Incidental Mutation 'IGL01960:Dnmt3b'
| ID |
182377 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Dnmt3b
|
| Ensembl Gene |
ENSMUSG00000027478 |
| Gene Name |
DNA methyltransferase 3B |
| Synonyms |
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL01960
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
2 |
| Chromosomal Location |
153491370-153529650 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 153518631 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Arginine
at position 578
(K578R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105395
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056495]
[ENSMUST00000072997]
[ENSMUST00000081628]
[ENSMUST00000088976]
[ENSMUST00000103150]
[ENSMUST00000103151]
[ENSMUST00000109771]
[ENSMUST00000109774]
[ENSMUST00000109772]
[ENSMUST00000109773]
|
| AlphaFold |
O88509 |
| PDB Structure |
Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000056495
AA Change: K599R
PolyPhen 2
Score 0.409 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
AA Change: K599R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
low complexity region
|
380 |
389 |
N/A |
INTRINSIC |
|
PDB:3A1A|A
|
421 |
560 |
8e-55 |
PDB |
|
Blast:RING
|
483 |
532 |
6e-28 |
BLAST |
|
Pfam:DNA_methylase
|
582 |
732 |
3.1e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000072997
AA Change: K598R
PolyPhen 2
Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
AA Change: K598R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
low complexity region
|
380 |
389 |
N/A |
INTRINSIC |
|
PDB:3A1A|A
|
421 |
560 |
8e-55 |
PDB |
|
Blast:RING
|
483 |
532 |
6e-28 |
BLAST |
|
Pfam:DNA_methylase
|
581 |
731 |
4.5e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000081628
AA Change: K578R
PolyPhen 2
Score 0.832 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
AA Change: K578R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
PDB:3A1A|A
|
401 |
540 |
1e-54 |
PDB |
|
Blast:RING
|
463 |
512 |
7e-28 |
BLAST |
|
Pfam:DNA_methylase
|
561 |
711 |
4.4e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000088976
AA Change: K598R
PolyPhen 2
Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
AA Change: K598R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
low complexity region
|
380 |
389 |
N/A |
INTRINSIC |
|
PDB:3A1A|A
|
421 |
560 |
7e-55 |
PDB |
|
Blast:RING
|
483 |
532 |
5e-28 |
BLAST |
|
Pfam:DNA_methylase
|
581 |
727 |
2.9e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000103150
AA Change: K578R
PolyPhen 2
Score 0.832 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
AA Change: K578R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
PDB:3A1A|A
|
401 |
540 |
8e-55 |
PDB |
|
Blast:RING
|
463 |
512 |
6e-28 |
BLAST |
|
Pfam:DNA_methylase
|
561 |
707 |
4.2e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000103151
AA Change: K578R
PolyPhen 2
Score 0.832 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
AA Change: K578R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
PDB:3A1A|A
|
401 |
540 |
8e-55 |
PDB |
|
Blast:RING
|
463 |
512 |
6e-28 |
BLAST |
|
Pfam:DNA_methylase
|
561 |
707 |
4.2e-15 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000109771
AA Change: K599R
PolyPhen 2
Score 0.409 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
AA Change: K599R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
