Mutagenetix > Incidental Mutation

Incidental Mutation 'R7490:Dnmt3a'

580696

Institutional Source

Beutler Lab

Gene Symbol

Dnmt3a

Ensembl Gene

ENSMUSG00000020661

Gene Name

DNA methyltransferase 3A

Synonyms

MMRRC Submission

045564-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.449) question?

Stock #

R7490 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

3806007-3914443 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 3904204 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 792 (G792D)

Ref Sequence

ENSEMBL: ENSMUSP00000020991 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000111186] [ENSMUST00000172689] [ENSMUST00000172913] [ENSMUST00000174483] [ENSMUST00000174817]

AlphaFold

O88508

Predicted Effect

probably damaging
Transcript: ENSMUST00000020991
AA Change: G792D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: G792D

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: G573D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000106817
Gene: ENSMUSG00000020661
AA Change: G573D

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 damaging
Transcript: ENSMUST00000172689
AA Change: G573D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000133543
Gene: ENSMUSG00000020661
AA Change: G573D

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: ENSMUST00000172913

SMART Domains

Protein: ENSMUSP00000134496
Gene: ENSMUSG00000020661

Domain	Start	End	E-Value	Type
PDB:2QRV\|H	1	69	3e-46	PDB
SCOP:d6mhta_	2	66	6e-11	SMART

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: ENSMUST00000174733

SMART Domains

Protein: ENSMUSP00000134492
Gene: ENSMUSG00000020661

Domain	Start	End	E-Value	Type
Pfam:DNA_methylase	16	104	8.2e-10	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000174817
AA Change: G792D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: G792D

