Mutagenetix > Incidental Mutation

Incidental Mutation 'R0384:Dnmt3l'

31183

Institutional Source

Beutler Lab

Gene Symbol

Dnmt3l

Ensembl Gene

ENSMUSG00000000730

Gene Name

DNA methyltransferase 3-like

Synonyms

D6Ertd14e, ecat7

MMRRC Submission

038590-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0384 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

77878121-77899456 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 77888571 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 158 (I158F)

Ref Sequence

ENSEMBL: ENSMUSP00000116970 (fasta)

Gene Model

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

AlphaFold

Q9CWR8

Predicted Effect

possibly damaging
Transcript: ENSMUST00000000746
AA Change: I158F

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000000746
Gene: ENSMUSG00000000730
AA Change: I158F

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

possibly damaging
Transcript: ENSMUST00000138785
AA Change: I158F

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000121562
Gene: ENSMUSG00000000730
AA Change: I158F

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

possibly damaging
Transcript: ENSMUST00000151242
AA Change: I158F

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000116970
Gene: ENSMUSG00000000730
AA Change: I158F

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

0.1795

Coding Region Coverage

1x: 99.1%
3x: 98.1%
10x: 95.8%
20x: 91.7%

Validation Efficiency

100% (72/72)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam8	T	A	7: 139,566,725 (GRCm39)		probably benign	Het
Akr1b8	T	C	6: 34,341,265 (GRCm39)		probably benign	Het
Arhgef39	A	G	4: 43,498,613 (GRCm39)	L117P	probably damaging	Het
Atp13a1	A	T	8: 70,249,974 (GRCm39)	Q356L	possibly damaging	Het
Bmp2k	T	A	5: 97,178,984 (GRCm39)		probably benign	Het
Ccdc141	A	G	2: 76,857,992 (GRCm39)	V1063A	probably damaging	Het
Col20a1	T	C	2: 180,640,955 (GRCm39)	Y568H	probably benign	Het
Crabp2	T	C	3: 87,860,328 (GRCm39)	V134A	possibly damaging	Het
Cyp19a1	T	C	9: 54,080,025 (GRCm39)	K265E	probably benign	Het
Cyp2j9	T	C	4: 96,474,122 (GRCm39)	H106R	probably benign	Het
Dcps	T	C	9: 35,087,239 (GRCm39)	K9R	probably damaging	Het
Dnajc6	C	T	4: 101,456,153 (GRCm39)	T47I	probably damaging	Het
Dnhd1	T	G	7: 105,369,321 (GRCm39)	S4315A	possibly damaging	Het
Dock3	A	G	9: 106,779,094 (GRCm39)		probably benign	Het
Eefsec	A	G	6: 88,258,632 (GRCm39)		probably null	Het
Fam204a	T	C	19: 60,209,728 (GRCm39)	M1V	probably null	Het
Fam98b	T	C	2: 117,098,328 (GRCm39)	V266A	possibly damaging	Het
Fat2	A	T	11: 55,160,291 (GRCm39)	I3274N	possibly damaging	Het
Fbh1	A	G	2: 11,754,389 (GRCm39)	I198T	probably damaging	Het
Fer	T	C	17: 64,231,179 (GRCm39)		probably benign	Het
Fhad1	T	A	4: 141,729,737 (GRCm39)	M89L	probably benign	Het
Fjx1	C	A	2: 102,281,452 (GRCm39)	C161F	probably damaging	Het
