Mutagenetix > Incidental Mutation

Incidental Mutation 'R2069:Dnmt3l'

226960

Institutional Source

Beutler Lab

Gene Symbol

Dnmt3l

Ensembl Gene

ENSMUSG00000000730

Gene Name

DNA (cytosine-5-)-methyltransferase 3-like

Synonyms

D6Ertd14e, ecat7

MMRRC Submission

040074-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2069 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

78041947-78063622 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 78052732 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 156 (V156A)

Ref Sequence

ENSEMBL: ENSMUSP00000116970 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000746] [ENSMUST00000123940] [ENSMUST00000131825] [ENSMUST00000138785] [ENSMUST00000139539] [ENSMUST00000151242]

AlphaFold

Q9CWR8

Predicted Effect

probably damaging
Transcript: ENSMUST00000000746
AA Change: V156A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000000746
Gene: ENSMUSG00000000730
AA Change: V156A

Domain	Start	End	E-Value	Type
low complexity region	22	32	N/A	INTRINSIC
PDB:2PVC\|C	38	415	1e-163	PDB
SCOP:d1fp0a1	123	191	5e-3	SMART
Blast:RING	130	179	1e-18	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000123940

SMART Domains

Protein: ENSMUSP00000123015
Gene: ENSMUSG00000000730

Domain	Start	End	E-Value	Type
PDB:2QRV\|G	1	120	1e-38	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000131825

SMART Domains

Protein: ENSMUSP00000119571
Gene: ENSMUSG00000000730

Domain	Start	End	E-Value	Type
PDB:2QRV\|G	1	120	1e-38	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000138785
AA Change: V156A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000121562
Gene: ENSMUSG00000000730
AA Change: V156A

Domain	Start	End	E-Value	Type
low complexity region	22	32	N/A	INTRINSIC
PDB:2PVC\|C	38	415	1e-163	PDB
SCOP:d1fp0a1	123	191	5e-3	SMART
Blast:RING	130	179	1e-18	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000139539

SMART Domains

Protein: ENSMUSP00000117827
Gene: ENSMUSG00000000730

Domain	Start	End	E-Value	Type
PDB:2QRV\|G	1	120	1e-38	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144446

Predicted Effect

probably damaging
Transcript: ENSMUST00000151242
AA Change: V156A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000116970
Gene: ENSMUSG00000000730
AA Change: V156A

Domain	Start	End	E-Value	Type
low complexity region	22	32	N/A	INTRINSIC
PDB:2PVC\|C	38	415	1e-163	PDB
SCOP:d1fp0a1	123	191	5e-3	SMART
Blast:RING	130	179	1e-18	BLAST

Meta Mutation Damage Score

0.3129

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

100% (104/104)