low complexity region
|
380 |
389 |
N/A |
INTRINSIC |
|
PDB:3A1A|A
|
421 |
560 |
8e-55 |
PDB |
|
Blast:RING
|
483 |
532 |
6e-28 |
BLAST |
|
Pfam:DNA_methylase
|
582 |
732 |
3.1e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000109774
AA Change: K598R
PolyPhen 2
Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
AA Change: K598R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
low complexity region
|
380 |
389 |
N/A |
INTRINSIC |
|
PDB:3A1A|A
|
421 |
560 |
8e-55 |
PDB |
|
Blast:RING
|
483 |
532 |
6e-28 |
BLAST |
|
Pfam:DNA_methylase
|
581 |
731 |
4.5e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000109772
AA Change: K598R
PolyPhen 2
Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
AA Change: K598R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
low complexity region
|
380 |
389 |
N/A |
INTRINSIC |
|
PDB:3A1A|A
|
421 |
560 |
7e-55 |
PDB |
|
Blast:RING
|
483 |
532 |
5e-28 |
BLAST |
|
Pfam:DNA_methylase
|
581 |
727 |
2.9e-15 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000109773
AA Change: K578R
PolyPhen 2
Score 0.832 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
AA Change: K578R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
97 |
N/A |
INTRINSIC |
|
low complexity region
|
157 |
179 |
N/A |
INTRINSIC |
|
PWWP
|
230 |
288 |
2.43e-26 |
SMART |
|
PDB:3A1A|A
|
401 |
540 |
1e-54 |
PDB |
|
Blast:RING
|
463 |
512 |
7e-28 |
BLAST |
|
Pfam:DNA_methylase
|
561 |
711 |
4.4e-15 |
PFAM |
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: This is one of two related genes encoding de novo DNA methyltransferases, which are responsible for the establishment of DNA methylation patterns in embryos. Loss of function of this gene results in severe developmental defects and loss of viability. Mutation of the related gene in humans causes immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. There is a pseudogene for this gene located adjacent to this gene in the same region of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Nov 2012]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit growth retardation and rostral neural tube defects, and die prenatally. Mutants exhibit slight under-methylation of endogenous viral DNA and substantial demethylation of minor satellite DNA. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrb2 |
G |
A |
4: 129,906,177 (GRCm39) |
|
probably benign |
Het |
| Adh7 |
T |
C |
3: 137,932,043 (GRCm39) |
I219T |
probably damaging |
Het |
| Ankmy1 |
C |
A |
1: 92,799,385 (GRCm39) |
|
probably benign |
Het |
| Aoc1 |
A |
G |
6: 48,885,537 (GRCm39) |
I681V |
probably benign |
Het |
| Arfgap3 |
T |
C |
15: 83,197,758 (GRCm39) |
T333A |
probably benign |
Het |
| Cdc42ep4 |
A |
G |
11: 113,619,830 (GRCm39) |
V187A |
probably benign |
Het |
| Cyp4f40 |
G |
A |
17: 32,878,535 (GRCm39) |
G26R |
probably benign |
Het |
| Dnah7b |
T |
A |
1: 46,163,497 (GRCm39) |
|
probably benign |
Het |
| Dnajb4 |
T |
C |
3: 151,892,176 (GRCm39) |
E219G |
probably damaging |
Het |
| Dst |
A |
T |
1: 34,329,570 (GRCm39) |
D4649V |
probably damaging |
Het |
| Fam20c |
T |
C |
5: 138,792,075 (GRCm39) |
S391P |
probably damaging |
Het |
| Fbxw10 |
A |
T |
11: 62,767,582 (GRCm39) |
Y801F |
probably damaging |
Het |
| Frem2 |
T |
G |
3: 53,429,725 (GRCm39) |
E2775A |
probably benign |
Het |
