Incidental Mutation 'R2359:Dnmt3a'
| ID |
247082 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Dnmt3a
|
| Ensembl Gene |
ENSMUSG00000020661 |
| Gene Name |
DNA methyltransferase 3A |
| Synonyms |
|
| MMRRC Submission |
040341-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.404)
|
| Stock # |
R2359 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
3856007-3964443 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 3951599 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 659
(S659P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000134009
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020991]
[ENSMUST00000111186]
[ENSMUST00000172509]
[ENSMUST00000172689]
[ENSMUST00000174483]
[ENSMUST00000174817]
[ENSMUST00000174774]
|
| AlphaFold |
O88508 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000020991
AA Change: S659P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: S659P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
15 |
37 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
55 |
101 |
6.44e-5 |
PROSPERO |
|
low complexity region
|
109 |
124 |
N/A |
INTRINSIC |
|
low complexity region
|
160 |
177 |
N/A |
INTRINSIC |
|
low complexity region
|
204 |
215 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
241 |
283 |
6.44e-5 |
PROSPERO |
|
PWWP
|
286 |
344 |
1.36e-24 |
SMART |
|
low complexity region
|
412 |
430 |
N/A |
INTRINSIC |
|
low complexity region
|
438 |
453 |
N/A |
INTRINSIC |
|
PDB:3A1B|A
|
454 |
610 |
2e-99 |
PDB |
|
Blast:RING
|
533 |
582 |
1e-17 |
BLAST |
|
Pfam:DNA_methylase
|
630 |
772 |
2.1e-14 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000111186
AA Change: S440P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000106817
Gene: ENSMUSG00000020661
AA Change: S440P
| Domain | Start | End | E-Value | Type |
|---|
|
PWWP
|
67 |
125 |
1.36e-24 |
SMART |
|
low complexity region
|
193 |
211 |
N/A |
INTRINSIC |
|
low complexity region
|
219 |
234 |
N/A |
INTRINSIC |
|
PDB:3A1B|A
|
235 |
391 |
1e-101 |
PDB |
|
Blast:RING
|
314 |
363 |
4e-16 |
BLAST |
|
Pfam:DNA_methylase
|
411 |
554 |
9.5e-15 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172509
|
| SMART Domains |
Protein: ENSMUSP00000133869
Gene: ENSMUSG00000020661
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
35 |
50 |
N/A |
INTRINSIC |
|
low complexity region
|
86 |
103 |
N/A |
INTRINSIC |
|
low complexity region
|
130 |
141 |
N/A |
INTRINSIC |
|
PWWP
|
212 |
270 |
1.36e-24 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000172689
AA Change: S440P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000133543
Gene: ENSMUSG00000020661
AA Change: S440P
| Domain | Start | End | E-Value | Type |
|---|
|
PWWP
|
67 |
125 |
1.36e-24 |
SMART |
|
low complexity region
|
193 |
211 |
N/A |
INTRINSIC |
|
low complexity region
|
219 |
234 |
N/A |
INTRINSIC |
|
PDB:3A1B|A
|
235 |
391 |
1e-101 |
PDB |
|
Blast:RING
|
314 |
363 |
4e-16 |
BLAST |
|
Pfam:DNA_methylase
|
411 |
554 |
9.5e-15 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172749
|
| SMART Domains |
Protein: ENSMUSP00000134567
Gene: ENSMUSG00000020661
| Domain | Start | End | E-Value | Type |
|---|
|
PWWP
|
61 |
119 |
7.62e-19 |
SMART |
|
low complexity region
|
151 |
169 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174272
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174483
|
| SMART Domains |
Protein: ENSMUSP00000133938
