Mutagenetix > Incidental Mutation

Incidental Mutation 'RF004:Dnmt1'

602696

Institutional Source

Beutler Lab

Gene Symbol

Dnmt1

Ensembl Gene

ENSMUSG00000004099

Gene Name

DNA methyltransferase 1

Synonyms

MTase, Dnmt1o, Cxxc9, MommeD2

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

RF004 (G1)

Quality Score

217.468

Status

Not validated

Chromosome

Chromosomal Location

20818501-20871084 bp(-) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

GCACAGTTCCTACCTCGTT to GCACAGTTCCTACCTCGTTTTGGGGGCGGAACACAGTTCCTACCTCGTT at 20821423 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000150433 (fasta)

Gene Model

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

AlphaFold

P13864

Predicted Effect

probably null
Transcript: ENSMUST00000004202

SMART Domains

Protein: ENSMUSP00000004202
Gene: ENSMUSG00000004099

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 null
Transcript: ENSMUST00000177754

SMART Domains

Protein: ENSMUSP00000136982
Gene: ENSMUSG00000004099

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 null
Transcript: ENSMUST00000178110

SMART Domains

Protein: ENSMUSP00000136669
Gene: ENSMUSG00000004099

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

probably null
Transcript: ENSMUST00000216540

Coding Region Coverage

1x: 99.8%
3x: 99.6%
10x: 99.1%
20x: 97.6%

Validation Efficiency

100% (34/34)

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110059E24Rik	T	A	19: 21,575,645 (GRCm39)	H126L	probably benign	Het
4930407I10Rik	A	T	15: 81,943,550 (GRCm39)	Q54L	possibly damaging	Het
4930433I11Rik	AACC	A	7: 40,642,479 (GRCm39)		probably benign	Het
Adora2a	A	T	10: 75,168,988 (GRCm39)	T151S	probably benign	Het
Ankhd1	GCGGCG	GCGGCGTCGGCG	18: 36,693,963 (GRCm39)		probably benign	Het
Ankrd36	A	G	11: 5,612,411 (GRCm39)	K1248E	possibly damaging	Het
Anks1b	G	A	10: 89,869,087 (GRCm39)	G49D	probably damaging	Het
Arl11	T	C	14: 61,548,304 (GRCm39)	V38A	probably damaging	Het
Atp2c2	A	T	8: 120,479,561 (GRCm39)	N726Y	probably damaging	Het
Bcat1	T	C	6: 144,953,349 (GRCm39)	K413R	probably benign	Het
Cd244a	C	G	1: 171,405,490 (GRCm39)	Q292E	probably benign	Het
Chp1	T	A	2: 119,411,195 (GRCm39)	D123E	probably damaging	Het
Cpeb4	ACTCT	ACTCTCT	11: 31,877,634 (GRCm39)		probably benign	Het
Ddx6	A	G	9: 44,535,789 (GRCm39)	T173A	possibly damaging	Het
Dlg2	T	A	7: 90,501,885 (GRCm39)	C66S	probably benign	Het
Dnah2	T	A	11: 69,328,013 (GRCm39)	Q3370L	probably benign	Het
Dop1a	T	C	9: 86,436,244 (GRCm39)	V2420A	probably benign	Het
Gm8369	GTGTGT	GTGTGTATGTGT	19: 11,489,118 (GRCm39)		probably benign	Het
Igkv6-25	TTGACGGA	T	6: 70,192,647 (GRCm39)		probably null	Het
Iqgap1	G	A	7: 80,370,623 (GRCm39)	A1582V	probably benign	Het
Lmnb1	T	C	18: 56,864,046 (GRCm39)	I217T	possibly damaging	Het
Mamld1	CAG	CAGTAG	X: 70,162,437 (GRCm39)		probably null	Het
Map2k2	A	T	10: 80,951,002 (GRCm39)	H149L	probably benign	Het
Med12l	CAG	CAGAAG	3: 59,183,390 (GRCm39)		probably benign	Het
Mmp1a	TG	TGG	9: 7,465,083 (GRCm38)		probably null	Het
Nxph2	G	A	2: 23,290,080 (GRCm39)	R144Q	probably damaging	Het
Or2t48	CA	C	11: 58,419,983 (GRCm39)		probably null	Het
Or51f1e	T	TTAG	7: 102,747,516 (GRCm39)		probably null	Het
Or51f1e	GTTAT	GTTATTAT	7: 102,747,512 (GRCm39)			Het
Or51f1e	AT	ATTCT	7: 102,747,515 (GRCm39)		probably benign	Het
Or51q1	TCC	TCCC	7: 103,629,110 (GRCm39)		probably null	Het
Or52n20	A	G	7: 104,320,248 (GRCm39)	E113G	probably damaging	Het
Or8d2	T	C	9: 38,760,114 (GRCm39)	F235L	probably benign	Het
Padi4	A	T	4: 140,487,269 (GRCm39)	V211E	probably damaging	Het
Prdm10	A	C	9: 31,270,422 (GRCm39)	D902A	probably damaging	Het
Prps1l1	A	G	12: 35,035,398 (GRCm39)	D171G	probably damaging	Het
Rasal3	A	T	17: 32,610,081 (GRCm39)	N1035K	probably damaging	Het
Rassf6	GGTCCTGTAGAGCAATGGGGATTC	GGTCCTGTAGAGCAATGGGGATTCTGCATCACTCATTGTCCTGTAGAGCAATGGGGATTC	5: 90,756,778 (GRCm39)		probably benign	Het
Rbm26	A	G	14: 105,388,931 (GRCm39)	V320A	probably damaging	Het
S1pr1	A	T	3: 115,506,536 (GRCm39)	Y19*	probably null	Het
Slc22a16	A	C	10: 40,479,642 (GRCm39)	L571F	possibly damaging	Het
Smarca2	CAGC	CAGCCCAAGC	19: 26,608,420 (GRCm39)		probably benign	Het
Ssx2ip	A	T	3: 146,132,195 (GRCm39)	K219*	probably null	Het
Trav15-2-dv6-2	AAG	AAGCAG	14: 53,887,212 (GRCm39)		probably benign	Het
Trav15-2-dv6-2	GGGAG	GGGAGGAG	14: 53,887,207 (GRCm39)		probably benign	Het
Trav15-2-dv6-2	GAA	GAATAA	14: 53,887,211 (GRCm39)		probably null	Het
Tsen15	A	G	1: 152,259,470 (GRCm39)	V63A	probably damaging	Het
Ttc21a	A	G	9: 119,795,838 (GRCm39)	Y1224C	probably damaging	Het
Usp54	T	A	14: 20,611,368 (GRCm39)	E1149D	possibly damaging	Het
Vmn2r37	A	T	7: 9,220,686 (GRCm39)	S392R	probably damaging	Het
Wdr97	GAGGAGGA	G	15: 76,247,373 (GRCm39)		probably null	Het
Zfp663	G	T	2: 165,200,363 (GRCm39)	H72Q	probably benign	Het
Zfp683	TGTGG	TGTGGTGG	4: 133,786,185 (GRCm39)		probably benign	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
R6143:Dnmt1	UTSW	9	20,838,430 (GRCm39)	missense	probably benign	0.30
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
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'- TGGCCTCTGCTGGAACTTAG -3'
(R):5'- GGGCAGACACTCTACCTAAAG -3'

Sequencing Primer
(F):5'- CCTCTGCTGGAACTTAGGAAGTGAG -3'
(R):5'- TGCAGGCTGGACAGTATGGC -3'

Posted On

2019-12-04