Incidental Mutation 'R3729:Lemd3'
| ID |
270888 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lemd3
|
| Ensembl Gene |
ENSMUSG00000048661 |
| Gene Name |
LEM domain containing 3 |
| Synonyms |
Man1 |
| MMRRC Submission |
040719-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R3729 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
120759318-120815237 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 120763920 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 780
(D780G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000113103
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000119093]
[ENSMUST00000119944]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000118291
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000119093
AA Change: D802G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: D802G
| Domain | Start | End | E-Value | Type |
|---|
|
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: D780G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: D780G
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
0.1880 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
100% (48/48) |
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acacb |
A |
G |
5: 114,345,409 (GRCm39) |
D954G |
probably damaging |
Het |
| Acvr1 |
T |
C |
2: 58,352,925 (GRCm39) |
K345R |
probably null |
Het |
| Aldoart2 |
A |
G |
12: 55,613,104 (GRCm39) |
Y343C |
probably damaging |
Het |
| Arpp21 |
T |
A |
9: 111,895,047 (GRCm39) |
Y739F |
possibly damaging |
Het |
| Cachd1 |
C |
A |
4: 100,832,077 (GRCm39) |
Y746* |
probably null |
Het |
| Card14 |
T |
C |
11: 119,224,758 (GRCm39) |
V595A |
probably damaging |
Het |
| Dhx33 |
T |
C |
11: 70,879,978 (GRCm39) |
D344G |
probably benign |
Het |
| Dnah12 |
T |
A |
14: 26,427,220 (GRCm39) |
D171E |
probably benign |
Het |
| Fat3 |
A |
G |
9: 16,158,337 (GRCm39) |
|
probably benign |
Het |
| Fmnl3 |
A |
G |
15: 99,219,745 (GRCm39) |
F668L |
probably damaging |
Het |
| Frmpd4 |
G |
A |
X: 166,269,803 (GRCm39) |
T493M |
probably damaging |
Het |
| Gcn1 |
A |
T |
5: 115,721,453 (GRCm39) |
|
probably benign |
Het |
| Hspbp1 |
G |
T |
7: 4,680,808 (GRCm39) |
Q223K |
probably damaging |
Het |
| Ighv1-19 |
C |
A |
12: 114,672,497 (GRCm39) |
C40F |
probably damaging |
Het |
| Igkv4-90 |
A |
G |
6: 68,784,665 (GRCm39) |
F10L |
probably benign |
Het |
| Kctd5 |
T |
C |
17: 24,278,212 (GRCm39) |
D146G |
probably benign |
Het |
| Kif4-ps |
A |
G |
12: 101,112,369 (GRCm39) |
E166G |
probably damaging |
Het |
| Manba |
G |
A |
3: 135,260,611 (GRCm39) |
V599I |
probably benign |
Het |
| Map2 |
A |
G |
1: 66,451,605 (GRCm39) |
E247G |
possibly damaging |
Het |
| Mfsd1 |
T |
C |
3: 67,490,298 (GRCm39) |
F50L |
probably benign |
Het |
| Mier2 |
T |
C |
10: 79,380,876 (GRCm39) |
|
probably benign |
Het |
| Mslnl |
G |
A |
17: 25,961,908 (GRCm39) |
V128M |
probably damaging |
Het |
| Nol10 |
A |
T |
12: 17,474,674 (GRCm39) |
K622I |
probably benign |
Het |
| Or5p62 |
A |
T |
7: 107,771,516 (GRCm39) |
I145N |
probably benign |
Het |
| Or8d2b |
T |
C |
9: 38,788,547 (GRCm39) |
F25S |
probably damaging |
Het |
| Phtf1 |
A |
G |
3: 103,893,095 (GRCm39) |
M120V |
probably benign |
Het |
| Prrx1 |
A |
G |
1: 163,089,446 (GRCm39) |
L127P |
probably damaging |
Het |
| Rbsn |
T |
C |
6: 92,168,316 (GRCm39) |
M373V |
possibly damaging |
Het |
| Sec24b |
T |
C |
3: 129,827,482 (GRCm39) |
K203R |
possibly damaging |
Het |
| Shroom3 |
G |
T |
5: 93,090,945 (GRCm39) |
V1151F |
probably damaging |
Het |
| Slc16a10 |
G |
C |
10: 39,932,620 (GRCm39) |
H314D |
possibly damaging |
Het |
| Slc4a7 |
A |
T |
14: 14,729,276 (GRCm38) |
E47D |
probably damaging |
Het |
| Taf12 |
C |
A |
4: 132,010,265 (GRCm39) |
P78Q |
probably damaging |
Het |
| Tnn |
A |
G |
1: 159,973,810 (GRCm39) |
C186R |
probably damaging |
Het |
| Trim46 |
T |
A |
3: 89,142,256 (GRCm39) |
T721S |
probably benign |
Het |
| Trip4 |
T |
C |
9: 65,788,224 (GRCm39) |
N74D |
possibly damaging |
Het |
| Tssk5 |
C |
T |
15: 76,257,096 (GRCm39) |
R262H |
probably benign |
Het |
| Vegfa |
T |
C |
17: 46,335,446 (GRCm39) |
I105V |
possibly damaging |
Het |
| Vmn2r14 |
T |
C |
5: 109,364,095 (GRCm39) |
Y607C |
probably damaging |
Het |
| Wdr83 |
G |
T |
8: 85,806,968 (GRCm39) |
H66Q |
probably damaging |
Het |
| Zfp280b |
A |
G |
10: 75,874,936 (GRCm39) |
T272A |
probably benign |
Het |
| Zfp960 |
T |
A |
17: 17,308,633 (GRCm39) |
L449H |
probably damaging |
Het |
|
| Other mutations in Lemd3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
|
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 |
|
R7007:Lemd3
|
UTSW |
10 |
120,788,137 (GRCm39) |
missense |
probably benign |
0.28 |
|
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'- TCTCTGTGTCAAAGGTCAAACC -3'
(R):5'- CTTGCTCAGCTGGAGTAGAG -3'
Sequencing Primer
(F):5'- GGTCAAACCTTTGCTTAGAATTTAAC -3'
(R):5'- GCAGCCTTAGAGATCACA -3'
|
| Posted On |
2015-03-18 |
Incidental Mutation