Mutagenetix > Incidental Mutation

Incidental Mutation 'R6143:Dnmt1'

488683

Institutional Source

Beutler Lab

Gene Symbol

Dnmt1

Ensembl Gene

ENSMUSG00000004099

Gene Name

DNA methyltransferase 1

Synonyms

MTase, Dnmt1o, Cxxc9, MommeD2

MMRRC Submission

044290-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6143 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

20818501-20871084 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 20838430 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 211 (E211G)

Ref Sequence

ENSEMBL: ENSMUSP00000136669 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004202] [ENSMUST00000177754] [ENSMUST00000178110] [ENSMUST00000216540]

AlphaFold

P13864

Predicted Effect

probably benign
Transcript: ENSMUST00000004202
AA Change: E330G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000004202
Gene: ENSMUSG00000004099
AA Change: E330G

Domain	Start	End	E-Value	Type
DMAP_binding	16	106	1.7e-13	SMART
low complexity region	121	143	N/A	INTRINSIC
low complexity region	156	166	N/A	INTRINSIC
low complexity region	180	194	N/A	INTRINSIC
low complexity region	273	290	N/A	INTRINSIC
low complexity region	306	328	N/A	INTRINSIC
Pfam:DNMT1-RFD	405	540	4.8e-46	PFAM
low complexity region	610	625	N/A	INTRINSIC
Pfam:zf-CXXC	648	694	2.7e-17	PFAM
low complexity region	701	711	N/A	INTRINSIC
low complexity region	719	731	N/A	INTRINSIC
BAH	758	884	4.62e-31	SMART
BAH	935	1103	1.79e-37	SMART
low complexity region	1110	1124	N/A	INTRINSIC
Pfam:DNA_methylase	1142	1596	1.3e-49	PFAM
low complexity region	1600	1619	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000177754
AA Change: E211G

PolyPhen 2 Score 0.300 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000136982
Gene: ENSMUSG00000004099
AA Change: E211G

Domain	Start	End	E-Value	Type
low complexity region	3	25	N/A	INTRINSIC
low complexity region	37	47	N/A	INTRINSIC
low complexity region	61	75	N/A	INTRINSIC
low complexity region	154	171	N/A	INTRINSIC
low complexity region	187	209	N/A	INTRINSIC
Pfam:DNMT1-RFD	286	421	3.4e-40	PFAM
low complexity region	491	506	N/A	INTRINSIC
Pfam:zf-CXXC	529	575	2.3e-17	PFAM
low complexity region	582	592	N/A	INTRINSIC
low complexity region	600	612	N/A	INTRINSIC
BAH	639	765	4.62e-31	SMART
BAH	816	984	1.79e-37	SMART
low complexity region	991	1005	N/A	INTRINSIC
Pfam:DNA_methylase	1023	1477	1.3e-49	PFAM
low complexity region	1481	1500	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000178110
AA Change: E211G

PolyPhen 2 Score 0.300 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000136669
Gene: ENSMUSG00000004099
AA Change: E211G

Domain	Start	End	E-Value	Type
low complexity region	3	25	N/A	INTRINSIC
low complexity region	38	48	N/A	INTRINSIC
low complexity region	62	76	N/A	INTRINSIC
low complexity region	155	172	N/A	INTRINSIC
low complexity region	188	210	N/A	INTRINSIC
Pfam:DNMT1-RFD	287	422	2.6e-40	PFAM
low complexity region	492	507	N/A	INTRINSIC
Pfam:zf-CXXC	530	576	4.7e-17	PFAM
low complexity region	583	593	N/A	INTRINSIC
low complexity region	601	613	N/A	INTRINSIC
BAH	640	766	4.62e-31	SMART
BAH	817	985	1.79e-37	SMART
low complexity region	992	1006	N/A	INTRINSIC
Pfam:DNA_methylase	1024	1478	8e-50	PFAM
low complexity region	1482	1501	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000215545

