Incidental Mutation 'R0920:Ldb3'
| ID |
82832 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ldb3
|
| Ensembl Gene |
ENSMUSG00000021798 |
| Gene Name |
LIM domain binding 3 |
| Synonyms |
ZASP, cypher |
| MMRRC Submission |
039070-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0920 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
14 |
| Chromosomal Location |
34248560-34310639 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 34289460 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 249
(T249A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000022330
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000022327]
[ENSMUST00000022328]
[ENSMUST00000022330]
[ENSMUST00000064098]
[ENSMUST00000090040]
[ENSMUST00000227819]
[ENSMUST00000228044]
|
| AlphaFold |
Q9JKS4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000022327
AA Change: T249A
PolyPhen 2
Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000022327
Gene: ENSMUSG00000021798
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
PDZ
|
11 |
84 |
1.68e-16 |
SMART |
|
low complexity region
|
138 |
147 |
N/A |
INTRINSIC |
|
ZM
|
186 |
211 |
1.33e-8 |
SMART |
|
low complexity region
|
214 |
229 |
N/A |
INTRINSIC |
|
low complexity region
|
309 |
353 |
N/A |
INTRINSIC |
|
low complexity region
|
359 |
376 |
N/A |
INTRINSIC |
|
low complexity region
|
418 |
473 |
N/A |
INTRINSIC |
|
LIM
|
546 |
597 |
2.72e-16 |
SMART |
|
LIM
|
605 |
656 |
2.65e-19 |
SMART |
|
LIM
|
664 |
717 |
1.04e-17 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000022328
AA Change: T249A
PolyPhen 2
Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000022328
Gene: ENSMUSG00000021798
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
PDZ
|
11 |
84 |
1.68e-16 |
SMART |
|
low complexity region
|
138 |
147 |
N/A |
INTRINSIC |
|
ZM
|
186 |
211 |
1.33e-8 |
SMART |
|
low complexity region
|
214 |
229 |
N/A |
INTRINSIC |
|
low complexity region
|
297 |
314 |
N/A |
INTRINSIC |
|
low complexity region
|
356 |
411 |
N/A |
INTRINSIC |
|
LIM
|
484 |
535 |
2.72e-16 |
SMART |
|
LIM
|
543 |
594 |
2.65e-19 |
SMART |
|
LIM
|
602 |
655 |
1.04e-17 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000022330
AA Change: T249A
PolyPhen 2
Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000022330
Gene: ENSMUSG00000021798
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
PDZ
|
11 |
84 |
1.68e-16 |
SMART |
|
low complexity region
|
138 |
147 |
N/A |
INTRINSIC |
|
ZM
|
186 |
211 |
1.33e-8 |
SMART |
|
low complexity region
|
214 |
229 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000064098
AA Change: T205A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000066784
Gene: ENSMUSG00000021798
AA Change: T205A
| Domain | Start | End | E-Value | Type |
|---|
|
PDZ
|
11 |
84 |
1.68e-16 |
SMART |
|
ZM
|
148 |
173 |
5.18e-11 |
SMART |
|
low complexity region
|
265 |
309 |
N/A |
INTRINSIC |
|
low complexity region
|
315 |
332 |
N/A |
INTRINSIC |
|
low complexity region
|
374 |
429 |
N/A |
INTRINSIC |
|
LIM
|
502 |
553 |
2.72e-16 |
SMART |
|
LIM
|
561 |
612 |
2.65e-19 |
SMART |
|
LIM
|
620 |
673 |
1.04e-17 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000090040
AA Change: T210A
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000087494
Gene: ENSMUSG00000021798
AA Change: T210A
| Domain | Start | End | E-Value | Type |
|---|
|
PDZ
|
11 |
84 |
1.68e-16 |
SMART |
|
ZM
|
148 |
173 |
5.18e-11 |
SMART |
|