Gene: ENSMUSG00000020661
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
35 |
50 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000174817
AA Change: S659P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: S659P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
15 |
37 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
55 |
101 |
6.44e-5 |
PROSPERO |
|
low complexity region
|
109 |
124 |
N/A |
INTRINSIC |
|
low complexity region
|
160 |
177 |
N/A |
INTRINSIC |
|
low complexity region
|
204 |
215 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
241 |
283 |
6.44e-5 |
PROSPERO |
|
PWWP
|
286 |
344 |
1.36e-24 |
SMART |
|
low complexity region
|
412 |
430 |
N/A |
INTRINSIC |
|
low complexity region
|
438 |
453 |
N/A |
INTRINSIC |
|
PDB:3A1B|A
|
454 |
610 |
2e-99 |
PDB |
|
Blast:RING
|
533 |
582 |
1e-17 |
BLAST |
|
Pfam:DNA_methylase
|
630 |
772 |
2.1e-14 |
PFAM |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000174733
AA Change: S44P
|
| SMART Domains |
Protein: ENSMUSP00000134492
Gene: ENSMUSG00000020661
AA Change: S44P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DNA_methylase
|
16 |
104 |
8.2e-10 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174774
|
| SMART Domains |
Protein: ENSMUSP00000134529
Gene: ENSMUSG00000020661
| Domain | Start | End | E-Value | Type |
|---|
|
PWWP
|
67 |
125 |
1.36e-24 |
SMART |
|
| Meta Mutation Damage Score |
0.8872 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.3%
|
| Validation Efficiency |
95% (41/43) |
| 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 causes developmental defects in multiple different organ systems. There is a pseudogene for this gene located on chromosome 3. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Nov 2012]
PHENOTYPE: Homozygotes for a targeted null mutation become runted and die around four weeks of age. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam24 |
A |
G |
8: 41,133,984 (GRCm39) |
E484G |
possibly damaging |
Het |
| Akr1c20 |
C |
T |
13: 4,573,276 (GRCm39) |
G13D |
probably damaging |
Het |
| Alkbh3 |
T |
C |
2: 93,838,458 (GRCm39) |
T38A |
probably benign |
Het |
| Anxa9 |
A |
C |
3: 95,210,062 (GRCm39) |
L99R |
probably damaging |
Het |
| Arfgef2 |
A |
T |
2: 166,702,539 (GRCm39) |
Y826F |
probably damaging |
Het |
| Arid2 |
G |
T |
15: 96,259,759 (GRCm39) |
L306F |
probably damaging |
Het |
| Ccdc141 |
C |
T |
2: 77,000,746 (GRCm39) |
V29M |
probably damaging |
Het |
| Cd55b |
A |
G |
1: 130,345,858 (GRCm39) |
S187P |
probably damaging |
Het |
| Cep63 |
A |
C |
9: 102,471,763 (GRCm39) |
L526V |
possibly damaging |
Het |
| Chtf8 |
G |
T |
8: 107,612,048 (GRCm39) |
|
probably null |
Het |
| Clca4b |
T |
A |
3: 144,631,003 (GRCm39) |
S286C |
probably damaging |
Het |
| Cpsf1 |
A |
G |
15: 76,481,873 (GRCm39) |
V1080A |
probably benign |
Het |
| Csf2rb2 |
C |
T |
15: 78,176,976 (GRCm39) |
V165I |
probably benign |
Het |
| Cyp2c40 |
A |
T |
19: 39,766,398 (GRCm39) |
V399E |
probably damaging |
Het |
| Efcab3 |
T |
C |
11: 104,630,106 (GRCm39) |
S967P |
possibly damaging |
Het |
| Efr3b |
G |
A |
12: 4,030,136 (GRCm39) |
|
probably benign |
Het |
| Epha8 |
A |
G |
4: 136,673,343 (GRCm39) |
I147T |
probably damaging |
Het |
| Fbxo48 |
G |
A |
11: 16,903,602 (GRCm39) |
W76* |
probably null |
Het |
| Ggt6 |
A |
T |
11: 72,328,377 (GRCm39) |
L254F |
possibly damaging |
Het |
| Gm4204 |
T |
A |