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700019A02Rik	T	C	1: 53,163,230	D132G	possibly damaging	Het
Abca5	T	C	11: 110,277,611	E1424G	possibly damaging	Het
Adamts4	C	T	1: 171,256,600	Q549*	probably null	Het
Adcy4	A	G	14: 55,770,433	I893T	possibly damaging	Het
Ago1	A	T	4: 126,439,505	*858R	probably null	Het
Ank2	T	A	3: 126,958,889	I393L	probably damaging	Het
Ankrd44	T	C	1: 54,648,300	T987A	probably benign	Het
Ap2a1	G	T	7: 44,902,789	N790K	probably benign	Het
Aqr	A	G	2: 114,158,868		probably null	Het
Arel1	G	T	12: 84,941,911	F21L	probably damaging	Het
Atp1a3	T	C	7: 24,987,470	D743G	probably damaging	Het
Atp9a	A	T	2: 168,675,352	F354I	probably benign	Het
Bag6	A	G	17: 35,140,842	H259R	unknown	Het
BC028528	CTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTT	CTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTT	3: 95,888,136		probably benign	Het
BC028528	GTCACTGGTTCTGTG	GTCACTGGTTCTGTGTTCACTGGTTCTGTG	3: 95,888,166		probably benign	Het
BC028528	TGGTT	TGGTTCTGTGGTCACGGGTT	3: 95,888,186		probably benign	Het
Bckdk	T	A	7: 127,904,973	S15T	unknown	Het
C4b	G	T	17: 34,731,080	Y1405*	probably null	Het
Camk4	G	A	18: 32,939,545		probably null	Het
Car11	T	A	7: 45,700,318	W16R	probably benign	Het
Ccdc80	A	C	16: 45,096,400	E506D	probably damaging	Het
Chmp6	C	T	11: 119,915,443	Q32*	probably null	Het
Colq	G	A	14: 31,545,086	P166S	possibly damaging	Het
Ctxn3	T	C	18: 57,477,285	M58T	probably damaging	Het
Cxcl3	A	T	5: 90,786,657	I93L	unknown	Het
Dnaaf2	T	C	12: 69,197,606	Y227C	probably damaging	Het
Dner	CGCTGCTGCTGCTGCTGCTGCTGCTGC	CGCTGCTGCTGCTGCTGCTGCTGC	1: 84,585,549		probably benign	Het
Dsg4	T	A	18: 20,451,936		probably null	Het
Ecm2	C	T	13: 49,530,342	Q599*	probably null	Het
Fbxl13	T	A	5: 21,523,060	R550*	probably null	Het
Gm4302	A	T	10: 100,341,583	Q243L	unknown	Het
Gm7168	A	T	17: 13,949,013	Y214F	probably benign	Het
Gtf3c1	C	T	7: 125,647,491	D1549N	probably damaging	Het
Gtf3c5	A	T	2: 28,571,141	D320E	probably damaging	Het
Hivep1	T	A	13: 42,157,650	V1122D	probably damaging	Het
Ibtk	T	C	9: 85,718,934		probably null	Het
Irs1	T	A	1: 82,287,264	Q1077L	probably damaging	Het
Ivd	A	T	2: 118,876,892	M296L	possibly damaging	Het
Katnal1	T	C	5: 148,891,682	D318G	probably null	Het
L3mbtl3	C	T	10: 26,339,231	V194I	unknown	Het
Malt1	C	A	18: 65,448,211	Q237K	probably benign	Het
March11	C	T	15: 26,311,101	A221V	possibly damaging	Het
Mgea5	G	A	19: 45,767,447	R586*	probably null	Het
Nfe2l3	A	G	6: 51,457,544	I361M	possibly damaging	Het
Nrg1	G	A	8: 31,818,654	R493C	probably damaging	Het
Olfr1019	A	T	2: 85,840,963	V276E	probably damaging	Het
Olfr1212	A	C	2: 88,959,048	Y194S	probably benign	Het
Olfr453	T	C	6: 42,744,805	I256T	probably damaging	Het
Olfr577	G	A	7: 102,973,810	P61S	probably damaging	Het
Olfr828	A	T	9: 18,815,933	Y120*	probably null	Het
Olfr980	T	A	9: 40,006,424	H175L	probably damaging	Het
Orai3	C	T	7: 127,773,627	A100V	possibly damaging	Het
Oxsm	T	A	14: 16,241,066	M328L	probably benign	Het
Pan2	T	C	10: 128,308,440	V186A	probably benign	Het
Pkd1l1	T	A	11: 8,916,265	D980V		Het
Ppp1r16b	T	C	2: 158,761,468	Y438H	probably damaging	Het
Ppp4c	A	T	7: 126,787,332	H164Q	probably damaging	Het
Prl8a2	C	A	13: 27,352,770	T125K	possibly damaging	Het
Rasa2	T	C	9: 96,566,122	N494S	possibly damaging	Het
Rpl18a	T	C	8: 70,895,506	D147G	probably benign	Het
Scg3	T	C	9: 75,669,277	D272G	possibly damaging	Het
Serpinb6c	T	A	13: 33,893,835	D184V	probably benign	Het
Simc1	T	G	13: 54,524,349	L170R	possibly damaging	Het
Slx4	T	C	16: 3,980,131	E1463G	possibly damaging	Het
Stk31	T	A	6: 49,439,232		probably null	Het
Tas1r3	A	G	4: 155,862,023	I375T	probably damaging	Het
Tbc1d24	T	C	17: 24,182,520	D405G	probably damaging	Het
Tcerg1l	G	A	7: 138,259,828	P391S	probably damaging	Het
Tiam1	T	C	16: 89,898,195	S125G	probably benign	Het
Trim16	C	A	11: 62,834,123	H246N	probably damaging	Het
Tti1	T	A	2: 157,995,472	N896I	probably damaging	Het
Ubash3a	A	G	17: 31,232,312	N395S	probably damaging	Het
Uggt1	T	C	1: 36,164,508	I1014V	probably benign	Het
Vmn1r30	T	A	6: 58,435,229	Q206L	possibly damaging	Het
Washc5	T	A	15: 59,337,204	N1057I	probably benign	Het
Xpo4	GGTATTAGCGGAGT	GGT	14: 57,602,621		probably null	Het
Zcchc14	A	T	8: 121,605,017	S536T	unknown	Het

