Mutagenetix > Incidental Mutations

Incidental Mutation 'R6314:Dnmt3l'

509948

Institutional Source

Beutler Lab

Gene Symbol

Dnmt3l

Ensembl Gene

ENSMUSG00000000730

Gene Name

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

Synonyms

D6Ertd14e, ecat7

MMRRC Submission

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6314 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

78041947-78063622 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 78059687 bp

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 58 (Y58F)

Ref Sequence

ENSEMBL: ENSMUSP00000119571 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000000746
AA Change: Y353F

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

SMART Domains

Protein: ENSMUSP00000000746
Gene: ENSMUSG00000000730
AA Change: Y353F

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
AA Change: Y58F

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

SMART Domains

Protein: ENSMUSP00000123015
Gene: ENSMUSG00000000730
AA Change: Y58F

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

Predicted Effect

probably benign
Transcript: ENSMUST00000131825
AA Change: Y58F

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000119571
Gene: ENSMUSG00000000730
AA Change: Y58F

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

Predicted Effect

probably benign
Transcript: ENSMUST00000138785
AA Change: Y353F

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

SMART Domains

Protein: ENSMUSP00000121562
Gene: ENSMUSG00000000730
AA Change: Y353F

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
AA Change: Y58F

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

SMART Domains

Protein: ENSMUSP00000117827
Gene: ENSMUSG00000000730
AA Change: Y58F

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144446

Predicted Effect

probably benign
Transcript: ENSMUST00000151242
AA Change: Y353F

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

SMART Domains

Protein: ENSMUSP00000116970
Gene: ENSMUSG00000000730
AA Change: Y353F

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

0.0846

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.2%
20x: 97.5%

Validation Efficiency

98% (54/55)

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4833423E24Rik	T	C	2: 85,502,176	N168S	probably benign	Het
4930449I24Rik	A	C	5: 146,504,892	E283A	possibly damaging	Het
6430531B16Rik	A	C	7: 139,976,489	L195R	possibly damaging	Het
9130204L05Rik	A	T	3: 91,088,376	V73E	possibly damaging	Het
Aadacl2	A	T	3: 60,017,403	R130S	probably damaging	Het
Adam22	A	T	5: 8,127,365	C581*	probably null	Het
Adss	T	A	1: 177,767,768	Y402F	probably damaging	Het
Agfg1	A	T	1: 82,858,434	Q13H	probably damaging	Het
Ankdd1a	C	T	9: 65,508,061	A227T	possibly damaging	Het
Armc8	A	G	9: 99,535,884	S74P	probably benign	Het
Atn1	A	T	6: 124,747,050		probably benign	Het
BC027072	T	G	17: 71,752,457	Q75P	probably benign	Het
Ddx5	T	C	11: 106,788,521		probably benign	Het
Depdc1a	T	A	3: 159,498,414	H33Q	probably damaging	Het
Efemp1	C	T	11: 28,914,603	T219I	probably benign	Het
Enpp2	T	C	15: 54,865,970	N436D	probably damaging	Het
Epb41l4a	A	G	18: 33,874,155	V261A	probably damaging	Het
Erap1	A	T	13: 74,674,775	K802N	probably damaging	Het
Fcrl6	T	A	1: 172,598,619		probably null	Het
Fv1	A	T	4: 147,869,699		probably null	Het
Gdpd4	T	A	7: 97,973,953	M257K	probably damaging	Het
Gorab	T	C	1: 163,397,089	S48G	probably damaging	Het
Gxylt2	A	T	6: 100,798,203	H361L	probably damaging	Het
Hk1	A	G	10: 62,292,444	Y300H	possibly damaging	Het
Hk3	T	C	13: 55,013,580	R156G	probably benign	Het
Hook3	T	A	8: 26,088,108	M118L	probably benign	Het
Lmnb2	G	A	10: 80,909,970	R92C	probably damaging	Het
Lsr	A	G	7: 30,958,599	L380P	probably damaging	Het
Mettl16	A	T	11: 74,796,006	R204*	probably null	Het
Olfr1353	A	G	10: 78,970,345	H232R	probably benign	Het
Olfr186	A	T	16: 59,027,457	I150K	probably benign	Het
Olfr866	C	A	9: 20,027,662	S92I	probably damaging	Het
Orc3	C	A	4: 34,579,797	G494C	possibly damaging	Het
Pip5k1a	G	T	3: 95,068,121	T346K	probably damaging	Het
Pitx1	A	T	13: 55,826,353	S222T	possibly damaging	Het
Pm20d1	T	C	1: 131,816,016	V473A	possibly damaging	Het
Pnpla6	C	T	8: 3,521,572	L168F	probably benign	Het
Pramef12	T	C	4: 144,394,587	D289G	probably damaging	Het
Reln	C	A	5: 22,152,484	E195*	probably null	Het
Sec24b	A	T	3: 130,007,245		probably null	Het
Selenbp1	A	G	3: 94,937,265	N78D	probably damaging	Het
Serpina1d	T	A	12: 103,764,700	T340S	probably benign	Het
Slc13a2	CGTTATCTGT	CGT	11: 78,403,480		probably benign	Het
Snap29	T	C	16: 17,419,319	M98T	probably benign	Het
Son	G	T	16: 91,660,410		probably benign	Het
Tgfbi	A	T	13: 56,626,163	T252S	probably benign	Het
Thsd7a	T	C	6: 12,554,997	N296S	possibly damaging	Het
Tmem225	C	G	9: 40,150,720	T210S	probably benign	Het
Tmem245	A	T	4: 56,888,592	V778D	possibly damaging	Het
Tor4a	T	C	2: 25,194,782	R370G	possibly damaging	Het
Tubgcp3	T	C	8: 12,648,625	H442R	probably benign	Het
Vmn1r20	A	T	6: 57,432,057	M123L	probably benign	Het
Zfp622	T	C	15: 25,986,981	V273A	probably benign	Het
Zhx1	C	T	15: 58,054,002	V283I	probably benign	Het