MGI Phenotype

FUNCTION: CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a nuclear protein that is a catalytically inactive regulatory factor of DNA methyltransferases. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mutants in this imprinted gene lack appropriate methylation of the maternal allele and this, in turn, causes azoospermia in homozygous males; and heterozygous progeny of homozygous females die by midgestation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 104 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930519G04Rik	T	C	5: 114,874,280 (GRCm38)	V86A	probably benign	Het
Abcc3	A	T	11: 94,364,417 (GRCm38)	I601N	probably damaging	Het
Abl2	T	A	1: 156,620,827 (GRCm38)		probably null	Het
Adgrf4	C	T	17: 42,666,898 (GRCm38)	R518Q	possibly damaging	Het
Ahi1	C	T	10: 20,959,996 (GRCm38)	T76I	probably damaging	Het
Arhgap42	C	T	9: 9,035,600 (GRCm38)	G247D	probably damaging	Het
Arid2	C	T	15: 96,362,590 (GRCm38)	L407F	probably damaging	Het
Atp13a1	T	C	8: 69,799,773 (GRCm38)	F606L	probably benign	Het
Avl9	T	A	6: 56,736,435 (GRCm38)		probably benign	Het
B3glct	C	T	5: 149,709,380 (GRCm38)	A65V	probably damaging	Het
Bcorl1	T	C	X: 48,401,917 (GRCm38)		probably benign	Het
Bdp1	T	C	13: 100,050,988 (GRCm38)	T1624A	probably benign	Het
Bmp15	A	G	X: 6,316,021 (GRCm38)	M263T	probably benign	Het
Brd8	T	C	18: 34,614,479 (GRCm38)	K110E	probably damaging	Het
Cachd1	A	G	4: 100,990,844 (GRCm38)	D1052G	probably damaging	Het
Capn9	G	A	8: 124,605,711 (GRCm38)	G430R	possibly damaging	Het
Ccdc113	G	A	8: 95,557,296 (GRCm38)	E333K	probably benign	Het
Ccnl2	A	T	4: 155,812,481 (GRCm38)		probably null	Het
Ccr9	T	C	9: 123,779,364 (GRCm38)	F37S	probably benign	Het
Cdh7	A	T	1: 110,138,159 (GRCm38)	D721V	probably damaging	Het
Ceacam10	A	T	7: 24,778,372 (GRCm38)	N104I	probably damaging	Het
Cenpk	T	A	13: 104,236,176 (GRCm38)		probably benign	Het
Cfi	A	G	3: 129,858,804 (GRCm38)		probably null	Het
Chd1	T	C	17: 15,742,294 (GRCm38)	F771S	probably damaging	Het
Chil4	G	A	3: 106,219,455 (GRCm38)	L4F	probably benign	Het
Cilp	G	A	9: 65,278,090 (GRCm38)	R489Q	possibly damaging	Het
Cntnap5b	G	A	1: 100,358,725 (GRCm38)	G402R	probably benign	Het
Coq8b	A	G	7: 27,257,377 (GRCm38)	E485G	probably damaging	Het
Cse1l	A	G	2: 166,941,492 (GRCm38)	S733G	probably benign	Het
Dnah5	G	A	15: 28,312,388 (GRCm38)		probably null	Het
Duox1	A	T	2: 122,333,062 (GRCm38)	T792S	probably benign	Het
Duox2	T	C	2: 122,287,108 (GRCm38)	D915G	probably benign	Het
Efcab5	A	T	11: 77,172,321 (GRCm38)	M115K	probably benign	Het
Eif2s1	G	A	12: 78,877,185 (GRCm38)	D139N	probably benign	Het
Erg	A	G	16: 95,361,078 (GRCm38)	F390L	probably damaging	Het
Fam193b	A	T	13: 55,542,998 (GRCm38)	S650R	probably damaging	Het
Fbp2	T	A	13: 62,854,061 (GRCm38)	K113N	possibly damaging	Het
Fnbp4	T	G	2: 90,758,372 (GRCm38)	S496A	probably damaging	Het
Gab3	C	A	X: 75,000,095 (GRCm38)	R475L	probably damaging	Het
Gsap	T	C	5: 21,226,839 (GRCm38)		probably benign	Het
Gucy1a2	C	T	9: 3,582,697 (GRCm38)	L160F	probably damaging	Het
Hivep1	C	T	13: 42,183,786 (GRCm38)	A2447V	possibly damaging	Het
Insc	G	T	7: 114,804,593 (GRCm38)		probably null	Het
Jph2	A	G	2: 163,339,685 (GRCm38)	S520P	possibly damaging	Het
Kidins220	T	A	12: 24,987,006 (GRCm38)		probably benign	Het
Krtap29-1	A	G	11: 99,978,612 (GRCm38)	S148P	probably damaging	Het
Ltbp2	A	C	12: 84,793,733 (GRCm38)	C1000G	probably damaging	Het
Map2k3	T	C	11: 60,950,027 (GRCm38)	F294S	probably damaging	Het