1: 135,159,927 (GRCm39) |
|
noncoding transcript |
Het |
| Golph3l |
A |
G |
3: 95,499,275 (GRCm39) |
|
probably null |
Het |
| Gtf2h3 |
A |
G |
5: 124,728,939 (GRCm39) |
K166R |
probably damaging |
Het |
| Hsp90aa1 |
A |
G |
12: 110,661,003 (GRCm39) |
|
probably null |
Het |
| Hyi |
A |
G |
4: 118,217,538 (GRCm39) |
R79G |
probably benign |
Het |
| Igbp1b |
G |
A |
6: 138,634,713 (GRCm39) |
P244S |
probably damaging |
Het |
| Ipo8 |
G |
A |
6: 148,717,975 (GRCm39) |
|
probably benign |
Het |
| Larp4b |
C |
A |
13: 9,208,199 (GRCm39) |
T391K |
probably damaging |
Het |
| Lrba |
T |
C |
3: 86,256,057 (GRCm39) |
V1133A |
probably benign |
Het |
| Med13 |
C |
T |
11: 86,181,861 (GRCm39) |
|
probably benign |
Het |
| Ncapd2 |
A |
G |
6: 125,156,379 (GRCm39) |
|
probably benign |
Het |
| Neurl1b |
T |
C |
17: 26,660,569 (GRCm39) |
F299L |
probably benign |
Het |
| Nosip |
G |
A |
7: 44,723,450 (GRCm39) |
A39T |
possibly damaging |
Het |
| Nsd1 |
A |
G |
13: 55,361,524 (GRCm39) |
D164G |
possibly damaging |
Het |
| Ntn1 |
G |
A |
11: 68,276,438 (GRCm39) |
T170M |
probably damaging |
Het |
| Polrmt |
A |
T |
10: 79,572,396 (GRCm39) |
L1079Q |
probably damaging |
Het |
| Prxl2c |
A |
T |
13: 64,460,465 (GRCm39) |
C12S |
probably benign |
Het |
| Rab30 |
A |
G |
7: 92,485,005 (GRCm39) |
D129G |
possibly damaging |
Het |
| Rwdd2b |
C |
T |
16: 87,233,809 (GRCm39) |
S97N |
probably benign |
Het |
| Slitrk3 |
T |
G |
3: 72,956,678 (GRCm39) |
D698A |
possibly damaging |
Het |
| Smarcd2 |
T |
C |
11: 106,157,990 (GRCm39) |
M93V |
probably benign |
Het |
| Tmprss4 |
A |
G |
9: 45,097,130 (GRCm39) |
V45A |
probably benign |
Het |
| Vmn1r22 |
A |
T |
6: 57,877,974 (GRCm39) |
M1K |
probably null |
Het |
| Vps13a |
A |
G |
19: 16,630,043 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Dnmt3a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00844:Dnmt3a
|
APN |
12 |
3,955,622 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02255:Dnmt3a
|
APN |
12 |
3,922,886 (GRCm39) |
splice site |
probably benign |
|
|
IGL02815:Dnmt3a
|
APN |
12 |
3,954,226 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03372:Dnmt3a
|
APN |
12 |
3,952,666 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Chromos
|
UTSW |
12 |
3,951,665 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Compaction
|
UTSW |
12 |
3,916,192 (GRCm39) |
nonsense |
probably null |
|
|
R0028:Dnmt3a
|
UTSW |
12 |
3,950,337 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0306:Dnmt3a
|
UTSW |
12 |
3,916,096 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R0843:Dnmt3a
|
UTSW |
12 |
3,922,886 (GRCm39) |
splice site |
probably benign |
|
|
R1055:Dnmt3a
|
UTSW |
12 |
3,922,864 (GRCm39) |
missense |
probably benign |
0.05 |
|
R1465:Dnmt3a
|
UTSW |
12 |
3,916,088 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1465:Dnmt3a
|
UTSW |
12 |
3,916,088 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1585:Dnmt3a
|
UTSW |
12 |
3,951,660 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1680:Dnmt3a
|
UTSW |
12 |
3,923,361 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1753:Dnmt3a
|
UTSW |
12 |
3,923,342 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R2055:Dnmt3a
|
UTSW |
12 |
3,922,859 (GRCm39) |
missense |
probably benign |
0.44 |
|
R2219:Dnmt3a
|
UTSW |
12 |
3,899,654 (GRCm39) |
utr 5 prime |
probably benign |
|
|
R2267:Dnmt3a
|
UTSW |
12 |
3,947,551 (GRCm39) |