Fkbp7	T	A	2: 76,496,168 (GRCm39)		probably benign	Het
Gm42669	T	A	5: 107,656,664 (GRCm39)	C976S	probably benign	Het
Gm4845	T	C	1: 141,184,823 (GRCm39)		noncoding transcript	Het
Herc1	T	A	9: 66,388,332 (GRCm39)		probably benign	Het
Hook3	C	T	8: 26,534,263 (GRCm39)		probably null	Het
Idh2	C	T	7: 79,748,005 (GRCm39)	A232T	probably damaging	Het
Itga2b	A	T	11: 102,356,188 (GRCm39)		probably null	Het
Klk1b21	T	C	7: 43,754,917 (GRCm39)	Y71H	probably benign	Het
Kndc1	A	T	7: 139,490,515 (GRCm39)	N339I	possibly damaging	Het
Ky	C	T	9: 102,419,289 (GRCm39)	T432I	probably benign	Het
Map4	C	T	9: 109,863,696 (GRCm39)	T307I	probably damaging	Het
Matn1	T	C	4: 130,671,787 (GRCm39)	L18P	probably benign	Het
Mindy4	G	A	6: 55,193,669 (GRCm39)	D121N	probably damaging	Het
Mpv17l	A	T	16: 13,758,863 (GRCm39)	I96L	probably benign	Het
Msto1	G	A	3: 88,817,646 (GRCm39)	Q441*	probably null	Het
Muc5ac	A	G	7: 141,365,988 (GRCm39)	H2048R	possibly damaging	Het
Musk	T	C	4: 58,373,711 (GRCm39)	*879Q	probably null	Het
Nat8f2	T	C	6: 85,845,350 (GRCm39)	Y4C	possibly damaging	Het
Ncaph2	T	A	15: 89,253,594 (GRCm39)	I282N	probably benign	Het
Nid1	A	G	13: 13,638,421 (GRCm39)	T114A	probably benign	Het
Npr1	C	A	3: 90,372,474 (GRCm39)	G113C	probably damaging	Het
Nrxn1	G	A	17: 90,515,775 (GRCm39)	P193S	probably damaging	Het
Nwd2	T	C	5: 63,963,025 (GRCm39)	F870L	probably benign	Het
Or10h1b	A	G	17: 33,395,522 (GRCm39)	I45V	probably damaging	Het
Or4c122	A	G	2: 89,079,414 (GRCm39)	I208T	possibly damaging	Het
Or6c5c	T	A	10: 129,298,909 (GRCm39)	Y121*	probably null	Het
Or8k30	T	A	2: 86,339,727 (GRCm39)	I308K	possibly damaging	Het
Phf14	A	G	6: 11,997,019 (GRCm39)		probably benign	Het
Pnpla5	G	T	15: 84,004,920 (GRCm39)	L144M	probably damaging	Het
Prdm2	T	C	4: 142,862,258 (GRCm39)	E344G	probably benign	Het
Psmd12	T	C	11: 107,376,547 (GRCm39)	V61A	probably benign	Het
Relt	T	C	7: 100,496,712 (GRCm39)	D385G	probably benign	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Scg2	T	A	1: 79,413,266 (GRCm39)	I446F	probably benign	Het
Sema3b	G	A	9: 107,478,165 (GRCm39)	L407F	probably damaging	Het
Slc25a13	A	T	6: 6,042,600 (GRCm39)	Y601*	probably null	Het
Sun5	C	T	2: 153,700,885 (GRCm39)	V270I	probably benign	Het
Tex52	A	G	6: 128,356,496 (GRCm39)	Y63C	probably damaging	Het
Tmem138	A	G	19: 10,552,186 (GRCm39)		probably benign	Het
Tnpo3	A	G	6: 29,582,163 (GRCm39)		probably null	Het
Tspoap1	A	T	11: 87,657,280 (GRCm39)	Q364L	probably damaging	Het
Ttc41	T	C	10: 86,599,811 (GRCm39)	L1037P	probably damaging	Het
Ugcg	T	A	4: 59,220,387 (GRCm39)	D393E	possibly damaging	Het
Vmn1r184	T	C	7: 25,967,076 (GRCm39)	I274T	probably benign	Het
Vmn2r27	A	G	6: 124,200,871 (GRCm39)	V362A	probably benign	Het
Vmn2r87	T	A	10: 130,307,712 (GRCm39)	Y842F	probably benign	Het
Vps8	T	A	16: 21,325,575 (GRCm39)		probably benign	Het

