Mutagenetix > Incidental Mutations

Incidental Mutation 'R4812:Dnmt3l'

369567

Institutional Source

Beutler Lab

Gene Symbol

Dnmt3l

Ensembl Gene

ENSMUSG00000000730

Gene Name

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

Synonyms

D6Ertd14e, ecat7

MMRRC Submission

042431-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4812 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

78041947-78063622 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 78057294 bp

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 302 (I302V)

Ref Sequence

ENSEMBL: ENSMUSP00000116970 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000000746
AA Change: I302V

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000000746
Gene: ENSMUSG00000000730
AA Change: I302V

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: I7V

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000123015
Gene: ENSMUSG00000000730
AA Change: I7V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000131825
AA Change: I7V

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000119571
Gene: ENSMUSG00000000730
AA Change: I7V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000138785
AA Change: I302V

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000121562
Gene: ENSMUSG00000000730
AA Change: I302V

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: I7V

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000117827
Gene: ENSMUSG00000000730
AA Change: I7V

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: I302V

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000116970
Gene: ENSMUSG00000000730
AA Change: I302V

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

Validation Efficiency

93% (124/133)

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: 128 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017G19Rik	C	T	3: 40,521,484		noncoding transcript	Het
2410089E03Rik	T	G	15: 8,201,123		probably null	Het
Abca5	T	C	11: 110,301,821	D681G	probably damaging	Het
Actl11	T	C	9: 107,931,130	V884A	probably damaging	Het
Akr1c14	G	A	13: 4,079,165	V187M	probably damaging	Het
Apbb1	A	T	7: 105,574,025	N126K	probably damaging	Het
Armc4	T	G	18: 7,288,634	T78P	possibly damaging	Het
Bmt2	G	T	6: 13,677,800	R12S	unknown	Het
Btrc	G	A	19: 45,423,164	C9Y	possibly damaging	Het
C5ar1	A	C	7: 16,248,333		probably null	Het
C8a	C	T	4: 104,862,591		probably null	Het
Cabin1	A	G	10: 75,646,594	S2172P	possibly damaging	Het
Calcoco2	T	C	11: 96,107,450	D49G	probably damaging	Het
Camta1	C	T	4: 151,131,542	D974N	probably null	Het
Car6	T	C	4: 150,197,415	E47G	probably damaging	Het
Ccdc105	T	C	10: 78,749,216	H262R	probably benign	Het
Ccnd3	G	A	17: 47,597,580		probably null	Het
Celf5	A	T	10: 81,470,739	V30E	probably damaging	Het
Cfap46	T	A	7: 139,636,000	D1513V	probably damaging	Het
Cinp	T	C	12: 110,879,740	Y84C	probably damaging	Het
Cnih1	A	G	14: 46,776,544	I154T	probably damaging	Het
Col15a1	C	T	4: 47,262,479	P511L	possibly damaging	Het
Col4a4	C	T	1: 82,462,153	V1364M	unknown	Het
Crtam	A	G	9: 40,984,325	L38P	probably damaging	Het
Ctnna1	T	A	18: 35,239,477	V495D	probably damaging	Het
Cubn	T	C	2: 13,459,076	Y606C	probably damaging	Het
Cyp4f16	C	T	17: 32,546,678	A345V	probably null	Het
Dctn1	A	T	6: 83,189,937	M160L	probably benign	Het
Dip2c	T	A	13: 9,637,130	C366*	probably null	Het
Dnajc2	G	A	5: 21,763,486	S401L	probably benign	Het
Dvl2	T	C	11: 70,011,293		probably benign	Het
Edn1	T	G	13: 42,303,640	S50A	probably benign	Het
Efhc1	A	T	1: 20,990,647	R636W	probably damaging	Het
Epg5	T	A	18: 77,979,184	H1047Q	probably benign	Het
Etv1	T	G	12: 38,861,288	V371G	probably damaging	Het
Fam71e2	G	A	7: 4,759,072	T295M	probably damaging	Het
Fap	T	A	2: 62,519,021	I475F	probably damaging	Het
Fbxw15	T	C	9: 109,559,922	I140V	probably benign	Het
Fer	A	G	17: 63,934,297	T311A	probably benign	Het
Fh1	A	G	1: 175,601,459	W497R	probably damaging	Het
Flot2	T	A	11: 78,053,365	L45Q	probably damaging	Het
Flt1	C	A	5: 147,683,939	A132S	probably benign	Het
Fmnl1	T	C	11: 103,198,564		probably benign	Het
Ggta1	C	T	2: 35,402,723	V203I	probably benign	Het
Gm19345	C	T	7: 19,857,873	V204M	probably damaging	Het
Gm4204	T	A	1: 135,232,489		noncoding transcript	Het
Gm6124	C	G	7: 39,222,895		noncoding transcript	Het
Gprin3	T	A	6: 59,353,365	K652N	possibly damaging	Het
Gucy1b2	T	C	14: 62,415,897		probably null	Het