Other mutations in Dnmt3l

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00160:Dnmt3l	APN	10	78057355	missense	probably damaging	1.00
IGL00827:Dnmt3l	APN	10	78053996	missense	probably damaging	1.00
IGL01072:Dnmt3l	APN	10	78052771	missense	probably benign	0.09
IGL01118:Dnmt3l	APN	10	78057286	missense	probably damaging	0.97
IGL01553:Dnmt3l	APN	10	78063248	missense	probably benign	0.00
IGL02322:Dnmt3l	APN	10	78052738	missense	possibly damaging	0.90
IGL02323:Dnmt3l	APN	10	78063318	missense	probably damaging	1.00
IGL02618:Dnmt3l	APN	10	78054022	splice site	probably benign
IGL02701:Dnmt3l	APN	10	78055022	missense	probably benign	0.01
IGL02950:Dnmt3l	APN	10	78050951	missense	probably benign	0.01
R0318:Dnmt3l	UTSW	10	78055055	missense	probably damaging	1.00
R0384:Dnmt3l	UTSW	10	78052737	missense	possibly damaging	0.95
R0391:Dnmt3l	UTSW	10	78051916	splice site	probably benign
R1144:Dnmt3l	UTSW	10	78051905	missense	probably damaging	1.00
R2069:Dnmt3l	UTSW	10	78052732	missense	probably damaging	1.00
R2115:Dnmt3l	UTSW	10	78063296	missense	probably damaging	0.99
R2116:Dnmt3l	UTSW	10	78063296	missense	probably damaging	0.99
R2117:Dnmt3l	UTSW	10	78063296	missense	probably damaging	0.99
R4812:Dnmt3l	UTSW	10	78057294	missense	probably benign	0.06
R5001:Dnmt3l	UTSW	10	78059731	missense	probably null	1.00
R5039:Dnmt3l	UTSW	10	78052900	splice site	probably null
R5389:Dnmt3l	UTSW	10	78056831	splice site	probably null
R5799:Dnmt3l	UTSW	10	78052026	missense	possibly damaging	0.71
R5811:Dnmt3l	UTSW	10	78052095	missense	possibly damaging	0.78
R5875:Dnmt3l	UTSW	10	78053938	missense	probably benign
R6537:Dnmt3l	UTSW	10	78052064	missense	probably null	1.00
R8437:Dnmt3l	UTSW	10	78052768	missense	possibly damaging	0.94

Predicted Primers

PCR Primer
(F):5'- AGTTGATCAAAGTGGTCTCCAG -3'
(R):5'- TGACCAGTTCAGAGGCATGATC -3'

Sequencing Primer
(F):5'- GATCAAAGTGGTCTCCAGATTTTAC -3'
(R):5'- GAGTGATCATCATAATGAGTGTCCC -3'

Posted On

2018-04-02