Predicted Effect

probably benign
Transcript: ENSMUST00000216540
AA Change: E212G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 95.1%

Validation Efficiency

98% (62/63)

MGI Phenotype

FUNCTION: This gene encodes a methyltransferase that preferentially methylates cytosines of CpG residues in hemimethylated DNA to generate fully methylated CpG base pairs during DNA replication. This enzyme plays roles in diverse cellular processes including cell cycle regulation, DNA repair, and telomere maintenance. The encoded protein is composed of an N-terminal domain with a nuclear localization sequence and replication fork-targeting domain, a DNA-binding CXXC domain, two bromo-adjacent homology domains, and a C-terminal catalytic domain. Mouse embryonic stem cells mutant for this gene are viable, but when introduced into the germ line, cause a recessive lethal phenotype with mutant embryos displaying stunted growth and developmental defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mutations causing partial or severe loss of function were homozygous lethal by embryonic day 9.5, with lack of appropriate genomic imprinting observed at several loci. [provided by MGI curators]

Allele List at MGI

All alleles(109) : Targeted, knock-out(5) Targeted, other(11) Gene trapped(92) Chemically induced(1)

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730061H03Rik	A	G	14: 55,797,736 (GRCm39)		probably benign	Het
Abcd2	A	T	15: 91,075,150 (GRCm39)	V221E	possibly damaging	Het
Arhgap39	T	A	15: 76,614,606 (GRCm39)	K853*	probably null	Het
Art2a	T	C	7: 101,204,430 (GRCm39)	D36G	possibly damaging	Het
Atp13a1	C	T	8: 70,258,010 (GRCm39)	P922S	probably benign	Het
Brwd1	C	T	16: 95,804,156 (GRCm39)	G2005R	probably benign	Het
Bzw2	A	T	12: 36,170,725 (GRCm39)	M133K	probably benign	Het
Cacna1s	T	G	1: 136,004,496 (GRCm39)	S346A	probably damaging	Het
Cebpb	C	A	2: 167,531,220 (GRCm39)	D93E	probably benign	Het
Cep162	C	A	9: 87,094,904 (GRCm39)		probably null	Het
Col9a2	A	T	4: 120,911,060 (GRCm39)	Y565F	probably damaging	Het
Csgalnact1	T	A	8: 68,826,202 (GRCm39)	N372I	probably damaging	Het
Csmd1	T	C	8: 16,138,315 (GRCm39)	D1579G	probably damaging	Het
Cyfip2	A	C	11: 46,144,792 (GRCm39)	Y687*	probably null	Het
Cyp2d34	G	A	15: 82,504,977 (GRCm39)	R28W	probably benign	Het
Dbndd2	C	A	2: 164,330,206 (GRCm39)	Q13K	probably damaging	Het
Dnah5	T	A	15: 28,233,377 (GRCm39)	S245R	probably benign	Het
Dnajb5	A	T	4: 42,956,990 (GRCm39)	T226S	probably damaging	Het
Dnpep	G	A	1: 75,291,872 (GRCm39)	H214Y	probably damaging	Het
Drc3	G	A	11: 60,261,406 (GRCm39)	V186M	possibly damaging	Het
Dvl3	A	G	16: 20,345,789 (GRCm39)	D413G	possibly damaging	Het
