Incidental Mutation 'PIT4151001:Dnmt3b'
| ID |
557005 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Dnmt3b
|
| Ensembl Gene |
ENSMUSG00000027478 |
| Gene Name |
DNA methyltransferase 3B |
| Synonyms |
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
PIT4151001 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
153491370-153529650 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to G
at 153526399 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000072761
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056495]
[ENSMUST00000072997]
[ENSMUST00000081628]
[ENSMUST00000088976]
[ENSMUST00000103150]
[ENSMUST00000103151]
[ENSMUST00000109771]
[ENSMUST00000109772]
[ENSMUST00000109773]
[ENSMUST00000109774]
|
| AlphaFold |
O88509 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000056495
|
| SMART Domains |
Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
| 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 |
probably null
Transcript: ENSMUST00000072997
|
| SMART Domains |
Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
| 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 |
probably null
Transcript: ENSMUST00000081628
|
| SMART Domains |
Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
| 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 |
probably benign
Transcript: ENSMUST00000088976
|
| SMART Domains |
Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
| 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 |
probably benign
Transcript: ENSMUST00000103150
|
| SMART Domains |
Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
| 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: ENSMUST00000103151
|
| SMART Domains |
Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
| 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 null
Transcript: ENSMUST00000109771
|
| SMART Domains |
Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
| 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 |
probably benign
Transcript: ENSMUST00000109772
|
| SMART Domains |
Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
| 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 |
probably null
Transcript: ENSMUST00000109773
|
| SMART Domains |
Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
| 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 |
probably null
Transcript: ENSMUST00000109774
|
| SMART Domains |
Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
| 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 |
|
| Coding Region Coverage |
- 1x: 92.7%
- 3x: 90.4%
- 10x: 84.6%
- 20x: 72.1%
|
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca4 |
T |
C |
3: 121,930,670 (GRCm39) |
L1389P |
probably damaging |
Het |
| Acot10 |
C |
T |
15: 20,666,684 (GRCm39) |
G19D |
probably damaging |
Het |
| Adam20 |
G |
A |
8: 41,248,081 (GRCm39) |
V64I |
possibly damaging |
Het |
| Ak6 |
T |
A |
13: 100,791,603 (GRCm39) |
D15E |
probably damaging |
Het |
| Atp1a2 |
A |
G |
1: 172,118,288 (GRCm39) |
Y129H |
probably damaging |
Het |
| Caskin1 |
C |
T |
17: 24,721,193 (GRCm39) |
T511I |
probably damaging |
Het |
| Casp9 |
C |
T |
4: 141,521,259 (GRCm39) |
R32* |
probably null |
Het |
| Ccdc40 |
A |
G |
11: 119,133,277 (GRCm39) |
E445G |
probably damaging |
Het |
| Cct8 |
T |
C |
16: 87,284,545 (GRCm39) |
E273G |
probably damaging |
Het |
| Chd5 |
G |
A |
4: 152,462,986 (GRCm39) |
V1380I |
probably damaging |
Het |
| Coro2b |
C |
T |
9: 62,336,286 (GRCm39) |
G272D |
probably damaging |
Het |
| Cyp4a10 |
C |
A |
4: 115,382,072 (GRCm39) |
H251Q |
probably damaging |
Het |
| Dgki |
A |
T |
6: 37,040,916 (GRCm39) |
H298Q |
probably benign |
Het |
| Dzip1 |
A |
G |
14: 119,160,200 (GRCm39) |
F3L |
probably damaging |
