Incidental Mutation 'R4348:Mbd1'
| ID |
500637 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Mbd1
|
| Ensembl Gene |
ENSMUSG00000024561 |
| Gene Name |
methyl-CpG binding domain protein 1 |
| Synonyms |
PCM1, Cxxc3 |
| MMRRC Submission |
041103-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4348 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
74400676-74415803 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 74407487 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Leucine
at position 199
(R199L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000153428
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000097530]
[ENSMUST00000224047]
[ENSMUST00000224332]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000097530
AA Change: R199L
PolyPhen 2
Score 0.932 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561
AA Change: R199L
| Domain | Start | End | E-Value | Type |
|---|
|
MBD
|
3 |
76 |
3.94e-27 |
SMART |
|
low complexity region
|
82 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
123 |
153 |
N/A |
INTRINSIC |
|
Pfam:zf-CXXC
|
194 |
241 |
1.9e-13 |
PFAM |
|
Pfam:zf-CXXC
|
243 |
288 |
1.2e-13 |
PFAM |
|
low complexity region
|
358 |
368 |
N/A |
INTRINSIC |
|
low complexity region
|
513 |
527 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000224047
AA Change: R199L
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224159
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000224332
AA Change: R89L
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224907
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| 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 multiple domains: MBD at the N-terminus that functions both in binding to methylated DNA and in protein interactions; several CXXC-type zinc finger domains that mediate binding to non-methylated CpG dinucleotides; transcriptional repression domain (TRD) at the C-terminus that is involved in transcription repression and in protein interactions. Numerous alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Feb 2011]
PHENOTYPE: Homozygous null exhibited defects in adult hippocampal neurogenesis and function. Spatial learning was also impaired in mutant mice. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(3) : Targeted(2) Gene trapped(1)
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A2ml1 |
C |
T |
6: 128,557,349 (GRCm39) |
A115T |
probably benign |
Het |
| Aass |
A |
G |
6: 23,113,738 (GRCm39) |
F235L |
probably benign |
Het |
| Adamts1 |
T |
A |
16: 85,599,234 (GRCm39) |
D122V |
probably benign |
Het |
| Adcy6 |
A |
T |
15: 98,502,041 (GRCm39) |
V191E |
probably benign |
Het |
| Cngb3 |
G |
A |
4: 19,396,688 (GRCm39) |
R347Q |
probably damaging |
Het |
| Cntnap4 |
T |
A |
8: 113,480,554 (GRCm39) |
C334S |
probably damaging |
Het |
| D7Ertd443e |
ACCTAGGAGGTCCT |
ACCT |
7: 133,950,682 (GRCm39) |
|
probably null |
Het |
| Dnah12 |
T |
A |
14: 26,536,498 (GRCm39) |
M2138K |
possibly damaging |
Het |
| Ebf2 |
T |
C |
14: 67,476,871 (GRCm39) |
I138T |
probably damaging |
Het |
| Ect2l |
A |
G |
10: 18,012,736 (GRCm39) |
S784P |
probably damaging |
Het |
| Emilin2 |
T |
C |
17: 71,587,726 (GRCm39) |
M129V |
probably benign |
Het |
| Enah |
A |
T |
1: 181,749,985 (GRCm39) |
S266T |
possibly damaging |
Het |
| Fhip1b |
A |
G |
7: 105,034,556 (GRCm39) |
V422A |
probably damaging |
Het |
| Garem2 |
G |
A |
5: 30,310,366 (GRCm39) |
R26H |
possibly damaging |
Het |
| Gfy |
T |
C |
7: 44,827,040 (GRCm39) |
E352G |
probably benign |
Het |
| Gpatch11 |
T |
C |
17: 79,148,446 (GRCm39) |
L128P |
probably damaging |
Het |
| Inava |
C |
T |
1: 136,153,946 (GRCm39) |
V180I |
probably damaging |
Het |
| Kcns3 |
T |
C |
12: 11,141,382 (GRCm39) |
N439S |
possibly damaging |
Het |
| Llgl1 |
C |
T |
11: 60,600,394 (GRCm39) |
P581L |
probably benign |
Het |
| Mbd5 |
T |
A |
2: 49,146,339 (GRCm39) |
M183K |
probably benign |
Het |
| Mecom |
C |
A |
3: 30,020,887 (GRCm39) |
V452L |
possibly damaging |
Het |
| Nckap1l |
A |
G |
15: 103,395,246 (GRCm39) |
T909A |
probably damaging |
Het |
| Ntrk2 |
A |
G |
13: 59,026,073 (GRCm39) |
K464E |
probably damaging |
Het |
| Orc1 |
C |
T |
4: 108,450,649 (GRCm39) |
T127I |
probably damaging |
Het |
| Pcdh17 |
T |
C |
14: 84,685,060 (GRCm39) |
I509T |
probably damaging |
Het |
| Pcsk7 |
G |
A |
9: 45,830,646 (GRCm39) |
A475T |
probably damaging |
Het |
| Prb1b |
T |
G |
6: 132,290,624 (GRCm39) |
Y25S |
unknown |
Het |
| Prdm16 |
A |
G |
4: 154,561,124 (GRCm39) |
V136A |
probably benign |
Het |
| Ptch1 |
C |
T |
13: 63,682,143 (GRCm39) |
R537H |
probably damaging |
Het |
| Ptpn13 |
T |
A |
5: 103,717,592 (GRCm39) |
S1879R |