Dyrk4	C	T	6: 126,863,614 (GRCm39)		probably null	Het
Edc4	T	A	8: 106,612,506 (GRCm39)	D181E	probably damaging	Het
Enthd1	T	C	15: 80,393,487 (GRCm39)	Y247C	possibly damaging	Het
Gm5622	A	T	14: 51,892,372 (GRCm39)	R50S	possibly damaging	Het
Gpbp1	G	A	13: 111,603,389 (GRCm39)	T20I	probably damaging	Het
Hnrnpdl	A	T	5: 100,184,410 (GRCm39)	Y276*	probably null	Het
Hsd3b7	A	C	7: 127,400,404 (GRCm39)	E51A	probably damaging	Het
Ighv5-16	G	T	12: 113,802,238 (GRCm39)	F87L	probably damaging	Het
Iqsec1	C	T	6: 90,786,666 (GRCm39)		probably null	Het
Irgm2	A	T	11: 58,111,435 (GRCm39)	E387D	possibly damaging	Het
Klhl23	C	A	2: 69,664,040 (GRCm39)	P463Q	possibly damaging	Het
Mast4	A	T	13: 102,990,391 (GRCm39)	N43K	probably damaging	Het
Mme	T	G	3: 63,207,532 (GRCm39)		probably null	Het
Mrps31	T	G	8: 22,901,539 (GRCm39)	S20A	probably benign	Het
Myo5c	A	G	9: 75,157,091 (GRCm39)	R176G	probably damaging	Het
Naf1	T	C	8: 67,330,347 (GRCm39)	V291A	possibly damaging	Het
Nbeal1	A	T	1: 60,290,466 (GRCm39)	H1021L	possibly damaging	Het
Ncaph2	T	C	15: 89,248,206 (GRCm39)		probably null	Het
Neurod4	T	G	10: 130,106,869 (GRCm39)	Y135S	probably damaging	Het
Nrp2	A	T	1: 62,799,974 (GRCm39)	N396I	probably damaging	Het
Nvl	T	G	1: 180,962,560 (GRCm39)	T137P	probably benign	Het
Or5p59	A	G	7: 107,703,335 (GRCm39)	D273G	probably damaging	Het
Papola	T	C	12: 105,793,219 (GRCm39)	V513A	probably benign	Het
Pcdhgc4	T	A	18: 37,950,653 (GRCm39)	S690T	possibly damaging	Het
Pck1	A	T	2: 172,995,805 (GRCm39)	D101V	probably damaging	Het
Pdilt	T	A	7: 119,094,265 (GRCm39)	N329Y	probably damaging	Het
Pfkl	T	A	10: 77,825,447 (GRCm39)	R648W	probably damaging	Het
Prtn3	T	A	10: 79,716,382 (GRCm39)	I63N	probably damaging	Het
Psg22	C	T	7: 18,456,723 (GRCm39)	A163V	probably benign	Het
Pten	A	G	19: 32,777,485 (GRCm39)	T160A	possibly damaging	Het
Retreg2	A	G	1: 75,123,530 (GRCm39)	D449G	probably damaging	Het
Scn9a	T	C	2: 66,317,868 (GRCm39)	Y1531C	probably benign	Het
Sgk2	T	A	2: 162,841,174 (GRCm39)	C195S	probably damaging	Het
Slc19a3	C	T	1: 83,004,060 (GRCm39)	V14I	probably benign	Het
Snai2	A	T	16: 14,526,107 (GRCm39)	R253*	probably null	Het
Speg	G	A	1: 75,391,031 (GRCm39)	V1512I	probably damaging	Het
Srsf1	G	A	11: 87,940,425 (GRCm39)		probably benign	Het
Tctn3	G	T	19: 40,597,671 (GRCm39)	T190N	probably benign	Het
Tmprss11f	T	A	5: 86,687,558 (GRCm39)	I117L	probably benign	Het
Ttn	G	A	2: 76,682,413 (GRCm39)	R959*	probably null	Het
Vmn2r118	G	T	17: 55,899,871 (GRCm39)	L678I	possibly damaging	Het
Vps13b	T	C	15: 35,668,884 (GRCm39)	S1594P	probably damaging	Het
Vps13d	G	T	4: 144,875,135 (GRCm39)	H1791N	possibly damaging	Het

