART
Blast:RRM 814 893 4e-49 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000119944
AA Change: Y413N

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: Y413N

DomainStartEndE-ValueType
LEM 8 51 1.01e-20 SMART
low complexity region 66 87 N/A INTRINSIC
low complexity region 106 129 N/A INTRINSIC
low complexity region 150 161 N/A INTRINSIC
low complexity region 169 176 N/A INTRINSIC
low complexity region 195 229 N/A INTRINSIC
low complexity region 258 272 N/A INTRINSIC
low complexity region 346 355 N/A INTRINSIC
low complexity region 366 384 N/A INTRINSIC
low complexity region 418 429 N/A INTRINSIC
low complexity region 451 462 N/A INTRINSIC
transmembrane domain 480 502 N/A INTRINSIC
Pfam:MSC 518 758 5.7e-57 PFAM
PDB:4OZ1|B 790 897 2e-23 PDB
SCOP:d1jmta_ 791 872 5e-7 SMART
Blast:RRM 792 871 4e-49 BLAST
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This locus encodes a LEM domain-containing protein. The encoded protein functions to antagonize transforming growth factor-beta signaling at the inner nuclear membrane. Two transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis.[provided by RefSeq, Nov 2009]
PHENOTYPE: Homozygous mutation of this gene results in embryonic lethality at midgestation, defects in vascular remodeling and increased apoptosis in embryos, particularly in mesenchymal tissues. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1810009A15Rik T C 19: 8,890,053 L72P probably benign Het
4930407I10Rik C A 15: 82,064,105 H734Q probably benign Het
4932438A13Rik T A 3: 36,974,172 N2329K possibly damaging Het
4932438A13Rik C T 3: 37,026,154 S267L probably benign Het
Acadl A G 1: 66,838,363 V343A possibly damaging Het
Acot4 A T 12: 84,043,237 D236V probably damaging Het
App T A 16: 85,040,309 probably null Het
Arfgef1 G A 1: 10,194,411 T470I possibly damaging Het
Arhgef5 T C 6: 43,274,757 I814T probably benign Het
Atr A T 9: 95,875,690 R968* probably null Het
C130060K24Rik T A 6: 65,452,956 I212N probably benign Het
Capn7 C T 14: 31,352,444 T268I probably benign Het
Cbwd1 A G 19: 24,942,681 probably null Het
Cubn A T 2: 13,348,178 F1916L probably benign Het
Cubn A G 2: 13,489,917 V107A possibly damaging Het
Cyp11b1 T A 15: 74,835,842 T473S probably damaging Het
Cyr61 C T 3: 145,648,692 G155R probably damaging Het
Dip2c T G 13: 9,659,311 S1396A probably benign Het
Dyrk1b T C 7: 28,184,312 Y198H probably damaging Het
Echdc2 G T 4: 108,174,077 R206L probably benign Het
Ep400 C T 5: 110,696,032 R1594Q unknown Het
Fmnl2 G A 2: 53,036,508 R69Q Het
Fry T A 5: 150,405,327 H1308Q probably damaging Het
Fyb2 T A 4: 105,010,454 D667E probably benign Het
Gimap7 T A 6: 48,723,857 Y126N possibly damaging Het
Gm1979 A T 5: 26,000,180 W266R probably damaging Het
Gm28042 T A 2: 120,039,716 M712K possibly damaging Het
Gm3238 A G 10: 77,770,635 *231R probably null Het
Gm5592 C A 7: 41,286,407 A111E probably damaging Het
Gm7694 A G 1: 170,301,148 *271Q probably null Het
Ift81 T C 5: 122,594,560 M304V possibly damaging Het
Igfals T C 17: 24,880,574 L213P probably damaging Het
Ints3 G A 3: 90,421,804 P83S probably benign Het
Kcna10 T G 3: 107,195,540 S496A probably damaging Het
Kmt2d G A 15: 98,843,719 A4520V unknown Het
Lgr6 T C 1: 134,996,032 N453S probably damaging Het
Lmtk3 A C 7: 45,792,574 D352A probably damaging Het
Lrrc4c T C 2: 97,630,679 M550T possibly damaging Het
Maml2 A T 9: 13,621,089 Q533L Het
Mdn1 T A 4: 32,741,344 D3815E probably damaging Het
Megf8 C T 7: 25,329,928 A299V possibly damaging Het
Meis3 G T 7: 16,177,556 E59D probably benign Het
Mppe1 A G 18: 67,225,704 *398R probably null Het
Mtmr7 G A 8: 40,606,884 A62V possibly damaging Het
Mtus1 T A 8: 41,083,969 T237S possibly damaging Het
Ndfip2 T A 14: 105,287,759 V158E possibly damaging Het
