Incidental Mutation 'R7007:Lemd3'
ID 544777
Institutional Source Beutler Lab
Gene Symbol Lemd3
Ensembl Gene ENSMUSG00000048661
Gene Name LEM domain containing 3
Synonyms Man1
MMRRC Submission 045109-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7007 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 120759318-120815237 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 120788137 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Isoleucine at position 523 (F523I)
Ref Sequence ENSEMBL: ENSMUSP00000113103 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000119093] [ENSMUST00000119944]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000119093
AA Change: F523I

PolyPhen 2 Score 0.279 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: F523I

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 benign
Transcript: ENSMUST00000119944
AA Change: F523I

PolyPhen 2 Score 0.279 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: F523I

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: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 95% (63/66)
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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930474N05Rik C T 14: 35,817,121 (GRCm39) T57I probably benign Het
Adcy8 T C 15: 64,576,565 (GRCm39) N999S possibly damaging Het
Adgrv1 T A 13: 81,684,483 (GRCm39) I1073F possibly damaging Het
Akap3 A G 6: 126,843,439 (GRCm39) D686G probably damaging Het
Alg2 A T 4: 47,471,881 (GRCm39) I309N probably benign Het
Ankrd36 A G 11: 5,639,168 (GRCm39) E1360G probably benign Het
Aox1 C A 1: 58,370,051 (GRCm39) Q788K probably damaging Het
Apoc2 A T 7: 19,407,282 (GRCm39) D26E possibly damaging Het
Bbx G A 16: 50,022,851 (GRCm39) T703I possibly damaging Het
C2cd4d T C 3: 94,271,378 (GRCm39) Y215H probably benign Het
C3 C T 17: 57,525,809 (GRCm39) E858K probably benign Het
Ciita T C 16: 10,329,171 (GRCm39) L482P probably damaging Het
Cldn9 T C 17: 23,902,052 (GRCm39) E191G probably benign Het
Cnst T A 1: 179,438,133 (GRCm39) S566T probably damaging Het
Col5a2 A G 1: 45,417,609 (GRCm39) I1322T possibly damaging Het
Cp G A 3: 20,024,137 (GRCm39) V326M probably damaging Het
Cyp7b1 G A 3: 18,151,782 (GRCm39) Q144* probably null Het
Dnah10 T C 5: 124,864,490 (GRCm39) S2232P probably damaging Het
Dnah17 T C 11: 118,009,697 (GRCm39) E625G possibly damaging Het
Dnah7c T A 1: 46,571,910 (GRCm39) D794E probably benign Het
Dusp10 G A 1: 183,769,414 (GRCm39) V127M probably benign Het
Dysf G C 6: 84,090,962 (GRCm39) W1015C probably damaging Het
Fbxw17 T C 13: 50,577,808 (GRCm39) Y104H probably damaging Het
Gm6408 G A 5: 146,420,647 (GRCm39) E176K probably damaging Het
Gp1bb T A 16: 18,439,689 (GRCm39) D135V possibly damaging Het
Gprin1 C T 13: 54,886,069 (GRCm39) C735Y probably damaging Het
Heatr9 T A 11: 83,411,446 (GRCm39) M30L possibly damaging Het
Hhat G A 1: 192,376,134 (GRCm39) T333I possibly damaging Het
Htr5b A G 1: 121,438,223 (GRCm39) F336S probably damaging Het
Ippk T G 13: 49,590,181 (GRCm39) probably null Het
Jph1 T A 1: 17,074,410 (GRCm39) H11L possibly damaging Het
Kif12 T A 4: 63,084,717 (GRCm39) I534L probably benign Het
Lgsn C A 1: 31,229,508 (GRCm39) H76Q probably benign Het
Lipm T A 19: 34,089,497 (GRCm39) W152R probably damaging Het
Mei1 A T 15: 81,978,200 (GRCm39) R216W probably damaging Het
Mybpc1 C T 10: 88,389,274 (GRCm39) G379S probably damaging Het
Myh8 A G 11: 67,179,142 (GRCm39) T512A probably benign Het
Nf1 A G 11: 79,337,849 (GRCm39) probably null Het
Npc1 T C 18: 12,343,605 (GRCm39) T463A probably benign Het
Or12e10 A G 2: 87,640,230 (GRCm39) N22S probably damaging Het
Or2y13 G A 11: 49,415,011 (GRCm39) V154M probably benign Het
Or6c7 A T 10: 129,323,277 (GRCm39) I133F probably damaging Het
Osbpl11 T G 16: 33,047,309 (GRCm39) I424R possibly damaging Het
