Mutagenetix > Incidental Mutation

Incidental Mutation 'R7239:Dnmt3a'

563095

Institutional Source

Beutler Lab

Gene Symbol

Dnmt3a

Ensembl Gene

ENSMUSG00000020661

Gene Name

DNA methyltransferase 3A

Synonyms

MMRRC Submission

045346-MU

Accession Numbers

Essential gene?

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

Stock #

R7239 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

3856007-3964443 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 3922850 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Leucine at position 151 (Q151L)

Ref Sequence

ENSEMBL: ENSMUSP00000020991 (fasta)

Gene Model

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

AlphaFold

O88508

Predicted Effect

probably benign
Transcript: ENSMUST00000020991
AA Change: Q151L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: Q151L

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 benign
Transcript: ENSMUST00000172509
AA Change: Q77L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000133869
Gene: ENSMUSG00000020661
AA Change: Q77L

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 benign
Transcript: ENSMUST00000172719
AA Change: Q151L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000133501
Gene: ENSMUSG00000020661
AA Change: Q151L

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

SMART Domains

Protein: ENSMUSP00000133567
Gene: ENSMUSG00000020661
AA Change: Q26L

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

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 benign
Transcript: ENSMUST00000174817
AA Change: Q151L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: Q151L

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

Meta Mutation Damage Score

0.0846

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

99% (76/77)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	A	G	16: 21,472,268 (GRCm39)	V144A	probably damaging	Het
Abca5	A	T	11: 110,217,530 (GRCm39)	Y109N	possibly damaging	Het
Abcb5	T	C	12: 118,892,460 (GRCm39)	Q433R	probably benign	Het
Adamts7	G	A	9: 90,068,610 (GRCm39)		probably null	Het
Adgrv1	T	C	13: 81,624,731 (GRCm39)	D3746G	possibly damaging	Het
Arhgap29	C	T	3: 121,782,599 (GRCm39)	S159L	probably benign	Het
Arhgap5	T	A	12: 52,564,159 (GRCm39)	C377S	probably benign	Het
Atp1a3	G	A	7: 24,700,129 (GRCm39)	P77L	probably damaging	Het
B4galt1	T	C	4: 40,812,754 (GRCm39)	D257G	probably damaging	Het
Bin1	T	A	18: 32,539,224 (GRCm39)	N52K	probably damaging	Het
Catsperg2	A	G	7: 29,409,507 (GRCm39)	M562T	probably benign	Het
Ccdc33	G	A	9: 57,940,192 (GRCm39)	Q713*	probably null	Het
Cd96	A	T	16: 45,929,477 (GRCm39)	L156Q	probably damaging	Het
Clpb	A	G	7: 101,360,662 (GRCm39)	T231A	probably damaging	Het
Dnaaf9	C	A	2: 130,648,708 (GRCm39)	R258L	unknown	Het
Dock2	C	T	11: 34,181,677 (GRCm39)	V1629M	probably benign	Het
Edem1	G	A	6: 108,831,341 (GRCm39)	D601N	probably benign	Het
Eno2	C	T	6: 124,745,228 (GRCm39)	V20M	probably damaging	Het
Eny2	A	C	15: 44,297,250 (GRCm39)	D52A	probably benign	Het
Esp36	T	C	17: 38,728,132 (GRCm39)	R93G	possibly damaging	Het
Fam227a	A	G	15: 79,518,263 (GRCm39)		probably null	Het
Fat4	C	A	3: 39,037,989 (GRCm39)	H3880Q	possibly damaging	Het
Fbxw24	A	T	9: 109,434,598 (GRCm39)	V334E	possibly damaging	Het
Flrt1	T	C	19: 7,073,329 (GRCm39)	Q406R	probably benign	Het
Frmpd2	A	G	14: 33,274,034 (GRCm39)	N1092S	probably benign	Het