Nrbp2 T G 15: 76,090,897 T53P probably damaging Het
Nrde2 G A 12: 100,130,835 P902L probably benign Het
Olfr1383 A G 11: 49,524,554 Y277C probably damaging Het
Olfr509 T A 7: 108,645,672 K301N probably damaging Het
Olfr642 T A 7: 104,050,593 probably benign Het
Olfr739 T A 14: 50,425,335 M272K probably benign Het
Olfr771 T C 10: 129,160,055 M310V probably benign Het
Pcdha1 A G 18: 36,931,062 T260A probably damaging Het
Pdlim1 T G 19: 40,249,658 K98N probably damaging Het
Phrf1 G A 7: 141,254,929 G207R unknown Het
Pik3r6 A G 11: 68,528,563 K124R probably damaging Het
Polr2b T A 5: 77,340,421 F823I probably benign Het
Prss58 T C 6: 40,895,388 I234V probably damaging Het
Ptpn14 A T 1: 189,865,411 N766I probably benign Het
Repin1 T A 6: 48,597,822 S562T probably damaging Het
Rgr C T 14: 37,044,595 D165N probably damaging Het
Rho T C 6: 115,935,239 F221L probably damaging Het
Rictor C T 15: 6,772,154 S441L probably benign Het
Rnase2a A G 14: 51,255,791 I39T probably damaging Het
Rpl13a T G 7: 45,127,236 I43L probably benign Het
Rpp30 T C 19: 36,089,158 V97A probably benign Het
Scube3 T C 17: 28,167,049 Y755H probably damaging Het
Sec24a A T 11: 51,712,257 V788E probably damaging Het
Spns2 A T 11: 72,489,617 L60* probably null Het
Strc T C 2: 121,371,748 N1213S possibly damaging Het
Tec A T 5: 72,786,024 I116N possibly damaging Het
Tll1 A T 8: 64,093,954 D319E probably benign Het
Tmem121b T C 6: 120,493,427 T110A unknown Het
Tmem232 T A 17: 65,265,218 I593F probably damaging Het
Tpp2 A G 1: 43,970,466 I487V probably benign Het
Ubr4 C A 4: 139,408,867 C934* probably null Het
Vmn1r68 A G 7: 10,527,632 Y180H probably benign Het
Vmn2r25 T C 6: 123,839,923 D233G possibly damaging Het
Wdr6 A G 9: 108,576,361 W108R possibly damaging Het
Other mutations in Lemd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01488:Lemd3 APN 10 120933399 nonsense probably null
IGL01733:Lemd3 APN 10 120933663 nonsense probably null
IGL02127:Lemd3 APN 10 120926028 missense possibly damaging 0.58
IGL02171:Lemd3 APN 10 120933622 splice site probably benign
Culebra UTSW 10 120933633 missense probably damaging 1.00
R2044_Lemd3_698 UTSW 10 120933442 missense probably damaging 1.00
R0037:Lemd3 UTSW 10 120925456 missense possibly damaging 0.95
R0309:Lemd3 UTSW 10 120937110 missense possibly damaging 0.71
R0829:Lemd3 UTSW 10 120979083 missense probably benign
R1171:Lemd3 UTSW 10 120949341 missense possibly damaging 0.90
R1382:Lemd3 UTSW 10 120931736 missense probably damaging 0.99
R1954:Lemd3 UTSW 10 120978940 missense probably damaging 0.99
R2044:Lemd3 UTSW 10 120933442 missense probably damaging 1.00
R2197:Lemd3 UTSW 10 120978527 small deletion probably benign
R3118:Lemd3 UTSW 10 120947251 missense probably benign 0.00
R3697:Lemd3 UTSW 10 120978527 small deletion probably benign
R3729:Lemd3 UTSW 10 120928015 missense probably damaging 1.00
R4407:Lemd3 UTSW 10 120925430 missense possibly damaging 0.93
R4429:Lemd3 UTSW 10 120977988 missense probably benign 0.00
R4830:Lemd3 UTSW 10 120931948 missense probably damaging 0.99
R5316:Lemd3 UTSW 10 120952256 critical splice acceptor site probably null
R5355:Lemd3 UTSW 10 120933633 missense probably damaging 1.00
R5404:Lemd3 UTSW 10 120931958 nonsense probably null
R6754:Lemd3 UTSW 10 120933660 missense probably damaging 1.00
R7007:Lemd3 UTSW 10 120952232 missense probably benign 0.28
R7213:Lemd3 UTSW 10 120978240 nonsense probably null
R7700:Lemd3 UTSW 10 120978090 missense probably damaging 0.99
R7781:Lemd3 UTSW 10 120925773 missense probably damaging 1.00
R8681:Lemd3 UTSW 10 120931823 missense possibly damaging 0.80
Predicted Primers PCR Primer
(F):5'- TCCCGTTTAAACTGCTGGAG -3'
(R):5'- TCTAGACAGGAGCCGAAACC -3'

Sequencing Primer
(F):5'- AACTGCTGGAGAAGTTCCTC -3'
(R):5'- GAGGAGGGTGCGGGTGC -3'
Posted On2019-11-12