Other mutations in Dnmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00334:Dnmt1	APN	9	20,821,566 (GRCm39)	missense	possibly damaging	0.94
IGL01093:Dnmt1	APN	9	20,821,081 (GRCm39)	missense	possibly damaging	0.88
IGL01160:Dnmt1	APN	9	20,828,615 (GRCm39)	missense	possibly damaging	0.90
IGL01704:Dnmt1	APN	9	20,821,476 (GRCm39)	missense	probably damaging	1.00
IGL02105:Dnmt1	APN	9	20,819,178 (GRCm39)	missense	unknown
IGL02124:Dnmt1	APN	9	20,819,845 (GRCm39)	missense	probably damaging	1.00
IGL02188:Dnmt1	APN	9	20,853,034 (GRCm39)	nonsense	probably null
IGL02409:Dnmt1	APN	9	20,837,793 (GRCm39)	missense	probably benign	0.00
IGL02579:Dnmt1	APN	9	20,829,416 (GRCm39)	missense	possibly damaging	0.79
IGL02625:Dnmt1	APN	9	20,838,442 (GRCm39)	missense	probably benign	0.01
IGL02794:Dnmt1	APN	9	20,847,847 (GRCm39)	missense	probably benign
IGL02795:Dnmt1	APN	9	20,838,407 (GRCm39)	missense	probably benign	0.12
IGL02938:Dnmt1	APN	9	20,852,669 (GRCm39)	missense	probably benign	0.23
IGL03245:Dnmt1	APN	9	20,827,056 (GRCm39)	missense	probably damaging	0.99
IGL03303:Dnmt1	APN	9	20,838,006 (GRCm39)	missense	probably benign
Blankslate	UTSW	9	20,823,521 (GRCm39)	missense	possibly damaging	0.86
Midrash	UTSW	9	20,821,089 (GRCm39)	nonsense	probably null
Rashi	UTSW	9	20,833,408 (GRCm39)	missense	possibly damaging	0.94
B5639:Dnmt1	UTSW	9	20,819,264 (GRCm39)	splice site	probably benign
BB003:Dnmt1	UTSW	9	20,818,855 (GRCm39)	missense	unknown
BB013:Dnmt1	UTSW	9	20,818,855 (GRCm39)	missense	unknown
PIT4576001:Dnmt1	UTSW	9	20,823,071 (GRCm39)	missense	probably benign	0.28
R0071:Dnmt1	UTSW	9	20,819,916 (GRCm39)	missense	probably damaging	0.99
R0180:Dnmt1	UTSW	9	20,819,916 (GRCm39)	missense	probably damaging	0.99
R0368:Dnmt1	UTSW	9	20,853,053 (GRCm39)	missense	probably damaging	0.99
R0387:Dnmt1	UTSW	9	20,829,509 (GRCm39)	missense	probably damaging	1.00
R0529:Dnmt1	UTSW	9	20,822,846 (GRCm39)	missense	probably damaging	1.00
R0532:Dnmt1	UTSW	9	20,829,852 (GRCm39)	splice site	probably benign
R0612:Dnmt1	UTSW	9	20,829,489 (GRCm39)	missense	probably damaging	0.98
R1109:Dnmt1	UTSW	9	20,833,684 (GRCm39)	missense	probably damaging	1.00
R1298:Dnmt1	UTSW	9	20,852,752 (GRCm39)	missense	probably benign
R1345:Dnmt1	UTSW	9	20,819,814 (GRCm39)	missense	probably damaging	1.00
R1472:Dnmt1	UTSW	9	20,843,472 (GRCm39)	missense	probably benign	0.28
R1654:Dnmt1	UTSW	9	20,847,870 (GRCm39)	missense	possibly damaging	0.75
R1817:Dnmt1	UTSW	9	20,838,422 (GRCm39)	missense	probably benign
R1836:Dnmt1	UTSW	9	20,829,542 (GRCm39)	missense	probably damaging	1.00