Other mutations in Dnmt3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00844:Dnmt3a	APN	12	3905622	missense	probably damaging	1.00
IGL02255:Dnmt3a	APN	12	3872886	splice site	probably benign
IGL02815:Dnmt3a	APN	12	3904226	critical splice donor site	probably null
IGL03372:Dnmt3a	APN	12	3902666	missense	probably damaging	1.00
Chromos	UTSW	12	3901665	missense	probably damaging	1.00
Compaction	UTSW	12	3866192	nonsense	probably null
R0028:Dnmt3a	UTSW	12	3900337	missense	probably damaging	0.99
R0306:Dnmt3a	UTSW	12	3866096	missense	possibly damaging	0.69
R0843:Dnmt3a	UTSW	12	3872886	splice site	probably benign
R1055:Dnmt3a	UTSW	12	3872864	missense	probably benign	0.05
R1465:Dnmt3a	UTSW	12	3866088	missense	probably damaging	1.00
R1465:Dnmt3a	UTSW	12	3866088	missense	probably damaging	1.00
R1585:Dnmt3a	UTSW	12	3901660	missense	probably damaging	0.99
R1680:Dnmt3a	UTSW	12	3873361	missense	probably damaging	0.97
R1753:Dnmt3a	UTSW	12	3873342	missense	possibly damaging	0.54
R2055:Dnmt3a	UTSW	12	3872859	missense	probably benign	0.44
R2219:Dnmt3a	UTSW	12	3849654	utr 5 prime	probably benign
R2267:Dnmt3a	UTSW	12	3897551	splice site	probably null
R2359:Dnmt3a	UTSW	12	3901599	missense	probably damaging	1.00
R2384:Dnmt3a	UTSW	12	3901591	missense	probably damaging	1.00
R2403:Dnmt3a	UTSW	12	3899883	missense	probably damaging	1.00
R2884:Dnmt3a	UTSW	12	3896132	missense	probably damaging	1.00
R3027:Dnmt3a	UTSW	12	3849626	splice site	probably null
R4281:Dnmt3a	UTSW	12	3901665	missense	probably damaging	1.00
R4282:Dnmt3a	UTSW	12	3901665	missense	probably damaging	1.00
R4283:Dnmt3a	UTSW	12	3901665	missense	probably damaging	1.00
R4809:Dnmt3a	UTSW	12	3900352	missense	probably damaging	1.00
R5154:Dnmt3a	UTSW	12	3896008	missense	probably damaging	1.00
R5361:Dnmt3a	UTSW	12	3895643	missense	probably benign	0.13
R5483:Dnmt3a	UTSW	12	3899615	missense	probably damaging	1.00
R5768:Dnmt3a	UTSW	12	3885660	splice site	probably null
R5928:Dnmt3a	UTSW	12	3866096	missense	possibly damaging	0.69
R6432:Dnmt3a	UTSW	12	3902399	missense	probably damaging	0.99
R6552:Dnmt3a	UTSW	12	3907623	missense	probably damaging	1.00
R6783:Dnmt3a	UTSW	12	3897406	missense	probably damaging	0.99
R6850:Dnmt3a	UTSW	12	3897600	missense	probably benign	0.40
R7106:Dnmt3a	UTSW	12	3897591	missense	probably damaging	0.99
R7145:Dnmt3a	UTSW	12	3872844	missense	probably benign	0.01
R7149:Dnmt3a	UTSW	12	3902397	missense	probably damaging	1.00
R7239:Dnmt3a	UTSW	12	3872850	missense	probably benign	0.01
R7588:Dnmt3a	UTSW	12	3896080	missense	possibly damaging	0.91
R7684:Dnmt3a	UTSW	12	3897340	missense	probably benign	0.02
R8058:Dnmt3a	UTSW	12	3902768	missense	possibly damaging	0.92
R8316:Dnmt3a	UTSW	12	3896965	missense	probably benign	0.00
R8345:Dnmt3a	UTSW	12	3835234	missense	unknown
R8464:Dnmt3a	UTSW	12	3899635	missense	probably benign	0.03
R8914:Dnmt3a	UTSW	12	3866192	nonsense	probably null
R9131:Dnmt3a	UTSW	12	3866136	missense	probably benign	0.00
R9246:Dnmt3a	UTSW	12	3899204	missense	probably damaging	1.00
R9476:Dnmt3a	UTSW	12	3907707	missense	probably damaging	1.00
R9485:Dnmt3a	UTSW	12	3866121	missense	probably benign	0.01
R9598:Dnmt3a	UTSW	12	3896997	missense	probably benign	0.25
R9709:Dnmt3a	UTSW	12	3907701	missense	probably damaging	1.00
Z1176:Dnmt3a	UTSW	12	3904201	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TAGCCAGCACATGTGGGATG -3'
(R):5'- TGCAGTATCCACTTTCCTGAG -3'

Sequencing Primer
(F):5'- CAGCACATGTGGGATGGATTTAAG -3'
(R):5'- TTTCCTGAGAAAGTGTTTTAAAAAGC -3'

Posted On

2019-10-17