splice site |
probably null |
|
|
R2384:Dnmt3a
|
UTSW |
12 |
3,951,591 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2403:Dnmt3a
|
UTSW |
12 |
3,949,883 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2884:Dnmt3a
|
UTSW |
12 |
3,946,132 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3027:Dnmt3a
|
UTSW |
12 |
3,899,626 (GRCm39) |
splice site |
probably null |
|
|
R4281:Dnmt3a
|
UTSW |
12 |
3,951,665 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4282:Dnmt3a
|
UTSW |
12 |
3,951,665 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4283:Dnmt3a
|
UTSW |
12 |
3,951,665 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4809:Dnmt3a
|
UTSW |
12 |
3,950,352 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5154:Dnmt3a
|
UTSW |
12 |
3,946,008 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5361:Dnmt3a
|
UTSW |
12 |
3,945,643 (GRCm39) |
missense |
probably benign |
0.13 |
|
R5483:Dnmt3a
|
UTSW |
12 |
3,949,615 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5768:Dnmt3a
|
UTSW |
12 |
3,935,660 (GRCm39) |
splice site |
probably null |
|
|
R5928:Dnmt3a
|
UTSW |
12 |
3,916,096 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R6432:Dnmt3a
|
UTSW |
12 |
3,952,399 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6552:Dnmt3a
|
UTSW |
12 |
3,957,623 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6783:Dnmt3a
|
UTSW |
12 |
3,947,406 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6850:Dnmt3a
|
UTSW |
12 |
3,947,600 (GRCm39) |
missense |
probably benign |
0.40 |
|
R7106:Dnmt3a
|
UTSW |
12 |
3,947,591 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7145:Dnmt3a
|
UTSW |
12 |
3,922,844 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7149:Dnmt3a
|
UTSW |
12 |
3,952,397 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7239:Dnmt3a
|
UTSW |
12 |
3,922,850 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7490:Dnmt3a
|
UTSW |
12 |
3,954,204 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7588:Dnmt3a
|
UTSW |
12 |
3,946,080 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7684:Dnmt3a
|
UTSW |
12 |
3,947,340 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8058:Dnmt3a
|
UTSW |
12 |
3,952,768 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R8316:Dnmt3a
|
UTSW |
12 |
3,946,965 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8345:Dnmt3a
|
UTSW |
12 |
3,885,234 (GRCm39) |
missense |
unknown |
|
|
R8464:Dnmt3a
|
UTSW |
12 |
3,949,635 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8914:Dnmt3a
|
UTSW |
12 |
3,916,192 (GRCm39) |
nonsense |
probably null |
|
|
R9131:Dnmt3a
|
UTSW |
12 |
3,916,136 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9246:Dnmt3a
|
UTSW |
12 |
3,949,204 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9476:Dnmt3a
|
UTSW |
12 |
3,957,707 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9485:Dnmt3a
|
UTSW |
12 |
3,916,121 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9598:Dnmt3a
|
UTSW |
12 |
3,946,997 (GRCm39) |
missense |
probably benign |
0.25 |
|
R9709:Dnmt3a
|
UTSW |
12 |
3,957,701 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Dnmt3a
|
UTSW |
12 |
3,954,201 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCTGTCCTGGCTTTGGAAAG -3'
(R):5'- AGGAGTGGATGGCAATGTCC -3'
Sequencing Primer
(F):5'- TGAGGCACAGTCATAGCGC -3'
(R):5'- ATGGCAATGTCCCCAGGAG -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation