Mutagenetix > Incidental Mutation

Incidental Mutation 'R1465:Dnmt3a'

201087

Institutional Source

Beutler Lab

Gene Symbol

Dnmt3a

Ensembl Gene

ENSMUSG00000020661

Gene Name

DNA methyltransferase 3A

Synonyms

MMRRC Submission

039519-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.404) question?

Stock #

R1465 (G1)

Quality Score

168

Status

Not validated

Chromosome

Chromosomal Location

3856007-3964443 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 3916088 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 17 (E17G)

Ref Sequence

ENSEMBL: ENSMUSP00000133938 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000172509] [ENSMUST00000172719] [ENSMUST00000172816] [ENSMUST00000174483] [ENSMUST00000174817]

AlphaFold

O88508

Predicted Effect

probably benign
Transcript: ENSMUST00000020991
AA Change: E91G

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: E91G

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

noncoding transcript
Transcript: ENSMUST00000085826

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144896

Predicted Effect

probably benign
Transcript: ENSMUST00000172509
AA Change: E17G

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000133869
Gene: ENSMUSG00000020661
AA Change: E17G

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: ENSMUST00000172719
AA Change: E91G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000133501
Gene: ENSMUSG00000020661
AA Change: E91G

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	15	37	N/A	INTRINSIC
low complexity region	109	124	N/A	INTRINSIC
low complexity region	160	177	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000172816
AA Change: E17G

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

Predicted Effect

probably benign
Transcript: ENSMUST00000173197

SMART Domains

Protein: ENSMUSP00000133567
Gene: ENSMUSG00000020661

Domain	Start	End	E-Value	Type
low complexity region	36	53	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000174483
AA Change: E17G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000133938
Gene: ENSMUSG00000020661
AA Change: E17G

Domain	Start	End	E-Value	Type
low complexity region	35	50	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000174817
AA Change: E91G