low complexity region
|
270 |
314 |
N/A |
INTRINSIC |
|
low complexity region
|
320 |
337 |
N/A |
INTRINSIC |
|
low complexity region
|
379 |
434 |
N/A |
INTRINSIC |
|
LIM
|
507 |
558 |
2.72e-16 |
SMART |
|
LIM
|
566 |
617 |
2.65e-19 |
SMART |
|
LIM
|
625 |
678 |
1.04e-17 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226226
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000227819
AA Change: T210A
PolyPhen 2
Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000228044
AA Change: T210A
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.6%
- 20x: 95.9%
|
| Validation Efficiency |
100% (37/37) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]
PHENOTYPE: Homozygous mutation of this gene results in lethality within a few days after birth from muscle abnormalities. Mutant mice exhibit myopathy, dysphagia, heart vascular congestion, dilated heart ventricles, cyanosis, and respiratory distress. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl4fm2 |
T |
C |
4: 144,287,696 (GRCm39) |
|
probably benign |
Het |
| Adamts16 |
A |
G |
13: 70,911,680 (GRCm39) |
|
probably benign |
Het |
| Adgra3 |
A |
G |
5: 50,118,503 (GRCm39) |
V1015A |
probably benign |
Het |
| Armc5 |
G |
T |
7: 127,839,491 (GRCm39) |
A270S |
probably damaging |
Het |
| Cacng1 |
A |
C |
11: 107,596,682 (GRCm39) |
|
probably benign |
Het |
| Ccdc33 |
T |
C |
9: 57,940,955 (GRCm39) |
D429G |
probably damaging |
Het |
| Ccdc88b |
G |
T |
19: 6,824,017 (GRCm39) |
A1412E |
probably benign |
Het |
| Cfap298 |
C |
T |
16: 90,724,267 (GRCm39) |
E125K |
probably damaging |
Het |
| Clock |
A |
T |
5: 76,378,167 (GRCm39) |
S578T |
possibly damaging |
Het |
| Crp |
T |
C |
1: 172,526,089 (GRCm39) |
F58S |
probably damaging |
Het |
| Dlg5 |
T |
A |
14: 24,226,465 (GRCm39) |
Q125L |
probably damaging |
Het |
| Eif3i |
T |
C |
4: 129,489,050 (GRCm39) |
|
probably benign |
Het |
| Gucy1a2 |
A |
C |
9: 3,759,472 (GRCm39) |
D426A |
probably damaging |
Het |
| Hpcal1 |
C |
T |
12: 17,841,098 (GRCm39) |
|
probably benign |
Het |
| Inf2 |
T |
A |
12: 112,576,721 (GRCm39) |
|
probably benign |
Het |
| Kdm7a |
A |
G |
6: 39,128,256 (GRCm39) |
L525P |
probably damaging |
Het |
| Kirrel3 |
A |
T |
9: 34,939,648 (GRCm39) |
I152F |
probably damaging |
Het |
| Knl1 |
T |
A |
2: 118,900,309 (GRCm39) |
I670K |
probably benign |
Het |
| Krt76 |
T |
C |
15: 101,800,874 (GRCm39) |
T141A |
possibly damaging |
Het |
| Magi3 |
A |
T |
3: 103,941,507 (GRCm39) |
|
probably null |
Het |
| Mfn1 |
A |
G |
3: 32,588,385 (GRCm39) |
|
probably null |
Het |
| Myb |
G |
T |
10: 21,002,133 (GRCm39) |
T736K |
possibly damaging |
Het |
| Myo5b |
A |
C |
18: 74,758,712 (GRCm39) |
K231T |
probably benign |
Het |
| Myt1l |
T |
A |
12: 29,936,138 (GRCm39) |
C909S |
unknown |
Het |
| Npas4 |
C |
A |
19: 5,036,344 (GRCm39) |
E607* |
probably null |
Het |
| Nphp3 |
A |
G |
9: 103,909,106 (GRCm39) |
N772S |
probably benign |
Het |
| Nup88 |
G |
T |
11: 70,847,146 (GRCm39) |
P288Q |
possibly damaging |
Het |
| Or2l13 |
A |
T |
16: 19,305,680 (GRCm39) |
I31F |
probably benign |
Het |
| Pknox1 |
C |
A |
17: 31,815,865 (GRCm39) |
Q240K |
probably damaging |
Het |
| Plce1 |
A |
C |
19: 38,724,965 (GRCm39) |
T1439P |
probably damaging |
Het |
| Ppp1r42 |
T |
A |
1: 10,069,750 (GRCm39) |
N104I |
probably damaging |
Het |
| Prkar2a |
T |
A |
9: 108,596,496 (GRCm39) |
|
probably benign |
Het |
| Stox2 |
C |
T |
8: 47,646,053 (GRCm39) |
R469Q |