Other mutations in Dnmt3l

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00160:Dnmt3l	APN	10	77,893,189 (GRCm39)	missense	probably damaging	1.00
IGL00827:Dnmt3l	APN	10	77,889,830 (GRCm39)	missense	probably damaging	1.00
IGL01072:Dnmt3l	APN	10	77,888,605 (GRCm39)	missense	probably benign	0.09
IGL01118:Dnmt3l	APN	10	77,893,120 (GRCm39)	missense	probably damaging	0.97
IGL01553:Dnmt3l	APN	10	77,899,082 (GRCm39)	missense	probably benign	0.00
IGL02322:Dnmt3l	APN	10	77,888,572 (GRCm39)	missense	possibly damaging	0.90
IGL02323:Dnmt3l	APN	10	77,899,152 (GRCm39)	missense	probably damaging	1.00
IGL02618:Dnmt3l	APN	10	77,889,856 (GRCm39)	splice site	probably benign
IGL02701:Dnmt3l	APN	10	77,890,856 (GRCm39)	missense	probably benign	0.01
IGL02950:Dnmt3l	APN	10	77,886,785 (GRCm39)	missense	probably benign	0.01
R0318:Dnmt3l	UTSW	10	77,890,889 (GRCm39)	missense	probably damaging	1.00
R0391:Dnmt3l	UTSW	10	77,887,750 (GRCm39)	splice site	probably benign
R1144:Dnmt3l	UTSW	10	77,887,739 (GRCm39)	missense	probably damaging	1.00
R2069:Dnmt3l	UTSW	10	77,888,566 (GRCm39)	missense	probably damaging	1.00
R2115:Dnmt3l	UTSW	10	77,899,130 (GRCm39)	missense	probably damaging	0.99
R2116:Dnmt3l	UTSW	10	77,899,130 (GRCm39)	missense	probably damaging	0.99
R2117:Dnmt3l	UTSW	10	77,899,130 (GRCm39)	missense	probably damaging	0.99
R4812:Dnmt3l	UTSW	10	77,893,128 (GRCm39)	missense	probably benign	0.06
R5001:Dnmt3l	UTSW	10	77,895,565 (GRCm39)	missense	probably null	1.00
R5039:Dnmt3l	UTSW	10	77,888,734 (GRCm39)	splice site	probably null
R5389:Dnmt3l	UTSW	10	77,892,665 (GRCm39)	splice site	probably null
R5799:Dnmt3l	UTSW	10	77,887,860 (GRCm39)	missense	possibly damaging	0.71
R5811:Dnmt3l	UTSW	10	77,887,929 (GRCm39)	missense	possibly damaging	0.78
R5875:Dnmt3l	UTSW	10	77,889,772 (GRCm39)	missense	probably benign
R6314:Dnmt3l	UTSW	10	77,895,521 (GRCm39)	missense	probably benign	0.00
R6537:Dnmt3l	UTSW	10	77,887,898 (GRCm39)	missense	probably null	1.00
R8437:Dnmt3l	UTSW	10	77,888,602 (GRCm39)	missense	possibly damaging	0.94
R9108:Dnmt3l	UTSW	10	77,892,756 (GRCm39)	critical splice donor site	probably null
R9171:Dnmt3l	UTSW	10	77,895,518 (GRCm39)	missense	probably benign
R9205:Dnmt3l	UTSW	10	77,892,586 (GRCm39)	critical splice donor site	probably null
R9473:Dnmt3l	UTSW	10	77,886,022 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TGCAGCCACCATTCAGCCATTC -3'
(R):5'- TTTAAGGCAAAGCCTCAGCCCC -3'

Sequencing Primer
(F):5'- ATAGGCAGCTCATTCACCCTTAG -3'
(R):5'- TGGCAGATCCAGTCCCTC -3'

Posted On

2013-04-24