Gm904	C	A	13: 50,799,287 (GRCm39)	T82K	probably benign	Het
Gnas	G	C	2: 174,140,408 (GRCm39)	G252R	unknown	Het
Gpatch2l	A	G	12: 86,307,349 (GRCm39)		probably null	Het
H2ac6	A	T	13: 23,867,593 (GRCm39)	I103N	probably damaging	Het
Ift74	T	C	4: 94,541,187 (GRCm39)	V204A	probably benign	Het
Ikzf4	A	G	10: 128,477,113 (GRCm39)	L119P	probably damaging	Het
Ing3	G	A	6: 21,952,193 (GRCm39)	E56K	probably damaging	Het
Klhl25	T	C	7: 75,516,516 (GRCm39)	I474T	probably benign	Het
Klhl5	T	C	5: 65,318,529 (GRCm39)	V556A	probably damaging	Het
Krt14	A	T	11: 100,095,081 (GRCm39)	M382K	probably benign	Het
Lmcd1	T	C	6: 112,292,745 (GRCm39)	V199A	possibly damaging	Het
Lpcat4	T	A	2: 112,073,052 (GRCm39)	F200I	possibly damaging	Het
Lrp1b	T	C	2: 40,894,725 (GRCm39)	T2282A		Het
Lrrk1	T	C	7: 65,911,903 (GRCm39)	T1886A	probably benign	Het
Meis2	T	C	2: 115,889,484 (GRCm39)		probably null	Het
Mki67	C	T	7: 135,301,905 (GRCm39)	R1043K	possibly damaging	Het
Myct1	G	T	10: 5,554,601 (GRCm39)	R156L	possibly damaging	Het
Nckap5l	G	T	15: 99,324,090 (GRCm39)	H804Q	probably damaging	Het
Ndst3	T	G	3: 123,400,555 (GRCm39)	E450D	probably damaging	Het
Nipbl	A	T	15: 8,321,619 (GRCm39)		probably null	Het
Npy	A	G	6: 49,800,587 (GRCm39)	N4D	probably benign	Het
Or7g35	A	T	9: 19,496,487 (GRCm39)	Y218F	probably damaging	Het
Osgin2	T	C	4: 16,008,748 (GRCm39)	S18G	probably benign	Het
Pcdha9	T	G	18: 37,131,551 (GRCm39)	F207V	probably benign	Het
Pcdhb13	A	T	18: 37,577,697 (GRCm39)	I692F	probably damaging	Het
Pde3b	T	A	7: 114,015,384 (GRCm39)	V200E	probably damaging	Het
Ppp6r3	A	T	19: 3,543,981 (GRCm39)	L345I	probably benign	Het
Psd2	G	A	18: 36,113,472 (GRCm39)	A315T	probably damaging	Het
Rnf111	G	A	9: 70,376,655 (GRCm39)	T328I	probably damaging	Het
Rnf213	T	C	11: 119,349,614 (GRCm39)	L3825P		Het
Rtl1	C	T	12: 109,558,909 (GRCm39)	V977I	probably benign	Het
Scn1a	G	A	2: 66,108,000 (GRCm39)		probably null	Het
Slc25a2	G	T	18: 37,770,748 (GRCm39)	N260K	probably benign	Het
Sprtn	T	C	8: 125,626,983 (GRCm39)	V121A	probably damaging	Het
Ssx2ip	T	G	3: 146,133,771 (GRCm39)	L260W	probably damaging	Het
Syde1	G	A	10: 78,424,615 (GRCm39)	R406C	probably damaging	Het
Tab1	A	G	15: 80,017,372 (GRCm39)	R6G	probably benign	Het
Tenm4	G	A	7: 96,202,703 (GRCm39)	R106H	probably benign	Het
Tenm4	G	A	7: 96,385,020 (GRCm39)	V526I	possibly damaging	Het
Tfap2b	T	C	1: 19,304,404 (GRCm39)	F405L	probably damaging	Het
Trbv13-1	C	A	6: 41,093,325 (GRCm39)	T87K	probably benign	Het
Trmt44	G	T	5: 35,732,130 (GRCm39)	A87E	probably benign	Het
Ttll3	CAAAGTAA	CAAAGTAAAGTAA	6: 113,376,118 (GRCm39)		probably null	Het
Ttn	T	C	2: 76,617,634 (GRCm39)	D16279G	probably damaging	Het
Ttn	G	A	2: 76,711,672 (GRCm39)	R8290C	unknown	Het
Ugt2b37	T	A	5: 87,402,590 (GRCm39)	I14L	probably benign	Het
Vmn1r13	A	T	6: 57,187,611 (GRCm39)	M257L	probably benign	Het
Vmn1r184	C	T	7: 25,966,602 (GRCm39)	P116L	possibly damaging	Het
Zfp426	T	C	9: 20,381,887 (GRCm39)	T367A	probably benign	Het
Zfp647	A	T	15: 76,795,956 (GRCm39)	C235S	probably damaging	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
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
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'- TTGAGACCAGGGTCCAAAGG -3'
(R):5'- TCACTAGGGGACTTCCAACC -3'

Sequencing Primer
(F):5'- AGAAGCCATGCCCCTGAGTTC -3'
(R):5'- TAGGGGACTTCCAACCTCCAC -3'

Posted On

2019-06-26