Incidental Mutation 'R7008:Mbd4'
| ID |
544830 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Mbd4
|
| Ensembl Gene |
ENSMUSG00000030322 |
| Gene Name |
methyl-CpG binding domain protein 4 |
| Synonyms |
Med1 |
| MMRRC Submission |
045110-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.187)
|
| Stock # |
R7008 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
115817658-115830332 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 115827685 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 43
(T43A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000125619
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000032469]
[ENSMUST00000038234]
[ENSMUST00000112923]
[ENSMUST00000112925]
[ENSMUST00000122816]
[ENSMUST00000147282]
[ENSMUST00000203643]
[ENSMUST00000141305]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000032469
AA Change: T64A
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: T64A
| Domain | Start | End | E-Value | Type |
|---|
|
MBD
|
66 |
142 |
1.25e-29 |
SMART |
|
low complexity region
|
178 |
196 |
N/A |
INTRINSIC |
|
PDB:1NGN|A
|
400 |
554 |
1e-111 |
PDB |
|
SCOP:d1keaa_
|
405 |
545 |
1e-23 |
SMART |
|
Blast:ENDO3c
|
439 |
514 |
2e-6 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000038234
|
| SMART Domains |
Protein: ENSMUSP00000045468
Gene: ENSMUSG00000030323
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
1 |
39 |
7.1e1 |
SMART |
|
WD40
|
42 |
81 |
7.16e-10 |
SMART |
|
WD40
|
83 |
120 |
1.54e0 |
SMART |
|
WD40
|
122 |
160 |
1.43e0 |
SMART |
|
WD40
|
162 |
208 |
2.29e1 |
SMART |
|
WD40
|
210 |
249 |
1.91e1 |
SMART |
|
WD40
|
251 |
290 |
3.45e-3 |
SMART |
|
WD40
|
448 |
483 |
1.43e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000112923
|
| SMART Domains |
Protein: ENSMUSP00000108545
Gene: ENSMUSG00000030323
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
1 |
39 |
7.1e1 |
SMART |
|
WD40
|
42 |
81 |
7.16e-10 |
SMART |
|
WD40
|
83 |
120 |
1.54e0 |
SMART |
|
WD40
|
122 |
160 |
1.43e0 |
SMART |
|
Blast:WD40
|
163 |
267 |
3e-46 |
BLAST |
|
WD40
|
269 |
308 |
1.91e1 |
SMART |
|
WD40
|
310 |
349 |
3.45e-3 |
SMART |
|
WD40
|
507 |
542 |
1.43e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000112925
|
| SMART Domains |
Protein: ENSMUSP00000108547
Gene: ENSMUSG00000030323
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
1 |
39 |
7.1e1 |
SMART |
|
WD40
|
42 |
81 |
7.16e-10 |
SMART |
|
WD40
|
83 |
120 |
1.54e0 |
SMART |
|
WD40
|
122 |
160 |
1.43e0 |
SMART |
|
WD40
|
162 |
208 |
2.29e1 |
SMART |
|
WD40
|
210 |
249 |
1.91e1 |
SMART |
|
WD40
|
251 |
290 |
3.45e-3 |
SMART |
|
WD40
|
448 |
483 |
1.43e1 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000122816
AA Change: T64A
PolyPhen 2
Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322
AA Change: T64A
| Domain | Start | End | E-Value | Type |
|---|
|
MBD
|
66 |
142 |
7.6e-32 |
SMART |
|
low complexity region
|
178 |
196 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125889
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133830
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000147282
AA Change: T43A
PolyPhen 2
Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322
AA Change: T43A
| Domain | Start | End | E-Value | Type |
|---|
|
MBD
|
45 |
121 |
1.25e-29 |
SMART |
|
low complexity region
|
157 |
175 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000203243
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000203643
|
| SMART Domains |
Protein: ENSMUSP00000144930
Gene: ENSMUSG00000030322
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:HhH-GPD
|
56 |
168 |
2.7e-5 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000141305
|
| SMART Domains |
Protein: ENSMUSP00000138535
Gene: ENSMUSG00000030323
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
1 |
39 |
7.1e1 |
SMART |
|
WD40
|
42 |
81 |
7.16e-10 |
SMART |
|
WD40
|
83 |
120 |
1.54e0 |
SMART |
|
low complexity region