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: E91G

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

Coding Region Coverage

1x: 97.3%
3x: 96.5%
10x: 93.6%
20x: 86.6%

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 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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310030G06Rik	A	G	9: 50,651,866 (GRCm39)	Y121H	probably damaging	Het
Abca13	G	T	11: 9,349,303 (GRCm39)	G3626W	probably damaging	Het
Acvr1c	A	G	2: 58,174,973 (GRCm39)	Y192H	probably damaging	Het
Afm	A	T	5: 90,698,200 (GRCm39)	D534V	probably damaging	Het
Agl	T	C	3: 116,565,021 (GRCm39)	E1076G	probably benign	Het
Ahcyl	T	C	16: 45,974,211 (GRCm39)	K389E	probably benign	Het
Angptl3	A	T	4: 98,925,757 (GRCm39)	H361L	probably benign	Het
Apob	T	C	12: 8,061,421 (GRCm39)	F3301S	possibly damaging	Het
Arhgef33	T	A	17: 80,674,730 (GRCm39)	C376S	possibly damaging	Het
Ass1	A	G	2: 31,410,428 (GRCm39)	*413W	probably null	Het
Atp6v1h	T	A	1: 5,165,911 (GRCm39)	L127Q	probably damaging	Het
Bcl2l1	G	A	2: 152,671,870 (GRCm39)	S14F	probably damaging	Het
Bhmt1b	T	G	18: 87,775,382 (GRCm39)	F302V	probably damaging	Het
Birc6	G	A	17: 74,930,853 (GRCm39)	A2477T	probably benign	Het
Bpifb9a	G	A	2: 154,112,941 (GRCm39)	A589T	possibly damaging	Het
Casp9	C	A	4: 141,533,151 (GRCm39)	T252K	probably benign	Het
Cct4	G	A	11: 22,952,922 (GRCm39)	D533N	probably damaging	Het
Clcn6	A	C	4: 148,098,358 (GRCm39)	I555S	probably damaging	Het
Col4a4	A	T	1: 82,475,543 (GRCm39)		probably null	Het
Cyp2d10	A	T	15: 82,288,129 (GRCm39)		probably null	Het
D930048N14Rik	A	G	11: 51,545,740 (GRCm39)		probably benign	Het
Dhfr	A	G	13: 92,504,815 (GRCm39)		probably benign	Het
Dlg5	T	C	14: 24,204,764 (GRCm39)		probably null	Het
Dnah11	T	C	12: 118,002,430 (GRCm39)	E2240G	probably damaging	Het
Dock1	A	G	7: 134,384,138 (GRCm39)	T670A	probably benign	Het
Dpy19l2	A	G	9: 24,580,618 (GRCm39)	M241T	probably benign	Het
Dpy19l4	A	G	4: 11,296,034 (GRCm39)	S212P	probably damaging	Het
Ephb6	T	C	6: 41,593,040 (GRCm39)	F426S	probably damaging	Het
F5	A	T	1: 164,026,402 (GRCm39)	D1658V	probably benign	Het
Faah	A	T	4: 115,856,755 (GRCm39)	V469E	probably damaging	Het
Fas	T	C	19: 34,294,013 (GRCm39)	C123R	probably damaging	Het
Fhod1	T	C	8: 106,065,546 (GRCm39)		probably benign	Het
Filip1	A	G	9: 79,805,589 (GRCm39)	V55A	probably benign	Het
Frmpd1	G	A	4: 45,273,197 (GRCm39)	R372Q	probably damaging	Het
Glyctk	C	T	9: 106,034,806 (GRCm39)	G87S	probably damaging	Het
Golga3	T	C	5: 110,357,744 (GRCm39)	L1080P	probably damaging	Het
Gpr137	T	C	19: 6,915,812 (GRCm39)	T281A	probably benign	Het
Grap2	T	A	15: 80,532,612 (GRCm39)		probably null	Het
Hlcs	T	C	16: 94,069,151 (GRCm39)	D170G	probably damaging	Het
Hook1	A	G	4: 95,901,493 (GRCm39)	T484A	probably benign	Het
Hoxa5	T	A	6: 52,180,771 (GRCm39)	H187L	probably benign	Het
Inpp1	G	T	1: 52,829,253 (GRCm39)	S255R	probably benign	Het
Inpp4b	T	A	8: 82,494,786 (GRCm39)	V67E	probably damaging	Het
Iqgap3	A	G	3: 87,994,616 (GRCm39)	N105S	probably damaging	Het
Kcnq5	A	G	1: 21,539,692 (GRCm39)		probably null	Het
Klhl1	T	C	14: 96,477,649 (GRCm39)	N473S	probably benign	Het
Klk1b24	C	A	7: 43,840,785 (GRCm39)	T71N	probably benign	Het
Loxhd1	A	G	18: 77,468,269 (GRCm39)		probably null	Het
Lrp1b	C	T	2: 41,001,071 (GRCm39)	R2165Q	probably benign	Het
Lrp2bp	A	T	8: 46,478,272 (GRCm39)	Q328L	possibly damaging	Het
Lrrc63	T	A	14: 75,344,829 (GRCm39)	K419N	possibly damaging	Het
Lrrc9	A	G	12: 72,547,533 (GRCm39)	N150S	probably benign	Het
Lrrn4	C	A	2: 132,713,995 (GRCm39)	C317F	probably damaging	Het