R1957:Dnmt1	UTSW	9	20,838,442 (GRCm39)	missense	probably benign	0.01
R1958:Dnmt1	UTSW	9	20,838,442 (GRCm39)	missense	probably benign	0.01
R2097:Dnmt1	UTSW	9	20,821,084 (GRCm39)	missense	probably benign	0.00
R2145:Dnmt1	UTSW	9	20,848,451 (GRCm39)	splice site	probably benign
R2326:Dnmt1	UTSW	9	20,835,442 (GRCm39)	splice site	probably benign
R4199:Dnmt1	UTSW	9	20,849,414 (GRCm39)	missense	probably benign	0.00
R4456:Dnmt1	UTSW	9	20,821,138 (GRCm39)	missense	probably damaging	1.00
R4518:Dnmt1	UTSW	9	20,823,274 (GRCm39)	missense	probably benign	0.00
R4586:Dnmt1	UTSW	9	20,837,989 (GRCm39)	missense	probably benign	0.05
R4836:Dnmt1	UTSW	9	20,819,854 (GRCm39)	missense	probably damaging	1.00
R5014:Dnmt1	UTSW	9	20,823,550 (GRCm39)	missense	probably benign	0.07
R5338:Dnmt1	UTSW	9	20,864,015 (GRCm39)	missense	probably benign	0.44
R5385:Dnmt1	UTSW	9	20,829,776 (GRCm39)	missense	probably damaging	1.00
R5579:Dnmt1	UTSW	9	20,831,501 (GRCm39)	missense	probably damaging	1.00
R5645:Dnmt1	UTSW	9	20,833,443 (GRCm39)	missense	probably damaging	1.00
R5719:Dnmt1	UTSW	9	20,823,891 (GRCm39)	missense	possibly damaging	0.86
R5881:Dnmt1	UTSW	9	20,864,013 (GRCm39)	missense	probably damaging	0.97
R6039:Dnmt1	UTSW	9	20,837,716 (GRCm39)	intron	probably benign
R6039:Dnmt1	UTSW	9	20,837,716 (GRCm39)	intron	probably benign
R6342:Dnmt1	UTSW	9	20,821,089 (GRCm39)	nonsense	probably null
R6374:Dnmt1	UTSW	9	20,835,341 (GRCm39)	missense	possibly damaging	0.73
R6953:Dnmt1	UTSW	9	20,829,822 (GRCm39)	missense	probably benign
R6990:Dnmt1	UTSW	9	20,827,110 (GRCm39)	nonsense	probably null
R7089:Dnmt1	UTSW	9	20,819,785 (GRCm39)	missense	probably damaging	0.99
R7463:Dnmt1	UTSW	9	20,823,521 (GRCm39)	missense	possibly damaging	0.86
R7522:Dnmt1	UTSW	9	20,831,498 (GRCm39)	missense	probably damaging	0.99
R7695:Dnmt1	UTSW	9	20,825,281 (GRCm39)	missense	probably null	1.00
R7785:Dnmt1	UTSW	9	20,833,345 (GRCm39)	missense	probably damaging	0.98
R7926:Dnmt1	UTSW	9	20,818,855 (GRCm39)	missense	unknown
R8037:Dnmt1	UTSW	9	20,852,860 (GRCm39)	missense	probably damaging	0.99
R8038:Dnmt1	UTSW	9	20,852,860 (GRCm39)	missense	probably damaging	0.99
R8424:Dnmt1	UTSW	9	20,829,836 (GRCm39)	missense	probably benign	0.07
R8692:Dnmt1	UTSW	9	20,853,077 (GRCm39)	missense	probably damaging	1.00
R9016:Dnmt1	UTSW	9	20,847,855 (GRCm39)	missense	possibly damaging	0.67
R9101:Dnmt1	UTSW	9	20,852,839 (GRCm39)	missense	probably damaging	1.00
R9200:Dnmt1	UTSW	9	20,819,896 (GRCm39)	missense	probably benign	0.00
R9248:Dnmt1	UTSW	9	20,833,408 (GRCm39)	missense	possibly damaging	0.94