probably damaging |
Het |
| Rasgrp3 |
A |
T |
17: 75,818,975 (GRCm39) |
Q388L |
probably benign |
Het |
| Rnf31 |
AAC |
A |
14: 55,838,555 (GRCm39) |
|
probably null |
Het |
| Rnf38 |
A |
T |
4: 44,149,100 (GRCm39) |
N82K |
possibly damaging |
Het |
| Smco3 |
T |
A |
6: 136,808,692 (GRCm39) |
T61S |
possibly damaging |
Het |
| Ssx2ip |
T |
C |
3: 146,138,245 (GRCm39) |
V364A |
probably benign |
Het |
| Ttn |
A |
G |
2: 76,595,109 (GRCm39) |
I20347T |
possibly damaging |
Het |
| Vmn2r120 |
A |
T |
17: 57,829,466 (GRCm39) |
F477Y |
possibly damaging |
Het |
| Wee1 |
A |
G |
7: 109,730,165 (GRCm39) |
H423R |
probably damaging |
Het |
|
| Other mutations in Mbd1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00902:Mbd1
|
APN |
18 |
74,408,310 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
IGL01551:Mbd1
|
APN |
18 |
74,402,614 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02213:Mbd1
|
APN |
18 |
74,408,453 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02562:Mbd1
|
APN |
18 |
74,409,993 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02596:Mbd1
|
APN |
18 |
74,409,868 (GRCm39) |
splice site |
probably benign |
|
|
IGL02944:Mbd1
|
APN |
18 |
74,410,481 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02973:Mbd1
|
APN |
18 |
74,408,498 (GRCm39) |
splice site |
probably benign |
|
|
IGL03200:Mbd1
|
APN |
18 |
74,409,502 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL03247:Mbd1
|
APN |
18 |
74,407,825 (GRCm39) |
nonsense |
probably null |
|
|
IGL03340:Mbd1
|
APN |
18 |
74,407,553 (GRCm39) |
missense |
probably benign |
0.00 |
|
Shortbread
|
UTSW |
18 |
74,407,128 (GRCm39) |
critical splice donor site |
probably null |
|
|
FR4737:Mbd1
|
UTSW |
18 |
74,406,644 (GRCm39) |
small deletion |
probably benign |
|
|
P0016:Mbd1
|
UTSW |
18 |
74,407,609 (GRCm39) |
nonsense |
probably null |
|
|
R0385:Mbd1
|
UTSW |
18 |
74,406,312 (GRCm39) |
frame shift |
probably null |
|
|
R0630:Mbd1
|
UTSW |
18 |
74,409,798 (GRCm39) |
splice site |
probably benign |
|
|
R0717:Mbd1
|
UTSW |
18 |
74,406,668 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R1084:Mbd1
|
UTSW |
18 |
74,402,603 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1290:Mbd1
|
UTSW |
18 |
74,402,557 (GRCm39) |
missense |
possibly damaging |
0.59 |
|
R1575:Mbd1
|
UTSW |
18 |
74,408,490 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2065:Mbd1
|
UTSW |
18 |
74,409,955 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2192:Mbd1
|
UTSW |
18 |
74,410,449 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2308:Mbd1
|
UTSW |
18 |
74,409,548 (GRCm39) |
missense |
probably benign |
0.42 |
|
R2697:Mbd1
|
UTSW |
18 |
74,406,688 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R3407:Mbd1
|
UTSW |
18 |
74,410,438 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R4664:Mbd1
|
UTSW |
18 |
74,402,597 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R5460:Mbd1
|
UTSW |
18 |
74,402,581 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5860:Mbd1
|
UTSW |
18 |
74,409,768 (GRCm39) |
nonsense |
probably null |
|
|
R6431:Mbd1
|
UTSW |
18 |
74,406,762 (GRCm39) |
splice site |
probably null |
|
|
R6734:Mbd1
|
UTSW |
18 |
74,409,114 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6861:Mbd1
|
UTSW |
18 |
74,406,645 (GRCm39) |
|
|
|
|
R7363:Mbd1
|
UTSW |
18 |
74,406,357 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7543:Mbd1
|
UTSW |
18 |
74,407,520 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7657:Mbd1
|
UTSW |
18 |
74,407,804 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7871:Mbd1
|
UTSW |
18 |
74,407,128 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8960:Mbd1
|
UTSW |
18 |
74,406,890 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9161:Mbd1
|
UTSW |
18 |
74,407,792 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9774:Mbd1
|
UTSW |
18 |
74,408,274 (GRCm39) |
missense |
probably benign |
|
|
RF005:Mbd1
|
UTSW |
18 |
74,406,644 (GRCm39) |
small deletion |
probably benign |
|
|
RF011:Mbd1
|
UTSW |
18 |
74,406,681 (GRCm39) |
small deletion |
probably benign |
|
|
RF024:Mbd1
|
UTSW |
18 |
74,406,681 (GRCm39) |
small deletion |
probably benign |
|
|
RF024:Mbd1
|
UTSW |
18 |
74,406,644 (GRCm39) |
small deletion |
probably benign |
|
|
RF058:Mbd1
|
UTSW |
18 |
74,406,680 (GRCm39) |
frame shift |
probably null |
|
|
Z1177:Mbd1
|
UTSW |
18 |
74,410,010 (GRCm39) |
missense |
probably null |
0.72 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTTAACAGAGCCCTTCCTTGTAGG -3'
(R):5'- TGTGATGTCTGGAGTCAGCC -3'
Sequencing Primer
(F):5'- CTTCCTTGTAGGGAACATCATAGCG -3'
(R):5'- AGTCAGCCGGGGACTGAG -3'
|
| Posted On |
2017-12-01 |
Incidental Mutation