Pnma8b A T 7: 16,680,181 (GRCm39) K388N possibly damaging Het
Ppp1r26 A T 2: 28,341,171 (GRCm39) K267I probably damaging Het
Psmb5 A T 14: 54,854,166 (GRCm39) M104K probably damaging Het
Ptges2 T C 2: 32,292,318 (GRCm39) V378A probably benign Het
Rcan2 C T 17: 44,147,216 (GRCm39) S18F probably benign Het
Saxo5 A T 8: 3,526,309 (GRCm39) D154V probably damaging Het
Sf3b2 C T 19: 5,324,545 (GRCm39) R859Q probably benign Het
Slc7a1 G A 5: 148,289,256 (GRCm39) Het
Spata31d1a T A 13: 59,851,448 (GRCm39) T227S probably benign Het
Sptbn2 T A 19: 4,794,173 (GRCm39) V1459E possibly damaging Het
Srgap2 T C 1: 131,247,275 (GRCm39) I586V probably benign Het
St6galnac1 G A 11: 116,657,833 (GRCm39) R356* probably null Het
Taf5 T A 19: 47,059,650 (GRCm39) F265I probably damaging Het
Tkfc T A 19: 10,573,727 (GRCm39) I229L probably benign Het
Tmem132c T A 5: 127,436,679 (GRCm39) L56Q probably damaging Het
Togaram2 C T 17: 72,016,638 (GRCm39) A665V probably damaging Het
Ttn G A 2: 76,537,390 (GRCm39) T34846I probably benign Het
Tyr G A 7: 87,142,548 (GRCm39) A4V probably benign Het
Ubap2 A C 4: 41,206,221 (GRCm39) F549L probably damaging Het
Usp2 T C 9: 44,001,339 (GRCm39) S294P probably damaging Het
Vrk3 A G 7: 44,407,187 (GRCm39) N53D probably damaging Het
Zfp324 T C 7: 12,705,142 (GRCm39) S444P probably damaging Het
Zfp597 T C 16: 3,683,791 (GRCm39) I322V probably benign Het
Other mutations in Lemd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01488:Lemd3 APN 10 120,769,304 (GRCm39) nonsense probably null
IGL01733:Lemd3 APN 10 120,769,568 (GRCm39) nonsense probably null
IGL02127:Lemd3 APN 10 120,761,933 (GRCm39) missense possibly damaging 0.58
IGL02171:Lemd3 APN 10 120,769,527 (GRCm39) splice site probably benign
Culebra UTSW 10 120,769,538 (GRCm39) missense probably damaging 1.00
R2044_Lemd3_698 UTSW 10 120,769,347 (GRCm39) missense probably damaging 1.00
R0037:Lemd3 UTSW 10 120,761,361 (GRCm39) missense possibly damaging 0.95
R0309:Lemd3 UTSW 10 120,773,015 (GRCm39) missense possibly damaging 0.71
R0829:Lemd3 UTSW 10 120,814,988 (GRCm39) missense probably benign
R1171:Lemd3 UTSW 10 120,785,246 (GRCm39) missense possibly damaging 0.90
R1382:Lemd3 UTSW 10 120,767,641 (GRCm39) missense probably damaging 0.99
R1954:Lemd3 UTSW 10 120,814,845 (GRCm39) missense probably damaging 0.99
R2044:Lemd3 UTSW 10 120,769,347 (GRCm39) missense probably damaging 1.00
R2197:Lemd3 UTSW 10 120,814,432 (GRCm39) small deletion probably benign
R3118:Lemd3 UTSW 10 120,783,156 (GRCm39) missense probably benign 0.00
R3697:Lemd3 UTSW 10 120,814,432 (GRCm39) small deletion probably benign
R3729:Lemd3 UTSW 10 120,763,920 (GRCm39) missense probably damaging 1.00
R4407:Lemd3 UTSW 10 120,761,335 (GRCm39) missense possibly damaging 0.93
R4429:Lemd3 UTSW 10 120,813,893 (GRCm39) missense probably benign 0.00
R4830:Lemd3 UTSW 10 120,767,853 (GRCm39) missense probably damaging 0.99
R5316:Lemd3 UTSW 10 120,788,161 (GRCm39) critical splice acceptor site probably null
R5355:Lemd3 UTSW 10 120,769,538 (GRCm39) missense probably damaging 1.00
R5404:Lemd3 UTSW 10 120,767,863 (GRCm39) nonsense probably null
R6754:Lemd3 UTSW 10 120,769,565 (GRCm39) missense probably damaging 1.00
R7213:Lemd3 UTSW 10 120,814,145 (GRCm39) nonsense probably null
R7699:Lemd3 UTSW 10 120,813,995 (GRCm39) missense probably damaging 0.99
R7700:Lemd3 UTSW 10 120,813,995 (GRCm39) missense probably damaging 0.99
R7781:Lemd3 UTSW 10 120,761,678 (GRCm39) missense probably damaging 1.00
R8681:Lemd3 UTSW 10 120,767,728 (GRCm39) missense possibly damaging 0.80
R9031:Lemd3 UTSW 10 120,767,878 (GRCm39) missense possibly damaging 0.94
R9274:Lemd3 UTSW 10 120,814,717 (GRCm39) missense possibly damaging 0.92
Predicted Primers PCR Primer
(F):5'- GCAAACATTCTATTGTCAGGAGC -3'
(R):5'- TTCAGTTGTGATGGCGAAAAC -3'

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