Ltbp2	T	C	12: 84,860,074 (GRCm39)	S627G	probably damaging	Het
Macf1	A	T	4: 123,386,947 (GRCm39)	S1224T	probably damaging	Het
Meis2	A	C	2: 115,889,151 (GRCm39)	H200Q	probably benign	Het
Mesd	C	A	7: 83,544,790 (GRCm39)	A80E	probably benign	Het
Mtor	G	T	4: 148,610,450 (GRCm39)		probably benign	Het
Myo3a	T	C	2: 22,467,939 (GRCm39)	F398L	probably benign	Het
Nagpa	G	T	16: 5,019,392 (GRCm39)		probably benign	Het
Nanp	A	G	2: 150,872,749 (GRCm39)	C60R	probably benign	Het
Nectin2	T	G	7: 19,464,041 (GRCm39)	M313L	probably benign	Het
Nek4	C	T	14: 30,678,844 (GRCm39)	H123Y	probably damaging	Het
Nploc4	A	G	11: 120,299,607 (GRCm39)	V371A	probably damaging	Het
Ntrk3	T	C	7: 78,005,762 (GRCm39)		probably benign	Het
Or11g7	A	G	14: 50,690,634 (GRCm39)	T42A	possibly damaging	Het
Or13c7b	A	G	4: 43,820,723 (GRCm39)	F213L	probably benign	Het
Or52n4	T	C	7: 104,294,153 (GRCm39)	N140S	probably benign	Het
Or5b109	T	A	19: 13,212,265 (GRCm39)	V217E	possibly damaging	Het
Pcdh20	T	A	14: 88,706,673 (GRCm39)	Q209L	probably benign	Het
Pcdhb20	G	A	18: 37,637,750 (GRCm39)	R92H	probably damaging	Het
Pgap1	T	C	1: 54,567,714 (GRCm39)	H377R	probably benign	Het
Phyhipl	G	T	10: 70,406,798 (GRCm39)	P52Q	probably damaging	Het
Plekhg4	T	C	8: 106,107,672 (GRCm39)		probably benign	Het
Pwwp2a	T	A	11: 43,596,383 (GRCm39)	V516E	possibly damaging	Het
Rack1	T	C	11: 48,692,586 (GRCm39)	V69A	probably damaging	Het
Rexo5	T	A	7: 119,400,581 (GRCm39)		probably null	Het
Rnf123	T	C	9: 107,948,665 (GRCm39)		probably benign	Het
Rock1	G	T	18: 10,072,863 (GRCm39)	Q1161K	possibly damaging	Het
Rps6ka2	T	C	17: 7,560,266 (GRCm39)	L568P	probably damaging	Het
Seh1l	T	C	18: 67,917,054 (GRCm39)	S78P	probably damaging	Het
Serpinb3b	A	T	1: 107,083,573 (GRCm39)		probably null	Het
Setd1a	T	C	7: 127,387,512 (GRCm39)		probably benign	Het
Setx	G	T	2: 29,030,401 (GRCm39)		probably null	Het
Sh3bp1	T	C	15: 78,791,545 (GRCm39)		probably benign	Het
Shc2	G	T	10: 79,467,136 (GRCm39)	R146S	probably damaging	Het
Skap2	T	C	6: 51,886,348 (GRCm39)	T5A	probably benign	Het
Skor2	A	T	18: 76,964,340 (GRCm39)		probably benign	Het
Slc35a3	T	C	3: 116,480,983 (GRCm39)	I93M	probably benign	Het
Sohlh1	C	T	2: 25,733,359 (GRCm39)	G295D	probably damaging	Het
Speg	A	G	1: 75,405,128 (GRCm39)		probably benign	Het
Sult2a8	A	C	7: 14,150,208 (GRCm39)	C168G	probably benign	Het
Tax1bp1	T	C	6: 52,704,179 (GRCm39)		probably benign	Het
Tbc1d4	T	C	14: 101,685,124 (GRCm39)	I1176V	possibly damaging	Het
Tcof1	A	G	18: 60,952,026 (GRCm39)		probably benign	Het
Thada	A	T	17: 84,744,104 (GRCm39)	F735I	possibly damaging	Het
Tle1	A	C	4: 72,058,068 (GRCm39)	H52Q	probably damaging	Het
Tmem101	A	T	11: 102,044,155 (GRCm39)	V244E	probably damaging	Het
Tnfrsf26	C	A	7: 143,171,668 (GRCm39)	C95F	probably damaging	Het
Uspl1	T	C	5: 149,150,842 (GRCm39)	S482P	probably benign	Het
Vmn2r118	G	T	17: 55,917,935 (GRCm39)	N192K	probably benign	Het
Vmn2r14	C	T	5: 109,368,195 (GRCm39)	V266I	possibly damaging	Het
Vmn2r51	A	G	7: 9,834,249 (GRCm39)	I263T	probably damaging	Het
Zfp937	T	A	2: 150,080,967 (GRCm39)	C332*	probably null	Het
Zscan21	T	A	5: 138,123,470 (GRCm39)	S50T	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
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
R2359:Dnmt3a	UTSW	12	3,951,599 (GRCm39)	missense	probably damaging	1.00
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'- TGGCCCATCACTTGAACCCTTAAAC -3'
(R):5'- GGGATAGGTAAACACTGCACCTGC -3'

Sequencing Primer
(F):5'- ATCACTTGAACCCTTAAACCTTCG -3'
(R):5'- agcatcccttggcattacac -3'

Posted On

2014-05-23