Incidental Mutation 'R6754:Lemd3'
| ID |
530964 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lemd3
|
| Ensembl Gene |
ENSMUSG00000048661 |
| Gene Name |
LEM domain containing 3 |
| Synonyms |
Man1 |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6754 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
10 |
| Chromosomal Location |
120759318-120815237 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 120769565 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 589
(I589N)
|
| 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: I611N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: I611N
| 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: I589N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: I589N
| 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 |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.8%
- 10x: 98.9%
- 20x: 97.2%
|
| 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: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acsbg3 |
T |
C |
17: 57,190,358 (GRCm39) |
F352L |
probably damaging |
Het |
| Acta2 |
T |
C |
19: 34,222,383 (GRCm39) |
D246G |
probably damaging |
Het |
| Ank2 |
A |
G |
3: 126,890,488 (GRCm39) |
|
probably benign |
Het |
| Bmpr2 |
T |
A |
1: 59,909,439 (GRCm39) |
I971N |
probably damaging |
Het |
| C9 |
C |
A |
15: 6,519,424 (GRCm39) |
C8* |
probably null |
Het |
| Casp2 |
T |
A |
6: 42,246,264 (GRCm39) |
N207K |
probably damaging |
Het |
| Cd302 |
T |
G |
2: 60,102,451 (GRCm39) |
D56A |
probably benign |
Het |
| Cecr2 |
C |
T |
6: 120,734,539 (GRCm39) |
P605S |
probably damaging |
Het |
| Cep152 |
A |
G |
2: 125,429,588 (GRCm39) |
V723A |
probably damaging |
Het |
| Col17a1 |
C |
T |
19: 47,639,160 (GRCm39) |
|
probably null |
Het |
| Ctsk |
T |
C |
3: 95,409,996 (GRCm39) |
V168A |
probably damaging |
Het |
| Cyp2c54 |
A |
T |
19: 40,060,004 (GRCm39) |
N176K |
probably damaging |
Het |
| Dnah8 |
G |
A |
17: 30,967,542 (GRCm39) |
D2585N |
probably benign |
Het |
| F5 |
A |
G |
1: 164,021,332 (GRCm39) |
D1269G |
probably damaging |
Het |
| Fat3 |
C |
T |
9: 15,826,357 (GRCm39) |
E4532K |
possibly damaging |
Het |
| Hivep2 |
G |
A |
10: 14,005,382 (GRCm39) |
G660D |
probably benign |
Het |
| Hspb3 |
A |
T |
13: 113,799,688 (GRCm39) |
I114K |
probably damaging |
Het |
| Irag1 |
G |
A |
7: 110,528,719 (GRCm39) |
P43S |
probably damaging |
Het |
| Itgb7 |
T |
G |
15: 102,124,595 (GRCm39) |
*807C |
probably null |
Het |
| Kbtbd2 |
A |
G |
6: 56,756,239 (GRCm39) |
V499A |
probably damaging |
Het |
| Mettl13 |
T |
C |
1: 162,375,692 (GRCm39) |
Y45C |
probably damaging |
Het |
| Mllt6 |
C |
T |
11: 97,565,273 (GRCm39) |
T571I |
probably damaging |
Het |
| Nabp1 |
A |
G |
1: 51,513,699 (GRCm39) |
I99T |
probably damaging |
Het |
| Ndufa4 |
A |
G |
6: 11,906,052 (GRCm39) |
V33A |
probably benign |
Het |
| Nr1h5 |
A |
G |
3: 102,856,913 (GRCm39) |
S200P |
probably damaging |
Het |
| Ntsr1 |
G |
A |
2: 180,184,476 (GRCm39) |
R393H |
probably benign |
Het |
| Obi1 |
C |
T |
14: 104,740,850 (GRCm39) |
E191K |
probably damaging |
Het |
| Or14j4 |
T |
C |
17: 37,921,046 (GRCm39) |
N199D |
probably benign |
Het |
| Or4c116 |
G |
T |
2: 88,942,640 (GRCm39) |
T72N |
possibly damaging |
Het |
| Pcdhb21 |
A |
T |
18: 37,647,736 (GRCm39) |
K288N |
probably benign |
Het |
| Pla2g6 |
T |
C |
15: 79,190,510 (GRCm39) |
N351D |
probably benign |
Het |
| Polg |
T |
C |
7: 79,109,584 (GRCm39) |
E411G |
probably damaging |
Het |
| Prdm11 |
A |
G |
2: 92,844,137 (GRCm39) |
L31P |
probably damaging |
Het |
| Rab27b |
G |
A |
18: 70,129,174 (GRCm39) |
T40I |
probably damaging |
Het |
| Ruvbl2 |
T |
C |
7: 45,078,182 (GRCm39) |
D97G |
probably benign |
Het |
| Saxo4 |
A |
T |
19: 10,454,453 (GRCm39) |
Y328N |
probably damaging |
Het |
| Sema3a |
T |
C |
5: 13,649,243 (GRCm39) |
V664A |
possibly damaging |
Het |
| Sh2d3c |
T |
C |
2: 32,644,542 (GRCm39) |
S842P |
probably damaging |
Het |
| Spam1 |
A |
G |
6: 24,796,315 (GRCm39) |
T89A |
probably damaging |
Het |
| Stab1 |
C |
T |
14: 30,863,038 (GRCm39) |
G2187E |
probably benign |
Het |
| Tff2 |
C |
A |
17: 31,363,207 (GRCm39) |
A6S |
probably benign |
Het |
| Trim80 |
T |
C |
11: 115,339,000 (GRCm39) |
V610A |
probably damaging |
Het |
| Trp53bp1 |
A |
G |
2: 121,101,057 (GRCm39) |
V47A |
possibly damaging |
Het |
| Ufl1 |
G |
A |
4: 25,267,796 (GRCm39) |
Q292* |
probably null |
Het |
| Ulk1 |
A |
T |
5: 110,938,259 (GRCm39) |
V571E |
possibly damaging |
Het |
| Usp24 |
A |
T |
4: 106,217,617 (GRCm39) |
N447Y |
probably damaging |
Het |
| Vmn1r81 |
A |
T |
7: 11,993,774 (GRCm39) |
I278K |
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 |
|
|
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 |
|
|
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'- ACAGTAATGAAAGCACGCCG -3'
(R):5'- CTATTGGAATCATGAGAAGATGGTG -3'
Sequencing Primer
(F):5'- CTGGTGGACTGTAAAAACTGCACATC -3'
(R):5'- GGAATCATGAGAAGATGGTGTTTTTC -3'
|
| Posted On |
2018-08-01 |
Incidental Mutation