R9317:Dnmt1	UTSW	9	20,829,575 (GRCm39)	missense	probably damaging	0.99
R9352:Dnmt1	UTSW	9	20,840,384 (GRCm39)	missense	probably benign	0.00
R9438:Dnmt1	UTSW	9	20,827,190 (GRCm39)	missense	probably benign
RF003:Dnmt1	UTSW	9	20,821,427 (GRCm39)	nonsense	probably null
RF004:Dnmt1	UTSW	9	20,821,423 (GRCm39)	nonsense	probably null
RF011:Dnmt1	UTSW	9	20,821,440 (GRCm39)	nonsense	probably null
RF011:Dnmt1	UTSW	9	20,821,424 (GRCm39)	nonsense	probably null
RF015:Dnmt1	UTSW	9	20,821,425 (GRCm39)	nonsense	probably null
RF015:Dnmt1	UTSW	9	20,821,420 (GRCm39)	nonsense	probably null
RF017:Dnmt1	UTSW	9	20,821,422 (GRCm39)	nonsense	probably null
RF023:Dnmt1	UTSW	9	20,821,427 (GRCm39)	nonsense	probably null
RF024:Dnmt1	UTSW	9	20,821,434 (GRCm39)	small insertion	probably benign
RF024:Dnmt1	UTSW	9	20,821,426 (GRCm39)	nonsense	probably null
RF025:Dnmt1	UTSW	9	20,821,431 (GRCm39)	nonsense	probably null
RF025:Dnmt1	UTSW	9	20,821,416 (GRCm39)	nonsense	probably null
RF029:Dnmt1	UTSW	9	20,821,419 (GRCm39)	nonsense	probably null
RF034:Dnmt1	UTSW	9	20,821,416 (GRCm39)	nonsense	probably null
RF037:Dnmt1	UTSW	9	20,821,437 (GRCm39)	nonsense	probably null
RF037:Dnmt1	UTSW	9	20,821,429 (GRCm39)	nonsense	probably null
RF037:Dnmt1	UTSW	9	20,821,415 (GRCm39)	critical splice donor site	probably benign
RF042:Dnmt1	UTSW	9	20,821,415 (GRCm39)	nonsense	probably null
RF045:Dnmt1	UTSW	9	20,821,433 (GRCm39)	small insertion	probably benign
RF045:Dnmt1	UTSW	9	20,821,425 (GRCm39)	nonsense	probably null
RF047:Dnmt1	UTSW	9	20,821,421 (GRCm39)	nonsense	probably null
RF048:Dnmt1	UTSW	9	20,821,422 (GRCm39)	nonsense	probably null
RF054:Dnmt1	UTSW	9	20,821,435 (GRCm39)	nonsense	probably null
RF055:Dnmt1	UTSW	9	20,821,432 (GRCm39)	small insertion	probably benign
RF055:Dnmt1	UTSW	9	20,821,431 (GRCm39)	nonsense	probably null
RF055:Dnmt1	UTSW	9	20,821,424 (GRCm39)	nonsense	probably null
RF059:Dnmt1	UTSW	9	20,821,434 (GRCm39)	small insertion	probably benign
RF059:Dnmt1	UTSW	9	20,821,435 (GRCm39)	nonsense	probably null
RF060:Dnmt1	UTSW	9	20,821,438 (GRCm39)	nonsense	probably null
RF061:Dnmt1	UTSW	9	20,821,426 (GRCm39)	nonsense	probably null
X0026:Dnmt1	UTSW	9	20,825,210 (GRCm39)	missense	probably damaging	1.00
Z1176:Dnmt1	UTSW	9	20,837,850 (GRCm39)	missense	probably benign	0.00
Z1176:Dnmt1	UTSW	9	20,827,159 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TGCACGTCGATGACTGTCAG -3'
(R):5'- TCCTAATGTGCCCATGCTGG -3'

Sequencing Primer
(F):5'- TCGATGACTGTCAGGACGAG -3'
(R):5'- TAGGGTCTCACCAAGTATCTCAGG -3'

Posted On

2017-10-10