Incidental Mutation 'R4830:Lemd3'
ID372749
Institutional Source Beutler Lab
Gene Symbol Lemd3
Ensembl Gene ENSMUSG00000048661
Gene NameLEM domain containing 3
SynonymsMan1
MMRRC Submission 042446-MU
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R4830 (G1)
Quality Score225
Status Validated
Chromosome10
Chromosomal Location120923413-120979332 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 120931948 bp
ZygosityHeterozygous
Amino Acid Change Aspartic acid to Glycine at position 697 (D697G)
Ref Sequence ENSEMBL: ENSMUSP00000112661 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000119093] [ENSMUST00000119944]
Predicted Effect noncoding transcript
Transcript: ENSMUST00000118291
Predicted Effect probably damaging
Transcript: ENSMUST00000119093
AA Change: D697G

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: D697G

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: D675G

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: D675G

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
Meta Mutation Damage Score 0.2536 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.5%
Validation Efficiency 97% (71/73)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcd3 C A 3: 121,760,284 G643V probably damaging Het
Adamtsl1 A G 4: 86,356,382 E1225G probably damaging Het
Agbl5 G A 5: 30,890,715 R111H probably damaging Het
Ankle2 A C 5: 110,242,013 K446Q probably damaging Het
Boc A C 16: 44,490,157 M800R probably damaging Het
Ccnt1 A T 15: 98,543,451 N645K probably damaging Het
Cd93 G A 2: 148,443,379 Q16* probably null Het
Cpsf4l G T 11: 113,709,502 probably benign Het
Cuzd1 T A 7: 131,318,054 D111V probably damaging Het
Dab2 T C 15: 6,427,527 C232R probably benign Het
Dmpk A T 7: 19,087,528 Y237F probably damaging Het
Dnah6 T A 6: 73,044,762 T3526S possibly damaging Het
Dock2 T C 11: 34,273,767 probably null Het
Dsp G A 13: 38,192,864 V1542I probably benign Het
Dst T A 1: 34,198,505 probably null Het
Esd T C 14: 74,741,160 L54S probably damaging Het
Exd1 C T 2: 119,520,326 A485T probably benign Het
Gm3604 A T 13: 62,369,043 N500K probably damaging Het
Gm7102 C T 19: 61,175,926 G24R unknown Het
Grhl2 T A 15: 37,335,659 probably null Het
Gsto1 C T 19: 47,864,391 R222C probably benign Het
H2afy2 C T 10: 61,739,353 D355N possibly damaging Het
Inpp4a T A 1: 37,371,780 M343K probably damaging Het
Itpripl2 T C 7: 118,491,057 Q93R probably benign Het
Jakmip2 G A 18: 43,567,143 T450I probably benign Het
Kdm6b A T 11: 69,403,794 I1186N unknown Het
Kif1a T C 1: 93,021,209 probably null Het
Klhl20 T C 1: 161,098,376 K434R probably benign Het
Lipo1 A G 19: 33,776,587 S383P probably damaging Het
Ltn1 C A 16: 87,379,694 K1741N probably damaging Het
Lvrn A T 18: 46,905,351 T991S probably damaging Het
Mast3 C A 8: 70,788,915 R151L possibly damaging Het
Muc4 G C 16: 32,753,919 R1265P probably benign Het
Myoz1 T C 14: 20,655,309 K14E probably damaging Het
Neb G T 2: 52,192,520 Q5450K probably damaging Het
Nedd1 T A 10: 92,686,258 N639I probably damaging Het
Nlrp4e A T 7: 23,336,740 N673Y probably benign Het
Nop53 C T 7: 15,942,204 R190Q probably damaging Het
Notch4 T C 17: 34,570,118 Y468H probably damaging Het
Obscn T C 11: 59,067,607 T3507A probably damaging Het
Olfr724 T C 14: 49,960,224 N283D probably damaging Het
Opn5 T C 17: 42,611,296 H5R probably benign Het
Patl1 T C 19: 11,925,151 M349T probably benign Het
Phactr3 A G 2: 178,284,018 N362S probably damaging Het
Pirb C T 7: 3,717,603 G299S probably benign Het
Rapgef5 G A 12: 117,756,074 R579Q probably damaging Het
Rgl1 T C 1: 152,554,330 D234G probably benign Het
Serpinb3a C T 1: 107,048,586 E122K probably benign Het
Slc22a15 T C 3: 101,875,603 probably benign Het
Slc25a12 A T 2: 71,296,805 V344E probably damaging Het
Slc43a2 T C 11: 75,543,293 L99P probably damaging Het
Smim27 G T 4: 40,269,719 probably null Het
Smtn A G 11: 3,520,736 probably benign Het
Szt2 A T 4: 118,369,248 Y3001N unknown Het
Tgfbr3 G T 5: 107,109,719 P825T probably damaging Het
Tnpo3 T C 6: 29,568,938 T472A probably benign Het
Trf T A 9: 103,227,915 D66V probably damaging Het
Vmn1r124 A G 7: 21,259,699 C307R probably damaging Het
Vps13b T A 15: 35,452,224 F656Y possibly damaging Het
Zic1 G T 9: 91,362,531 S358R probably 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
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
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
R7699:Lemd3 UTSW 10 120978090 missense probably damaging 0.99
R7700:Lemd3 UTSW 10 120978090 missense probably damaging 0.99
R7781:Lemd3 UTSW 10 120925773 missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCGGCTGTATTAGGGAATCG -3'
(R):5'- CTCCATTATTCCATGAGGCCAG -3'

Sequencing Primer
(F):5'- CTGTATTAGGGAATCGCGGAC -3'
(R):5'- GGGGCACGGGTCACTGTTAG -3'
Posted On2016-03-01