probably damaging |
Het |
| Syna |
A |
G |
5: 134,587,956 (GRCm39) |
V331A |
probably benign |
Het |
| Vmn1r58 |
A |
T |
7: 5,413,788 (GRCm39) |
N147K |
probably benign |
Het |
| Zdhhc6 |
A |
T |
19: 55,300,133 (GRCm39) |
L148H |
probably damaging |
Het |
|
| Other mutations in Ldb3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01124:Ldb3
|
APN |
14 |
34,266,157 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01485:Ldb3
|
APN |
14 |
34,264,519 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01983:Ldb3
|
APN |
14 |
34,299,156 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0323:Ldb3
|
UTSW |
14 |
34,266,002 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0335:Ldb3
|
UTSW |
14 |
34,300,608 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R0483:Ldb3
|
UTSW |
14 |
34,258,541 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1524:Ldb3
|
UTSW |
14 |
34,277,313 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2161:Ldb3
|
UTSW |
14 |
34,289,353 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2246:Ldb3
|
UTSW |
14 |
34,251,432 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2865:Ldb3
|
UTSW |
14 |
34,251,460 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3113:Ldb3
|
UTSW |
14 |
34,251,418 (GRCm39) |
makesense |
probably null |
|
|
R3765:Ldb3
|
UTSW |
14 |
34,300,639 (GRCm39) |
splice site |
probably null |
|
|
R3870:Ldb3
|
UTSW |
14 |
34,289,440 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4018:Ldb3
|
UTSW |
14 |
34,274,128 (GRCm39) |
splice site |
probably benign |
|
|
R4797:Ldb3
|
UTSW |
14 |
34,277,470 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R4963:Ldb3
|
UTSW |
14 |
34,288,815 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5705:Ldb3
|
UTSW |
14 |
34,298,986 (GRCm39) |
missense |
probably null |
0.01 |
|
R6401:Ldb3
|
UTSW |
14 |
34,299,291 (GRCm39) |
missense |
probably benign |
0.33 |
|
R6549:Ldb3
|
UTSW |
14 |
34,263,854 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6682:Ldb3
|
UTSW |
14 |
34,274,221 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R6917:Ldb3
|
UTSW |
14 |
34,277,321 (GRCm39) |
missense |
probably null |
0.03 |
|
R7132:Ldb3
|
UTSW |
14 |
34,298,992 (GRCm39) |
missense |
probably benign |
0.25 |
|
R7327:Ldb3
|
UTSW |
14 |
34,293,759 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7488:Ldb3
|
UTSW |
14 |
34,289,402 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7760:Ldb3
|
UTSW |
14 |
34,264,460 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8755:Ldb3
|
UTSW |
14 |
34,299,256 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8845:Ldb3
|
UTSW |
14 |
34,258,634 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8954:Ldb3
|
UTSW |
14 |
34,277,301 (GRCm39) |
missense |
probably null |
0.17 |
|
R9179:Ldb3
|
UTSW |
14 |
34,277,312 (GRCm39) |
missense |
probably benign |
|
|
R9321:Ldb3
|
UTSW |
14 |
34,266,099 (GRCm39) |
nonsense |
probably null |
|
|
R9702:Ldb3
|
UTSW |
14 |
34,299,090 (GRCm39) |
missense |
probably benign |
0.03 |
|
Z1176:Ldb3
|
UTSW |
14 |
34,277,322 (GRCm39) |
missense |
probably benign |
0.21 |
|
Z1177:Ldb3
|
UTSW |
14 |
34,266,060 (GRCm39) |
missense |
probably damaging |
0.99 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCTGGAAGCCATATGACAAGGCATC -3'
(R):5'- ATGGGCAAGAAGCTGCTTTCCCAC -3'
Sequencing Primer
(F):5'- GCCATATGACAAGGCATCTGTTC -3'
(R):5'- CAGCTCTTCTGATAGCAGTGATG -3'
|
| Posted On |
2013-11-08 |
Incidental Mutation