| Frmd4b |
A |
T |
6: 97,272,741 (GRCm39) |
S830T |
possibly damaging |
Het |
| Gatad2a |
T |
G |
8: 70,362,598 (GRCm39) |
S581R |
possibly damaging |
Het |
| Gpcpd1 |
C |
T |
2: 132,381,818 (GRCm39) |
|
probably null |
Het |
| Igsf10 |
A |
G |
3: 59,226,158 (GRCm39) |
L2505P |
probably benign |
Het |
| Igsf9b |
A |
G |
9: 27,239,902 (GRCm39) |
D649G |
possibly damaging |
Het |
| Impact |
T |
C |
18: 13,107,815 (GRCm39) |
C28R |
probably benign |
Het |
| Ino80d |
G |
T |
1: 63,097,306 (GRCm39) |
Q863K |
probably damaging |
Het |
| Iqsec1 |
A |
C |
6: 90,653,762 (GRCm39) |
M675R |
probably damaging |
Het |
| Kcng3 |
C |
T |
17: 83,895,279 (GRCm39) |
V396I |
probably damaging |
Het |
| Klhl18 |
A |
T |
9: 110,279,814 (GRCm39) |
D60E |
probably benign |
Het |
| Krtap7-1 |
C |
T |
16: 89,305,156 (GRCm39) |
|
probably benign |
Het |
| Mal2 |
T |
A |
15: 54,461,941 (GRCm39) |
Y145* |
probably null |
Het |
| Mcpt8 |
A |
T |
14: 56,319,864 (GRCm39) |
|
probably null |
Het |
| Mdn1 |
A |
G |
4: 32,758,393 (GRCm39) |
D4810G |
probably benign |
Het |
| Med24 |
T |
C |
11: 98,598,368 (GRCm39) |
I766V |
probably benign |
Het |
| Mga |
G |
A |
2: 119,769,138 (GRCm39) |
V1477M |
probably damaging |
Het |
| Mybph |
T |
A |
1: 134,121,663 (GRCm39) |
V112E |
probably benign |
Het |
| Nmur2 |
A |
T |
11: 55,931,337 (GRCm39) |
S125T |
probably damaging |
Het |
| Or2w3 |
T |
C |
11: 58,556,691 (GRCm39) |
V102A |
probably benign |
Het |
| Or6c212 |
A |
G |
10: 129,558,756 (GRCm39) |
I219T |
probably damaging |
Het |
| Or8b44 |
A |
T |
9: 38,410,003 (GRCm39) |
I13F |
probably damaging |
Het |
| Otop3 |
A |
G |
11: 115,231,795 (GRCm39) |
N220S |
probably damaging |
Het |
| Pacsin1 |
T |
G |
17: 27,923,809 (GRCm39) |
|
probably null |
Het |
| Pcsk1 |
A |
G |
13: 75,241,286 (GRCm39) |
R89G |
possibly damaging |
Het |
| Pde2a |
A |
T |
7: 101,153,947 (GRCm39) |
E509V |
probably benign |
Het |
| Pex1 |
T |
C |
5: 3,677,588 (GRCm39) |
|
probably benign |
Het |
| Ppp4r4 |
T |
G |
12: 103,547,753 (GRCm39) |
|
probably benign |
Het |
| Pygb |
T |
A |
2: 150,655,403 (GRCm39) |
N251K |
probably benign |
Het |
| Rsf1 |
C |
T |
7: 97,310,782 (GRCm39) |
T504I |
probably benign |
Het |
| Slc5a11 |
A |
T |
7: 122,869,163 (GRCm39) |
T584S |
probably benign |
Het |
| Smad2 |
G |
A |
18: 76,395,555 (GRCm39) |
|
probably benign |
Het |
| Srsf6 |
G |
A |
2: 162,775,674 (GRCm39) |
R161H |
probably damaging |
Het |
| Tbx3 |
T |
A |
5: 119,820,708 (GRCm39) |
S573T |
probably benign |
Het |
| Tecpr1 |
C |
T |
5: 144,153,737 (GRCm39) |
R172Q |
probably benign |
Het |
| Ttn |
T |
A |
2: 76,619,244 (GRCm39) |
|
probably null |
Het |
| Ubr2 |
T |
C |
17: 47,284,893 (GRCm39) |
M542V |
probably benign |
Het |
| Unc80 |
T |
C |
1: 66,647,659 (GRCm39) |
|
probably benign |
Het |
| Vmn1r222 |
T |
A |
13: 23,416,315 (GRCm39) |
K299N |
probably benign |
Het |
| Wwp1 |
A |
T |
4: 19,662,115 (GRCm39) |
|
probably benign |
Het |
| Zbtb46 |
T |
A |
2: 181,065,928 (GRCm39) |
H74L |
possibly damaging |
Het |
| Zfp106 |
A |
T |
2: 120,354,524 (GRCm39) |
L1416I |
probably damaging |
Het |
| Zfp106 |
A |
G |
2: 120,369,803 (GRCm39) |
L73S |
probably benign |
Het |
| Zfp667 |
G |
A |
7: 6,308,336 (GRCm39) |
G335R |
probably benign |
Het |
|
| Other mutations in Dnmt3b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00793:Dnmt3b
