Incidental Mutation 'R5830:Ldb1'
| ID |
449293 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ldb1
|
| Ensembl Gene |
ENSMUSG00000025223 |
| Gene Name |
LIM domain binding 1 |
| Synonyms |
CLIM2 |
| MMRRC Submission |
043219-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5830 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
46020009-46033653 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 46022557 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Leucine
at position 307
(M307L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000139562
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026252]
[ENSMUST00000056931]
[ENSMUST00000137771]
[ENSMUST00000152946]
[ENSMUST00000156585]
[ENSMUST00000185355]
|
| AlphaFold |
P70662 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000026252
AA Change: M271L
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000026252
Gene: ENSMUSG00000025223
AA Change: M271L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LIM_bind
|
32 |
236 |
1e-72 |
PFAM |
|
low complexity region
|
264 |
287 |
N/A |
INTRINSIC |
|
PDB:2JTN|A
|
295 |
339 |
1e-22 |
PDB |
|
low complexity region
|
355 |
368 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000056931
AA Change: M271L
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000053680
Gene: ENSMUSG00000025223
AA Change: M271L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LIM_bind
|
32 |
236 |
1e-72 |
PFAM |
|
low complexity region
|
264 |
287 |
N/A |
INTRINSIC |
|
PDB:2JTN|A
|
295 |
339 |
1e-22 |
PDB |
|
low complexity region
|
355 |
368 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126320
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136203
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137771
AA Change: M271L
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000114667
Gene: ENSMUSG00000025223
AA Change: M271L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LIM_bind
|
32 |
236 |
5.4e-73 |
PFAM |
|
low complexity region
|
264 |
287 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000152946
AA Change: M271L
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000116909
Gene: ENSMUSG00000025223
AA Change: M271L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LIM_bind
|
33 |
189 |
1.1e-42 |
PFAM |
|
Pfam:LIM_bind
|
178 |
235 |
5.5e-15 |
PFAM |
|
low complexity region
|
264 |
287 |
N/A |
INTRINSIC |
|
PDB:2YPA|D
|
298 |
337 |
4e-21 |
PDB |
|
low complexity region
|
353 |
366 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000156585
AA Change: M307L
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000118546
Gene: ENSMUSG00000025223
AA Change: M307L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LIM_bind
|
69 |
225 |
5.9e-42 |
PFAM |
|
Pfam:LIM_bind
|
214 |
271 |
2.5e-14 |
PFAM |
|
low complexity region
|
300 |
323 |
N/A |
INTRINSIC |
|
PDB:2JTN|A
|
331 |
375 |
2e-22 |
PDB |
|
low complexity region
|
391 |
404 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000185355
AA Change: M307L
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000139562
Gene: ENSMUSG00000025223
AA Change: M307L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LIM_bind
|
68 |
272 |
5.6e-73 |
PFAM |
|
low complexity region
|
300 |
323 |
N/A |
INTRINSIC |
|
PDB:2JTN|A
|
331 |
375 |
2e-22 |
PDB |
|
low complexity region
|
391 |
404 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.4%
- 10x: 97.1%
- 20x: 90.6%
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Mice homozygous for disruptions in this gene die as embryos at E9.5-E10 with impaired primitive erythropoiesis and vascular development. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Apobec3 |
A |
T |
15: 79,783,268 (GRCm39) |
N115I |
possibly damaging |
Het |
| Arl14ep |
T |
C |
2: 106,799,539 (GRCm39) |
S101G |
possibly damaging |
Het |
| Atp6v0a2 |
C |
T |
5: 124,779,485 (GRCm39) |