Map4k2	C	A	19: 6,342,738 (GRCm38)		probably benign	Het
Mboat2	T	C	12: 24,951,443 (GRCm38)	V281A	probably benign	Het
Mdga2	G	A	12: 66,568,917 (GRCm38)	R570*	probably null	Het
Mlxipl	A	G	5: 135,107,005 (GRCm38)	D28G	probably damaging	Het
Morc2b	T	C	17: 33,136,760 (GRCm38)	I679M	probably benign	Het
Myh4	T	C	11: 67,246,366 (GRCm38)		probably benign	Het
Nfib	A	C	4: 82,498,615 (GRCm38)	L61R	probably damaging	Het
Noc2l	C	A	4: 156,241,450 (GRCm38)	Y227*	probably null	Het
Nrde2	A	G	12: 100,142,232 (GRCm38)	S367P	probably damaging	Het
Nup93	C	A	8: 94,243,739 (GRCm38)	P89T	probably damaging	Het
Obsl1	G	A	1: 75,486,756 (GRCm38)	T1764M	probably benign	Het
Or10a2	A	T	7: 107,074,619 (GRCm38)	K264*	probably null	Het
Or11h4	T	A	14: 50,736,576 (GRCm38)	E195D	possibly damaging	Het
Or4a68	C	T	2: 89,439,583 (GRCm38)	R232H	probably benign	Het
Or4k77	A	G	2: 111,369,095 (GRCm38)	I154M	probably benign	Het
Or6b9	A	T	7: 106,956,287 (GRCm38)	Y216*	probably null	Het
Or9r7	A	G	10: 130,126,205 (GRCm38)	I284T	possibly damaging	Het
Oxct1	G	T	15: 4,092,525 (GRCm38)	A319S	probably null	Het
P2ry10	A	G	X: 107,103,253 (GRCm38)	S265G	probably benign	Het
Peak1	A	T	9: 56,258,759 (GRCm38)	N628K	probably damaging	Het
Pkdrej	T	A	15: 85,821,231 (GRCm38)	Q168L	probably benign	Het
Plaat5	T	C	19: 7,612,638 (GRCm38)	S10P	possibly damaging	Het
Plec	A	G	15: 76,188,926 (GRCm38)	M604T	probably benign	Het
Pmfbp1	A	T	8: 109,532,103 (GRCm38)	N680I	possibly damaging	Het
Pnma8b	T	C	7: 16,945,789 (GRCm38)	W233R	probably damaging	Het
Pxn	A	G	5: 115,545,667 (GRCm38)	N186S	probably benign	Het
Rsad1	A	C	11: 94,549,125 (GRCm38)		probably benign	Het
Runx2	A	G	17: 44,735,342 (GRCm38)	I112T	probably benign	Het
S1pr2	A	T	9: 20,967,494 (GRCm38)	L346Q	probably damaging	Het
Skint6	A	G	4: 113,238,132 (GRCm38)	I110T	probably damaging	Het
Slc36a4	T	A	9: 15,726,980 (GRCm38)	F234Y	probably damaging	Het
Slitrk2	T	A	X: 66,654,629 (GRCm38)	V242D	probably damaging	Het
Sp100	A	G	1: 85,681,142 (GRCm38)		probably null	Het
Spryd3	A	C	15: 102,118,181 (GRCm38)	L352V	probably benign	Het
Ssc4d	A	C	5: 135,970,317 (GRCm38)	W11G	possibly damaging	Het
Stx17	T	A	4: 48,158,870 (GRCm38)	D83E	probably damaging	Het
Tlk2	A	T	11: 105,240,440 (GRCm38)	Q204L	probably benign	Het
Tnfrsf21	A	T	17: 43,037,938 (GRCm38)	H147L	possibly damaging	Het
Tnrc18	A	T	5: 142,766,087 (GRCm38)	D1154E	unknown	Het
Trap1	A	G	16: 4,068,336 (GRCm38)	S86P	probably benign	Het
Trim32	T	A	4: 65,614,776 (GRCm38)	C523*	probably null	Het
Ttc38	G	T	15: 85,838,788 (GRCm38)	D146Y	probably damaging	Het
Ttc9	T	A	12: 81,631,796 (GRCm38)	L131Q	probably damaging	Het
Ttn	C	T	2: 76,813,339 (GRCm38)	G11436R	probably damaging	Het
Ttn	T	C	2: 76,726,848 (GRCm38)		probably benign	Het
Ubash3b	G	A	9: 41,043,573 (GRCm38)	P92S	possibly damaging	Het
Ube4a	T	C	9: 44,948,099 (GRCm38)	N367S	probably damaging	Het
Ubr4	T	A	4: 139,479,540 (GRCm38)	H4899Q	possibly damaging	Het
Ufl1	C	T	4: 25,269,036 (GRCm38)	G265D	possibly damaging	Het
Vmn2r27	T	A	6: 124,224,483 (GRCm38)	I172F	probably damaging	Het
Vmn2r6	A	T	3: 64,556,098 (GRCm38)	H438Q	possibly damaging	Het
Vmn2r61	A	G	7: 42,300,001 (GRCm38)	D615G	probably benign	Het
Wdr24	T	A	17: 25,826,282 (GRCm38)	D330E	probably damaging	Het
Zbbx	A	T	3: 75,078,412 (GRCm38)	N444K	probably benign	Het
Zc3h7b	A	T	15: 81,792,328 (GRCm38)	Q757L	probably damaging	Het
Zpld2	T	G	4: 134,201,941 (GRCm38)	N351T	possibly damaging	Het