|
APN |
2 |
153,514,422 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
IGL00931:Dnmt3b
|
APN |
2 |
153,528,170 (GRCm39) |
splice site |
probably benign |
|
|
IGL01073:Dnmt3b
|
APN |
2 |
153,512,762 (GRCm39) |
splice site |
probably benign |
|
|
IGL01138:Dnmt3b
|
APN |
2 |
153,503,361 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02884:Dnmt3b
|
APN |
2 |
153,516,297 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03382:Dnmt3b
|
APN |
2 |
153,528,279 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4151001:Dnmt3b
|
UTSW |
2 |
153,526,399 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0062:Dnmt3b
|
UTSW |
2 |
153,514,192 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0122:Dnmt3b
|
UTSW |
2 |
153,518,618 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0147:Dnmt3b
|
UTSW |
2 |
153,503,377 (GRCm39) |
missense |
possibly damaging |
0.68 |
|
R0178:Dnmt3b
|
UTSW |
2 |
153,516,938 (GRCm39) |
missense |
probably benign |
0.41 |
|
R0751:Dnmt3b
|
UTSW |
2 |
153,516,762 (GRCm39) |
splice site |
probably null |
|
|
R1696:Dnmt3b
|
UTSW |
2 |
153,518,630 (GRCm39) |
nonsense |
probably null |
|
|
R1795:Dnmt3b
|
UTSW |
2 |
153,525,559 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R1889:Dnmt3b
|
UTSW |
2 |
153,518,679 (GRCm39) |
missense |
probably benign |
|
|
R2898:Dnmt3b
|
UTSW |
2 |
153,509,550 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R4201:Dnmt3b
|
UTSW |
2 |
153,512,337 (GRCm39) |
nonsense |
probably null |
|
|
R4630:Dnmt3b
|
UTSW |
2 |
153,512,235 (GRCm39) |
nonsense |
probably null |
|
|
R4870:Dnmt3b
|
UTSW |
2 |
153,512,284 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5648:Dnmt3b
|
UTSW |
2 |
153,519,118 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5814:Dnmt3b
|
UTSW |
2 |
153,514,417 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6311:Dnmt3b
|
UTSW |
2 |
153,515,925 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6625:Dnmt3b
|
UTSW |
2 |
153,507,233 (GRCm39) |
missense |
probably benign |
|
|
R6818:Dnmt3b
|
UTSW |
2 |
153,528,204 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7258:Dnmt3b
|
UTSW |
2 |
153,525,519 (GRCm39) |
splice site |
probably null |
|
|
R7473:Dnmt3b
|
UTSW |
2 |
153,526,370 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7570:Dnmt3b
|
UTSW |
2 |
153,518,619 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7627:Dnmt3b
|
UTSW |
2 |
153,519,500 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7709:Dnmt3b
|
UTSW |
2 |
153,514,140 (GRCm39) |
missense |
probably benign |
0.10 |
|
R8483:Dnmt3b
|
UTSW |
2 |
153,516,306 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8771:Dnmt3b
|
UTSW |
2 |
153,504,734 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R8775:Dnmt3b
|
UTSW |
2 |
153,511,711 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R8775-TAIL:Dnmt3b
|
UTSW |
2 |
153,511,711 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R8821:Dnmt3b
|
UTSW |
2 |
153,518,734 (GRCm39) |
missense |
probably benign |
0.15 |
|
R8850:Dnmt3b
|
UTSW |
2 |
153,515,933 (GRCm39) |
missense |
probably benign |
0.16 |
|
R9102:Dnmt3b
|
UTSW |
2 |
153,518,703 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9228:Dnmt3b
|
UTSW |
2 |
153,507,980 (GRCm39) |
missense |
probably benign |
0.01 |
|
| Posted On |
2014-05-07 |
Incidental Mutation