|
124 |
134 |
N/A |
INTRINSIC |
|
low complexity region
|
162 |
176 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]
PHENOTYPE: Mice homozygous for a null allele have an increased rate of DNA mutation, specifically at CpGs. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(8) : Targeted(6) Gene trapped(2)
|
| Other mutations in this stock |
Total: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ankrd17 |
T |
A |
5: 90,407,955 (GRCm39) |
I1421F |
possibly damaging |
Het |
| Arhgef11 |
C |
A |
3: 87,636,525 (GRCm39) |
T992K |
possibly damaging |
Het |
| Arid1b |
T |
C |
17: 5,341,254 (GRCm39) |
Y853H |
probably damaging |
Het |
| Bcl10 |
G |
T |
3: 145,639,054 (GRCm39) |
R232L |
probably benign |
Het |
| Best2 |
T |
A |
8: 85,739,840 (GRCm39) |
I76F |
possibly damaging |
Het |
| Card11 |
G |
C |
5: 140,859,148 (GRCm39) |
R1133G |
probably damaging |
Het |
| Card9 |
T |
C |
2: 26,247,811 (GRCm39) |
D180G |
possibly damaging |
Het |
| Ccdc162 |
T |
A |
10: 41,428,411 (GRCm39) |
E119V |
probably damaging |
Het |
| Ccdc168 |
T |
C |
1: 44,098,785 (GRCm39) |
D771G |
probably benign |
Het |
| Cd2bp2 |
T |
C |
7: 126,794,567 (GRCm39) |
D15G |
possibly damaging |
Het |
| Cdk7 |
A |
C |
13: 100,854,129 (GRCm39) |
M120R |
probably damaging |
Het |
| Cryba4 |
T |
A |
5: 112,399,648 (GRCm39) |
T2S |
probably benign |
Het |
| Cyp19a1 |
A |
T |
9: 54,100,609 (GRCm39) |
M26K |
probably benign |
Het |
| Dgcr2 |
A |
G |
16: 17,662,865 (GRCm39) |
S157P |
probably damaging |
Het |
| Dis3l |
A |
G |
9: 64,217,735 (GRCm39) |
F782S |
possibly damaging |
Het |
| Ephb4 |
T |
A |
5: 137,359,536 (GRCm39) |
S369T |
probably benign |
Het |
| Fhad1 |
CGG |
CG |
4: 141,645,602 (GRCm39) |
|
probably null |
Het |
| H1f4 |
T |
C |
13: 23,806,192 (GRCm39) |
K97E |
probably damaging |
Het |
| Igf2bp2 |
A |
T |
16: 21,900,582 (GRCm39) |
D118E |
probably benign |
Het |
| Iqgap3 |
GGAGAG |
GGAG |
3: 88,020,078 (GRCm39) |
|
probably null |
Het |
| Klhl5 |
T |
C |
5: 65,300,592 (GRCm39) |
S52P |
probably benign |
Het |
| Lrrc28 |
A |
T |
7: 67,245,459 (GRCm39) |
|
probably benign |
Het |
| Map4k4 |
T |
G |
1: 40,028,131 (GRCm39) |
D317E |
probably benign |
Het |
| Maz |
A |
T |
7: 126,623,784 (GRCm39) |
C66S |
probably damaging |
Het |
| Milr1 |
T |
A |
11: 106,642,140 (GRCm39) |
S11T |
probably damaging |
Het |
| Mthfd2l |
T |
A |
5: 91,107,587 (GRCm39) |
C150S |
probably damaging |
Het |
| Nemf |
A |
T |
12: 69,388,395 (GRCm39) |
N325K |
possibly damaging |
Het |
| Nemf |
C |
T |
12: 69,400,567 (GRCm39) |
|
probably null |
Het |
| Nod2 |
T |
A |
8: 89,390,285 (GRCm39) |
C197* |
probably null |
Het |
| Odf2l |
A |
G |
3: 144,838,495 (GRCm39) |
K241E |
probably damaging |
Het |
| Or4z4 |
G |
A |
19: 12,076,214 (GRCm39) |
T263I |
possibly damaging |
Het |
| Or5b124 |
A |
T |
19: 13,610,985 (GRCm39) |
N170I |
probably damaging |
Het |
| Osbpl10 |
T |
G |
9: 114,890,916 (GRCm39) |
D101E |
probably damaging |
Het |
| Osgin1 |
T |
C |
8: 120,168,233 (GRCm39) |
V20A |
possibly damaging |
Het |
| Pan3 |
T |
A |
5: 147,482,503 (GRCm39) |
C438S |
probably damaging |
Het |
| Plaa |
A |
G |
4: 94,457,586 (GRCm39) |
*795Q |
probably null |
Het |
| Prss35 |
T |
C |
9: 86,638,361 (GRCm39) |
V377A |
probably benign |
Het |
| Rab5c |
G |
A |
11: 100,610,789 (GRCm39) |
R40C |
probably damaging |
Het |
| Rasl12 |
G |
A |
9: 65,318,151 (GRCm39) |
V172M |
probably damaging |
Het |
| Rdh16f1 |
A |
G |
10: 127,626,775 (GRCm39) |
H276R |
probably benign |
Het |
| Runx2 |
G |
A |
17: 45,125,079 (GRCm39) |
P80L |
probably damaging |
Het |
| Sez6l |
T |
C |
5: 112,612,561 (GRCm39) |
Y460C |
probably damaging |
Het |
| Sipa1l1 |
T |
G |
12: 82,409,886 (GRCm39) |
M600R |
probably damaging |
Het |
| Slc11a2 |
T |
C |
15: 100,307,205 (GRCm39) |
Y92C |
probably damaging |
Het |
| Slc4a10 |
A |
G |
2: 62,117,266 (GRCm39) |
T712A |
probably benign |
Het |
| Sntb1 |
A |
T |