Het |
| Egf |
A |
G |
3: 129,496,198 (GRCm39) |
S807P |
probably benign |
Het |
| Emc10 |
C |
T |
7: 44,142,627 (GRCm39) |
R105H |
|
Het |
| Enthd1 |
T |
C |
15: 80,336,937 (GRCm39) |
E499G |
probably damaging |
Het |
| Eps8l1 |
G |
A |
7: 4,474,414 (GRCm39) |
S295N |
probably benign |
Het |
| Fer1l5 |
T |
A |
1: 36,450,728 (GRCm39) |
M1242K |
probably benign |
Het |
| Gm3415 |
A |
G |
5: 146,493,079 (GRCm39) |
R36G |
probably benign |
Het |
| Gm5797 |
C |
A |
14: 7,330,318 (GRCm38) |
M114I |
possibly damaging |
Het |
| Gmppa |
A |
T |
1: 75,418,468 (GRCm39) |
R284* |
probably null |
Het |
| Homer1 |
G |
C |
13: 93,485,724 (GRCm39) |
K118N |
probably damaging |
Het |
| Ivl |
TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG |
TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG |
3: 92,479,608 (GRCm39) |
|
probably benign |
Het |
| Kcnc4 |
G |
A |
3: 107,366,019 (GRCm39) |
A63V |
probably damaging |
Het |
| Kif11 |
T |
A |
19: 37,373,045 (GRCm39) |
I88N |
probably damaging |
Het |
| Krba1 |
T |
C |
6: 48,379,831 (GRCm39) |
F9S |
probably damaging |
Het |
| Nckap1 |
A |
G |
2: 80,350,714 (GRCm39) |
|
probably null |
Het |
| Nox4 |
A |
T |
7: 86,954,097 (GRCm39) |
Y134F |
probably benign |
Het |
| Or4a79 |
T |
A |
2: 89,552,237 (GRCm39) |
T73S |
probably benign |
Het |
| Or51f23c-ps1 |
T |
C |
7: 102,431,465 (GRCm39) |
S261P |
probably benign |
Het |
| Or52e15 |
A |
G |
7: 104,645,424 (GRCm39) |
L229P |
probably damaging |
Het |
| Or5m13b |
T |
A |
2: 85,754,386 (GRCm39) |
M258K |
probably damaging |
Het |
| Or5m8 |
T |
C |
2: 85,822,538 (GRCm39) |
C126R |
probably damaging |
Het |
| Or8k22 |
G |
T |
2: 86,163,173 (GRCm39) |
H176N |
possibly damaging |
Het |
| Pcdh17 |
G |
T |
14: 84,684,798 (GRCm39) |
V422L |
probably benign |
Het |
| Pcx |
T |
A |
19: 4,653,157 (GRCm39) |
V275E |
probably damaging |
Het |
| Pde6h |
A |
T |
6: 136,938,185 (GRCm39) |
M53L |
possibly damaging |
Het |
| Phactr3 |
A |
T |
2: 177,975,861 (GRCm39) |
E535D |
probably damaging |
Het |
| Pkn3 |
C |
A |
2: 29,980,539 (GRCm39) |
T810N |
probably damaging |
Het |
| Pnpla5 |
T |
C |
15: 84,002,827 (GRCm39) |
E252G |
probably damaging |
Het |
| Pramel21 |
T |
A |
4: 143,342,722 (GRCm39) |
C276* |
probably null |
Het |
| Psg17 |
A |
G |
7: 18,548,530 (GRCm39) |
S414P |
probably benign |
Het |
| Pzp |
T |
A |
6: 128,502,259 (GRCm39) |
Q30L |
probably benign |
Het |
| Reln |
A |
T |
5: 22,491,894 (GRCm39) |
F113I |
possibly damaging |
Het |
| Ret |
T |
C |
6: 118,141,702 (GRCm39) |
D975G |
probably benign |
Het |
| Sarnp |
A |
G |
10: 128,713,235 (GRCm39) |
I209V |
probably benign |
Het |
| Sorl1 |
A |
T |
9: 41,879,918 (GRCm39) |
V2210D |
probably damaging |
Het |
| Stard9 |
C |
T |
2: 120,533,237 (GRCm39) |
Q3165* |
probably null |
Het |
| Tmem64 |
A |
T |
4: 15,283,159 (GRCm39) |
I319F |
probably damaging |
Het |
| Vmn1r176 |
A |
T |
7: 23,534,808 (GRCm39) |
V115D |
probably damaging |
Het |
| Vmn1r2 |
A |
G |
4: 3,172,623 (GRCm39) |
T181A |
probably benign |
Het |
| Vmn2r2 |
T |
C |
3: 64,024,334 (GRCm39) |
E749G |
possibly damaging |
Het |
| Vps35 |
G |
A |
8: 86,010,677 (GRCm39) |
T222I |
possibly damaging |
Het |
| Zfp532 |
A |
G |
18: 65,757,485 (GRCm39) |
T473A |
probably damaging |
Het |
| Zfyve16 |
A |
G |
13: 92,657,712 (GRCm39) |
V733A |
probably damaging |
Het |
| Zranb1 |
T |
A |
7: 132,551,723 (GRCm39) |
S125T |
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 |
|
IGL01960:Dnmt3b
|
APN |
2 |
153,518,631 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGGGACACATAAAGAATCCCTTCC -3'
(R):5'- TGCAACTGAGAGATGACTGC -3'
Sequencing Primer
(F):5'- ATAAAGAATCCCTTCCAGTCTGTC -3'
(R):5'- CAACTGAGAGATGACTGCTTCTG -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation