Incidental Mutation 'RF005:Mbd1'
| ID |
602795 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Mbd1
|
| Ensembl Gene |
ENSMUSG00000024561 |
| Gene Name |
methyl-CpG binding domain protein 1 |
| Synonyms |
PCM1, Cxxc3 |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
RF005 (G1)
|
| Quality Score |
217.468 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
74400676-74415803 bp(+) (GRCm39) |
| Type of Mutation |
small deletion (8 aa in frame mutation) |
| DNA Base Change (assembly) |
TGTCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGC to TATCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGC
at 74406644 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000153085
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000097530]
[ENSMUST00000224047]
[ENSMUST00000224332]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000097530
|
| SMART Domains |
Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561
| 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 benign
Transcript: ENSMUST00000224047
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224159
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000224332
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224907
|
| Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.7%
- 10x: 99.4%
- 20x: 98.6%
|
| Validation Efficiency |
94% (65/69) |
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5430401F13Rik |
AGAAAGGAAAAGGTGGCCAG |
AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG |
6: 131,529,847 (GRCm39) |
|
probably benign |
Het |
| A030005L19Rik |
CTGCTG |
CTGCTGTGGATGCTG |
1: 82,891,306 (GRCm39) |
|
probably benign |
Het |
| Abca1 |
G |
T |
4: 53,049,125 (GRCm39) |
T1651N |
probably damaging |
Het |
| Adamtsl3 |
A |
G |
7: 82,261,603 (GRCm39) |
T40A |
|
Het |
| Adgra3 |
A |
T |
5: 50,170,729 (GRCm39) |
|
probably null |
Het |
| Apcs |
A |
T |
1: 172,721,809 (GRCm39) |
M179K |
probably damaging |
Het |
| Baiap2 |
G |
A |
11: 119,887,355 (GRCm39) |
E217K |
possibly damaging |
Het |
| Bltp3a |
A |
T |
17: 28,104,505 (GRCm39) |
D517V |
probably damaging |
Het |
| Ccdc69 |
A |
G |
11: 54,951,349 (GRCm39) |
L24P |
probably damaging |
Het |
| Cdh16 |
T |
G |
8: 105,343,684 (GRCm39) |
N604T |
probably damaging |
Het |
| Cfb |
C |
T |
17: 35,077,022 (GRCm39) |
V538I |
possibly damaging |
Het |
| Col6a3 |
A |
G |
1: 90,738,984 (GRCm39) |
S1022P |
probably benign |
Het |
| Cpeb1 |
A |
G |
7: 81,011,554 (GRCm39) |
L129S |
possibly damaging |
Het |
| Crybg1 |
A |
G |
10: 43,880,741 (GRCm39) |
V149A |
probably benign |
Het |
| Cyp4f16 |
C |
A |
17: 32,764,169 (GRCm39) |
|
probably null |
Het |
| Dlg5 |
G |
A |
14: 24,208,561 (GRCm39) |
Q882* |
probably null |
Het |
| Fsip2 |
T |
A |
2: 82,822,876 (GRCm39) |
I6203K |
probably benign |
Het |
| Gabre |
CCGGCT |
CCGGCTACGGCT |
X: 71,313,651 (GRCm39) |
|
probably null |
Het |
| Gprc5d |
A |
T |
6: 135,093,517 (GRCm39) |
L130Q |
probably damaging |
Het |
| H13 |
G |
A |
2: 152,511,589 (GRCm39) |
E30K |
probably damaging |
Het |
| Hmcn1 |
T |
A |
1: 150,510,897 (GRCm39) |
K3609* |
probably null |
Het |
| Hsdl2 |
GCTGCAG |
GCTGCAGCAGCAGCCACATCTGCAG |
4: 59,610,652 (GRCm39) |
|
probably benign |
Het |
| Kl |
A |
C |
5: 150,876,885 (GRCm39) |
Y235S |
probably benign |
Het |
| Map6d1 |
G |
A |
16: 20,059,750 (GRCm39) |
T105I |
probably benign |
Het |
| Mast4 |
GGTGGTGGTGG |
GGTGGTGGTGGTGGTGG |
13: 102,872,815 (GRCm39) |
|
probably benign |
Het |
| Mms22l |
A |
G |
4: 24,517,207 (GRCm39) |
I363V |
probably benign |
Het |
| Myo7a |
T |
C |
7: 97,742,824 (GRCm39) |
I391V |
probably benign |
Het |
| Nab2 |
A |
T |
10: 127,500,233 (GRCm39) |
D286E |
probably benign |
Het |
| Nrxn1 |
G |
A |
17: 90,670,304 (GRCm39) |
R1144C |
probably damaging |
Het |
| Or51q1 |
A |
G |
7: 103,628,768 (GRCm39) |
D123G |
probably damaging |
Het |
| Or52j3 |
T |
C |
7: 102,835,898 (GRCm39) |
I30T |
possibly damaging |
Het |
| Or5al5 |
T |
C |
2: 85,961,414 (GRCm39) |
M198V |
probably benign |
Het |
| Pan2 |
G |
A |
10: 128,151,404 (GRCm39) |
E842K |
probably benign |
Het |
| Pate11 |
T |
C |
9: 36,386,970 (GRCm39) |
S13P |
possibly damaging |
Het |
| Polr1has |
CACCACCACCACCACCACCAC |
CACCACCACCACCACCACCACAACCACCACCACCACCACCAC |
17: 37,275,940 (GRCm39) |
|
probably benign |
Het |
| Prex2 |
A |
C |
1: 11,255,390 (GRCm39) |
D1145A |
possibly damaging |
Het |
| Prop1 |
A |
C |
11: 50,841,957 (GRCm39) |
Y150D |
possibly damaging |
Het |
| Prp2 |
AGGCCCACAGCAGCGACCCCCTCAAGGCCCACCACCACCAGGTGGCCCACAGCCGAGACCCCCTCAAGGCCCACCACC |
AGGCCCACAGCCGAGACCCCCTCAAGGCCCACCACC |
6: 132,577,464 (GRCm39) |
|
probably benign |
Het |
| Psip1 |
T |
C |
4: 83,378,735 (GRCm39) |
I353M |
probably damaging |
Het |
| Rapgef1 |
C |
A |
2: 29,597,207 (GRCm39) |
|
probably null |
Het |
| Rgl1 |
G |
A |
1: 152,397,114 (GRCm39) |
S684L |
probably benign |
Het |
| Sbf2 |
T |
A |
7: 109,916,215 (GRCm39) |
D1552V |
probably damaging |
Het |
| Scpppq1 |
A |
C |
5: 104,222,725 (GRCm39) |
|
probably null |
Het |
| Serpinh1 |
C |
T |
7: 98,995,410 (GRCm39) |
V391M |
probably damaging |
Het |
| Slc35e4 |
A |
T |
11: 3,857,960 (GRCm39) |
L215Q |
possibly damaging |
Het |
| Tbl3 |
TCTT |
TCTTCTT |
17: 24,921,515 (GRCm39) |
|
probably benign |
Het |
| Tex15 |
T |
A |
8: 34,066,705 (GRCm39) |
M2045K |
probably benign |
Het |
| Tmprss15 |
T |
C |
16: 78,750,689 (GRCm39) |
*1070W |
probably null |
Het |
| Trav15-2-dv6-2 |
GAA |
GAACAA |
14: 53,887,211 (GRCm39) |
|
probably benign |
Het |
| Trav15-2-dv6-2 |
GGGAG |
GGGAGGAG |
14: 53,887,207 (GRCm39) |
|
probably benign |
Het |
| Trav15-2-dv6-2 |
GGAG |
GGAGGAG |
14: 53,887,208 (GRCm39) |
|
probably benign |
Het |
| Trim33 |
GCCCCGGCCCCCG |
GCCCCG |
3: 103,187,528 (GRCm39) |
|
probably null |
Het |
| Triobp |
GACAA |
GACAACCCCAGGACTCCCTGTGCCCAACGGAACAA |
15: 78,851,261 (GRCm39) |
|
probably benign |
Het |
| Tub |
C |
A |
7: 108,621,846 (GRCm39) |
Q95K |
probably benign |
Het |
| Usp9y |
T |
A |
Y: 1,435,046 (GRCm39) |
Q261L |
probably benign |
Het |
| Utp20 |
A |
T |
10: 88,661,319 (GRCm39) |
D29E |
probably damaging |
Het |
| Vill |
G |
A |
9: 118,889,507 (GRCm39) |
V148M |
probably damaging |
Het |
| Vmn2r120 |
C |
T |
17: 57,828,991 (GRCm39) |
E535K |
possibly damaging |
Het |
| Zfp451 |
A |
T |
1: 33,815,873 (GRCm39) |
Y692* |
probably null |
Het |
| Zfp599 |
A |
C |
9: 22,165,180 (GRCm39) |
V65G |
probably benign |
Het |
| Zfp808 |
T |
C |
13: 62,319,113 (GRCm39) |
V114A |
probably benign |
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 |
|
R4348:Mbd1
|
UTSW |
18 |
74,407,487 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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 |
|
|
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'- TAGGGCAATTGTGTCACATGG -3'
(R):5'- CAATTCTCACAGCACCTAGGG -3'
Sequencing Primer
(F):5'- GCACCCGGGCATTAATCTATGTG -3'
(R):5'- TTCTCACAGCACCTAGGGTAAAAAGG -3'
|
| Posted On |
2019-12-04 |
Incidental Mutation