15: 55,655,468 (GRCm39) |
Y249* |
probably null |
Het |
| Spatc1 |
A |
G |
15: 76,167,923 (GRCm39) |
I127M |
probably benign |
Het |
| Sting1 |
C |
A |
18: 35,868,224 (GRCm39) |
R292L |
probably damaging |
Het |
| Synj1 |
A |
T |
16: 90,790,833 (GRCm39) |
N109K |
probably damaging |
Het |
| Tdg |
T |
A |
10: 82,484,475 (GRCm39) |
M396K |
possibly damaging |
Het |
| Tmem252 |
T |
C |
19: 24,651,656 (GRCm39) |
V75A |
probably damaging |
Het |
| Trim40 |
T |
C |
17: 37,194,868 (GRCm39) |
Q142R |
probably damaging |
Het |
| Trip6 |
T |
C |
5: 137,311,228 (GRCm39) |
T163A |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,724,986 (GRCm39) |
|
probably benign |
Het |
| Wdr95 |
T |
C |
5: 149,535,005 (GRCm39) |
L721P |
probably benign |
Het |
| Zfp385c |
A |
T |
11: 100,521,513 (GRCm39) |
D182E |
probably damaging |
Het |
| Zfp597 |
A |
G |
16: 3,683,631 (GRCm39) |
F375S |
probably benign |
Het |
| Zfp658 |
T |
G |
7: 43,223,336 (GRCm39) |
F537C |
possibly damaging |
Het |
| Zgrf1 |
T |
C |
3: 127,355,421 (GRCm39) |
F216L |
probably benign |
Het |
|
| Other mutations in Mbd4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01516:Mbd4
|
APN |
6 |
115,826,491 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01545:Mbd4
|
APN |
6 |
115,827,758 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01657:Mbd4
|
APN |
6 |
115,826,598 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02406:Mbd4
|
APN |
6 |
115,825,986 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
E0370:Mbd4
|
UTSW |
6 |
115,826,116 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R0025:Mbd4
|
UTSW |
6 |
115,821,529 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0025:Mbd4
|
UTSW |
6 |
115,821,529 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0538:Mbd4
|
UTSW |
6 |
115,826,443 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2085:Mbd4
|
UTSW |
6 |
115,825,918 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4405:Mbd4
|
UTSW |
6 |
115,826,076 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R4464:Mbd4
|
UTSW |
6 |
115,826,463 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4780:Mbd4
|
UTSW |
6 |
115,826,345 (GRCm39) |
missense |
probably benign |
|
|
R4782:Mbd4
|
UTSW |
6 |
115,822,283 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R4799:Mbd4
|
UTSW |
6 |
115,822,283 (GRCm39) |
missense |
probably benign |
0.26 |
|
R4814:Mbd4
|
UTSW |
6 |
115,826,260 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R4860:Mbd4
|
UTSW |
6 |
115,825,887 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R4860:Mbd4
|
UTSW |
6 |
115,825,887 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R4976:Mbd4
|
UTSW |
6 |
115,827,685 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R5126:Mbd4
|
UTSW |
6 |
115,825,929 (GRCm39) |
splice site |
probably null |
|
|
R5202:Mbd4
|
UTSW |
6 |
115,826,363 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5485:Mbd4
|
UTSW |
6 |
115,827,679 (GRCm39) |
missense |
probably benign |
0.21 |
|
R6179:Mbd4
|
UTSW |
6 |
115,822,386 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6661:Mbd4
|
UTSW |
6 |
115,826,116 (GRCm39) |
nonsense |
probably null |
|
|
R7244:Mbd4
|
UTSW |
6 |
115,821,564 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7723:Mbd4
|
UTSW |
6 |
115,822,324 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R7755:Mbd4
|
UTSW |
6 |
115,821,546 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7837:Mbd4
|
UTSW |
6 |
115,826,500 (GRCm39) |
missense |
probably benign |
0.20 |
|
R8032:Mbd4
|
UTSW |
6 |
115,821,594 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9707:Mbd4
|
UTSW |
6 |
115,826,559 (GRCm39) |
missense |
probably benign |
0.04 |
|
| Predicted Primers |
PCR Primer
(F):5'- CAACCGCAGATTCTTGCTATC -3'
(R):5'- GGCACAAGACTAGCTCACTGAC -3'
Sequencing Primer
(F):5'- TCCTTTCCCATTACGGACAAAAATC -3'
(R):5'- AGTCTCATACTGCTGTGGGC -3'
|
| Posted On |
2019-05-13 |
Incidental Mutation