Other mutations in Dnmt3l

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00160:Dnmt3l	APN	10	78,057,355 (GRCm38)	missense	probably damaging	1.00
IGL00827:Dnmt3l	APN	10	78,053,996 (GRCm38)	missense	probably damaging	1.00
IGL01072:Dnmt3l	APN	10	78,052,771 (GRCm38)	missense	probably benign	0.09
IGL01118:Dnmt3l	APN	10	78,057,286 (GRCm38)	missense	probably damaging	0.97
IGL01553:Dnmt3l	APN	10	78,063,248 (GRCm38)	missense	probably benign	0.00
IGL02322:Dnmt3l	APN	10	78,052,738 (GRCm38)	missense	possibly damaging	0.90
IGL02323:Dnmt3l	APN	10	78,063,318 (GRCm38)	missense	probably damaging	1.00
IGL02618:Dnmt3l	APN	10	78,054,022 (GRCm38)	splice site	probably benign
IGL02701:Dnmt3l	APN	10	78,055,022 (GRCm38)	missense	probably benign	0.01
IGL02950:Dnmt3l	APN	10	78,050,951 (GRCm38)	missense	probably benign	0.01
R0318:Dnmt3l	UTSW	10	78,055,055 (GRCm38)	missense	probably damaging	1.00
R0384:Dnmt3l	UTSW	10	78,052,737 (GRCm38)	missense	possibly damaging	0.95
R0391:Dnmt3l	UTSW	10	78,051,916 (GRCm38)	splice site	probably benign
R1144:Dnmt3l	UTSW	10	78,051,905 (GRCm38)	missense	probably damaging	1.00
R2115:Dnmt3l	UTSW	10	78,063,296 (GRCm38)	missense	probably damaging	0.99
R2116:Dnmt3l	UTSW	10	78,063,296 (GRCm38)	missense	probably damaging	0.99
R2117:Dnmt3l	UTSW	10	78,063,296 (GRCm38)	missense	probably damaging	0.99
R4812:Dnmt3l	UTSW	10	78,057,294 (GRCm38)	missense	probably benign	0.06
R5001:Dnmt3l	UTSW	10	78,059,731 (GRCm38)	missense	probably null	1.00
R5039:Dnmt3l	UTSW	10	78,052,900 (GRCm38)	splice site	probably null
R5389:Dnmt3l	UTSW	10	78,056,831 (GRCm38)	splice site	probably null
R5799:Dnmt3l	UTSW	10	78,052,026 (GRCm38)	missense	possibly damaging	0.71
R5811:Dnmt3l	UTSW	10	78,052,095 (GRCm38)	missense	possibly damaging	0.78
R5875:Dnmt3l	UTSW	10	78,053,938 (GRCm38)	missense	probably benign
R6314:Dnmt3l	UTSW	10	78,059,687 (GRCm38)	missense	probably benign	0.00
R6537:Dnmt3l	UTSW	10	78,052,064 (GRCm38)	missense	probably null	1.00
R8437:Dnmt3l	UTSW	10	78,052,768 (GRCm38)	missense	possibly damaging	0.94
R9108:Dnmt3l	UTSW	10	78,056,922 (GRCm38)	critical splice donor site	probably null
R9171:Dnmt3l	UTSW	10	78,059,684 (GRCm38)	missense	probably benign
R9205:Dnmt3l	UTSW	10	78,056,752 (GRCm38)	critical splice donor site	probably null
R9473:Dnmt3l	UTSW	10	78,050,188 (GRCm38)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TTTTCCAACCTGCAGCCAG -3'
(R):5'- ATGCGCACATGGGATGCTAG -3'

Sequencing Primer
(F):5'- TGCAGCCAGCCCAACTCAG -3'
(R):5'- CACATGGGATGCTAGCCTACAG -3'

Posted On

2014-09-17