Mutagenetix > Incidental Mutation

Incidental Mutation 'R4518:Dnmt1'

334075

Institutional Source

Beutler Lab

Gene Symbol

Dnmt1

Ensembl Gene

ENSMUSG00000004099

Gene Name

DNA methyltransferase 1

Synonyms

MTase, Dnmt1o, Cxxc9, MommeD2

MMRRC Submission

041762-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4518 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

20818501-20871084 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 20823274 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 1055 (D1055E)

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: D1174E

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

SMART Domains

Protein: ENSMUSP00000004202
Gene: ENSMUSG00000004099
AA Change: D1174E

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: D1055E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000136982
Gene: ENSMUSG00000004099
AA Change: D1055E

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: D1055E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000136669
Gene: ENSMUSG00000004099
AA Change: D1055E

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: ENSMUST00000184490

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000214964

Predicted Effect

probably benign
Transcript: ENSMUST00000216540
AA Change: D1056E

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

Meta Mutation Damage Score

0.0906

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.9%

Validation Efficiency

98% (60/61)

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110082J24Rik	T	A	5: 30,311,006 (GRCm39)		probably null	Het
Abr	A	G	11: 76,363,344 (GRCm39)	S167P	possibly damaging	Het
Adamtsl2	T	C	2: 26,985,559 (GRCm39)	L481P	probably benign	Het
Atp8b3	C	T	10: 80,359,681 (GRCm39)	M984I	probably benign	Het
Brip1	G	A	11: 85,968,704 (GRCm39)	A827V	possibly damaging	Het
Carns1	T	G	19: 4,220,069 (GRCm39)	T389P	probably benign	Het
Ccdc88a	T	C	11: 29,432,651 (GRCm39)	I1219T	probably benign	Het
Cckar	T	C	5: 53,857,264 (GRCm39)	N311S	probably damaging	Het
Cenpc1	A	G	5: 86,195,446 (GRCm39)	S108P	possibly damaging	Het
Chpf	G	T	1: 75,451,689 (GRCm39)	S588R	probably damaging	Het
Clca3a2	T	A	3: 144,514,466 (GRCm39)	T414S	probably damaging	Het
Cntrl	A	G	2: 35,038,986 (GRCm39)	E1092G	probably damaging	Het
Crb2	C	A	2: 37,680,401 (GRCm39)	T443K	probably damaging	Het
Crppa	G	A	12: 36,523,179 (GRCm39)	V203I	possibly damaging	Het
Cwf19l1	A	G	19: 44,121,473 (GRCm39)	V25A	probably damaging	Het
Cyb561d1	T	C	3: 108,106,887 (GRCm39)	I111V	possibly damaging	Het
Dbn1	A	T	13: 55,624,042 (GRCm39)	I350N	possibly damaging	Het
Dnajb4	T	C	3: 151,890,813 (GRCm39)	I329V	probably benign	Het
Fam168a	C	T	7: 100,483,247 (GRCm39)	A176V	probably damaging	Het
Farp2	A	G	1: 93,548,363 (GRCm39)	E1016G	probably benign	Het
Fibcd1	A	T	2: 31,707,207 (GRCm39)	V350E	probably damaging	Het
Galnt3	C	A	2: 65,923,954 (GRCm39)	R438L	probably damaging	Het
Golga4	T	A	9: 118,388,076 (GRCm39)	S1733T	probably benign	Het
Golgb1	G	A	16: 36,749,625 (GRCm39)	E3076K	probably damaging	Het
Grm7	A	G	6: 110,891,507 (GRCm39)		probably null	Het
Hcn2	T	C	10: 79,560,536 (GRCm39)	V289A	probably benign	Het
Hipk1	G	T	3: 103,657,688 (GRCm39)	H799N	probably damaging	Het
Klf14	A	G	6: 30,934,867 (GRCm39)	S256P	possibly damaging	Het
Muc6	T	A	7: 141,230,489 (GRCm39)	T1214S	probably benign	Het
Nlrp2	T	A	7: 5,328,055 (GRCm39)	D666V	possibly damaging	Het
Ntng1	A	G	3: 109,842,329 (GRCm39)	I148T	probably damaging	Het
Or4k35	T	C	2: 111,100,263 (GRCm39)	M150V	probably benign	Het
Or7d9	A	G	9: 20,197,546 (GRCm39)	I184V	probably benign	Het
Or7g27	T	A	9: 19,250,556 (GRCm39)	S267T	possibly damaging	Het
Orc4	G	A	2: 48,827,501 (GRCm39)	P31S	probably benign	Het
Pabir3	G	A	X: 52,382,376 (GRCm39)	R94H	possibly damaging	Het
Pacs2	A	G	12: 113,024,289 (GRCm39)	D360G	probably benign	Het
Parp8	C	A	13: 117,032,209 (GRCm39)	L321F	possibly damaging	Het
Pdss2	T	A	10: 43,248,146 (GRCm39)	S217T	probably damaging	Het
Plekhn1	T	C	4: 156,309,988 (GRCm39)	S109G	probably damaging	Het
Prlr	C	A	15: 10,329,085 (GRCm39)	T520K	possibly damaging	Het
Prokr2	T	A	2: 132,216,012 (GRCm39)		probably null	Het
Rab3gap2	G	A	1: 184,999,265 (GRCm39)	V991I	probably benign	Het
Reln	T	C	5: 22,106,741 (GRCm39)	I3210V	probably benign	Het
Rims2	T	C	15: 39,300,922 (GRCm39)	Y218H	probably damaging	Het
Slc41a1	T	C	1: 131,766,863 (GRCm39)	V127A	probably damaging	Het
St8sia6	T	A	2: 13,797,562 (GRCm39)		probably null	Het
Tlr6	A	G	5: 65,112,247 (GRCm39)	F220S	possibly damaging	Het
Trmt1l	C	T	1: 151,324,094 (GRCm39)	Q314*	probably null	Het
Ubqlnl	C	T	7: 103,798,925 (GRCm39)	V191M	probably benign	Het
Vnn3	G	A	10: 23,743,124 (GRCm39)	V445M	possibly damaging	Het
Ypel1	A	T	16: 16,913,905 (GRCm39)	F173I	possibly damaging	Het
Zfhx4	T	C	3: 5,477,578 (GRCm39)	C3398R	probably damaging	Het
Zfyve16	T	C	13: 92,657,820 (GRCm39)	E697G	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
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
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'- TTCATGCCACTGAAGCCCTG -3'
(R):5'- AAGGATTCCACCAAGCAGG -3'

Sequencing Primer
(F):5'- ACTGAAGCCCTGGCAGG -3'
(R):5'- CTGACTCTGGCCTGGCTTTAG -3'

Posted On

2015-08-18