T200I |
probably damaging |
Het |
| Ccdc40 |
C |
A |
11: 119,133,572 (GRCm39) |
H571N |
probably benign |
Het |
| Cdc42bpb |
G |
A |
12: 111,312,016 (GRCm39) |
R99* |
probably null |
Het |
| Cdyl2 |
A |
G |
8: 117,321,823 (GRCm39) |
Y235H |
probably benign |
Het |
| Chmp2a |
T |
C |
7: 12,766,039 (GRCm39) |
D161G |
probably damaging |
Het |
| Ep400 |
A |
T |
5: 110,831,862 (GRCm39) |
W2091R |
unknown |
Het |
| Epha8 |
G |
A |
4: 136,663,701 (GRCm39) |
Q452* |
probably null |
Het |
| Fbn2 |
A |
G |
18: 58,247,541 (GRCm39) |
F451S |
probably benign |
Het |
| Fndc1 |
C |
A |
17: 8,007,918 (GRCm39) |
R72L |
possibly damaging |
Het |
| Gfpt2 |
A |
G |
11: 49,699,888 (GRCm39) |
E81G |
probably benign |
Het |
| Gpr155 |
A |
G |
2: 73,200,433 (GRCm39) |
V358A |
possibly damaging |
Het |
| Hnrnpk |
A |
T |
13: 58,545,548 (GRCm39) |
Y92* |
probably null |
Het |
| Il34 |
A |
G |
8: 111,475,323 (GRCm39) |
V71A |
probably damaging |
Het |
| Inpp5e |
A |
G |
2: 26,290,427 (GRCm39) |
F416L |
probably damaging |
Het |
| Iqgap2 |
C |
T |
13: 95,811,880 (GRCm39) |
R707H |
probably damaging |
Het |
| Kdsr |
A |
G |
1: 106,675,262 (GRCm39) |
S125P |
possibly damaging |
Het |
| Lrr1 |
T |
A |
12: 69,225,445 (GRCm39) |
S374T |
possibly damaging |
Het |
| Mtmr2 |
A |
G |
9: 13,713,274 (GRCm39) |
I412V |
probably benign |
Het |
| Ncor1 |
T |
C |
11: 62,235,589 (GRCm39) |
I298V |
possibly damaging |
Het |
| Ndst1 |
A |
G |
18: 60,836,910 (GRCm39) |
F384L |
probably damaging |
Het |
| Nlrc5 |
A |
G |
8: 95,199,542 (GRCm39) |
E51G |
probably damaging |
Het |
| Obox6 |
G |
A |
7: 15,568,382 (GRCm39) |
H165Y |
possibly damaging |
Het |
| Or5k17 |
T |
A |
16: 58,746,457 (GRCm39) |
H159L |
possibly damaging |
Het |
| Pde8b |
A |
T |
13: 95,178,398 (GRCm39) |
F582Y |
probably benign |
Het |
| Pik3r4 |
C |
A |
9: 105,522,023 (GRCm39) |
Y196* |
probably null |
Het |
| Pink1 |
A |
T |
4: 138,043,325 (GRCm39) |
M1K |
probably null |
Het |
| Scn7a |
A |
T |
2: 66,544,395 (GRCm39) |
Y365* |
probably null |
Het |
| Sec16a |
A |
T |
2: 26,330,853 (GRCm39) |
D387E |
probably benign |
Het |
| Sel1l |
A |
T |
12: 91,799,945 (GRCm39) |
F127Y |
probably damaging |
Het |
| Syt7 |
T |
A |
19: 10,399,151 (GRCm39) |
N82K |
probably damaging |
Het |
| Zfp358 |
G |
T |
8: 3,545,846 (GRCm39) |
V143L |
probably benign |
Het |
| Zkscan2 |
T |
C |
7: 123,079,323 (GRCm39) |
N878S |
possibly damaging |
Het |
|
| Other mutations in Ldb1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01603:Ldb1
|
APN |
19 |
46,024,014 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02069:Ldb1
|
APN |
19 |
46,021,617 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
IGL02380:Ldb1
|
APN |
19 |
46,022,929 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02441:Ldb1
|
APN |
19 |
46,024,195 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02677:Ldb1
|
APN |
19 |
46,024,594 (GRCm39) |
splice site |
probably benign |
|
|
R1585:Ldb1
|
UTSW |
19 |
46,022,903 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R3720:Ldb1
|
UTSW |
19 |
46,033,331 (GRCm39) |
start gained |
probably benign |
|
|
R4897:Ldb1
|
UTSW |
19 |
46,023,132 (GRCm39) |
missense |
probably benign |
|
|
R7663:Ldb1
|
UTSW |
19 |
46,023,963 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8482:Ldb1
|
UTSW |
19 |
46,024,709 (GRCm39) |
missense |
probably null |
0.99 |
|
R8887:Ldb1
|
UTSW |
19 |
46,023,294 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9742:Ldb1
|
UTSW |
19 |
46,023,858 (GRCm39) |
critical splice donor site |
probably null |
|
|
X0027:Ldb1
|
UTSW |
19 |
46,022,528 (GRCm39) |
missense |
probably damaging |
0.99 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGGAAGGAGTCAGGTCATGC -3'
(R):5'- CTCACTTCTGGGACTACAAGG -3'
Sequencing Primer
(F):5'- AGCACATGAGGAACTGTCTTTGC -3'
(R):5'- CACTTCTGGGACTACAAGGCTGAG -3'
|
| Posted On |
2016-12-20 |
Incidental Mutation