Hace1	C	A	10: 45,686,603	A738E	probably benign	Het
Hectd1	C	T	12: 51,827,351		probably null	Het
Hnrnpdl	T	C	5: 100,036,472		probably benign	Het
Hyou1	T	C	9: 44,387,121		probably benign	Het
Ifi44l	G	A	3: 151,759,699	A138V	probably benign	Het
Igkv16-104	A	T	6: 68,425,845	I41F	possibly damaging	Het
Ints7	T	A	1: 191,594,430	D171E	possibly damaging	Het
Kmt2a	A	T	9: 44,831,354		probably benign	Het
Kmt2e	T	C	5: 23,502,587	V1716A	possibly damaging	Het
Krtap5-1	G	A	7: 142,296,891	S60F	unknown	Het
Lama4	G	A	10: 39,072,769	V843I	probably benign	Het
Laptm5	A	G	4: 130,913,438		probably null	Het
Lbhd1	G	A	19: 8,889,174	A193T	probably damaging	Het
Lce3f	C	T	3: 92,992,940	P23S	unknown	Het
Lrmp	G	A	6: 145,148,011	G120S	probably damaging	Het
Mecom	A	C	3: 30,140,368	M1R	probably null	Het
Mindy4	A	C	6: 55,279,103	T531P	possibly damaging	Het
Mrpl3	A	G	9: 105,073,824	N263S	probably damaging	Het
Myo18b	T	C	5: 112,809,718	K1460E	possibly damaging	Het
Myof	A	G	19: 37,916,559	Y852H	probably damaging	Het
Nefl	T	G	14: 68,084,285	V108G	probably damaging	Het
Nid1	T	A	13: 13,506,468	L1061*	probably null	Het
Nim1k	T	A	13: 119,712,384	M325L	probably benign	Het
Nlrp1c-ps	T	C	11: 71,252,305		noncoding transcript	Het
Npsr1	C	T	9: 24,289,956	T59I	probably damaging	Het
Nr2c1	A	G	10: 94,188,252	T440A	probably benign	Het
Nup160	C	T	2: 90,725,691	T1245I	probably damaging	Het
Nup88	T	A	11: 70,965,726	T194S	probably damaging	Het
Oas3	A	G	5: 120,761,147		probably benign	Het
Olfr1129	A	G	2: 87,575,743	I220V	probably benign	Het
Olfr1274-ps	T	A	2: 90,401,096	M145K	probably benign	Het
Olfr1393	T	A	11: 49,280,457	I103K	possibly damaging	Het
Opn1sw	A	T	6: 29,378,039	M252K	probably damaging	Het
Oprm1	T	G	10: 6,832,698		probably benign	Het
Pcdha2	T	A	18: 36,939,808	V164E	probably benign	Het
Pclo	A	G	5: 14,540,025	T780A	unknown	Het
Pcnx2	T	A	8: 125,865,939	Q762L	probably benign	Het
Pcyt2	A	T	11: 120,614,425		probably benign	Het
Pdpr	A	G	8: 111,116,717	N294D	probably benign	Het
Perm1	T	A	4: 156,218,736	V579E	possibly damaging	Het
Pgk2	T	A	17: 40,207,390	K382N	possibly damaging	Het
Plcb4	T	A	2: 136,007,881	L205Q	probably damaging	Het
Plekha3	C	T	2: 76,686,631	T109I	probably damaging	Het
Pnn	T	A	12: 59,071,618	V329E	possibly damaging	Het
Ptpn13	A	G	5: 103,523,615	I469M	probably benign	Het
Rapgef3	A	G	15: 97,753,803	V603A	probably benign	Het
Rbms1	C	T	2: 60,792,769	V75I	possibly damaging	Het
Rbp3	T	A	14: 33,954,774	D226E	probably damaging	Het
Robo2	A	T	16: 73,916,288	N1189K	probably benign	Het
Rragd	A	G	4: 33,018,766	T270A	probably benign	Het
Rxfp1	T	A	3: 79,650,582	T530S	probably benign	Het
Ryr3	T	C	2: 112,912,236	E479G	probably damaging	Het
Scd2	A	T	19: 44,301,402	I279F	probably damaging	Het
Sh3d19	A	T	3: 86,123,767	D746V	probably damaging	Het
Shroom4	A	G	X: 6,624,126	K1133E	probably benign	Het
Sirpb1c	A	G	3: 15,833,222	V151A	probably damaging	Het
Slc26a2	A	T	18: 61,202,021	I120N	probably damaging	Het
Slco1a1	A	G	6: 141,918,593	S494P	probably damaging	Het
Srebf2	A	T	15: 82,203,825	T1061S	probably damaging	Het
Sspo	T	C	6: 48,490,510	L4202P	probably benign	Het
Synj2	G	A	17: 6,010,664	G215E	probably damaging	Het
Tbc1d19	T	C	5: 53,809,806	V16A	probably damaging	Het
Tiparp	T	C	3: 65,552,769	I495T	possibly damaging	Het
Tipin	A	G	9: 64,304,412	H260R	probably benign	Het
Tle1	A	G	4: 72,145,354	S221P	probably damaging	Het
Tmem94	T	A	11: 115,796,112	L1101*	probably null	Het
Trim43b	C	T	9: 89,091,480	D67N	probably benign	Het
Ubn2	T	A	6: 38,463,726	C178S	probably benign	Het
Vmn1r54	T	C	6: 90,269,325	F74L	probably benign	Het
Vmn2r24	A	G	6: 123,779,185	H72R	probably benign	Het
Wdr66	G	A	5: 123,287,305	V776I	probably benign	Het
Wnk1	C	T	6: 119,952,771	V850I	probably benign	Het
Zan	T	G	5: 137,456,285	Y1419S	unknown	Het
Zbtb14	T	A	17: 69,387,582	Y92N	probably damaging	Het
Zfand5	A	G	19: 21,277,737	K116E	probably benign	Het
Zfhx3	A	G	8: 108,947,961	E1881G	possibly damaging	Het
Zfp280b	A	G	10: 76,039,090	K268E	probably benign	Het
Zfp541	A	G	7: 16,079,110	I563V	probably benign	Het
Zfy2	T	A	Y: 2,106,334	I767L	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
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
R6314:Dnmt3l	UTSW	10	78059687	missense	probably benign	0.00
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'- ACTGCCAGGTGAACTTGCAC -3'
(R):5'- GCCTGATGTCCTCTTTGTAAGC -3'

Sequencing Primer
(F):5'- TGAACTTGCACGTGCTCAG -3'
(R):5'- TGTAAGCCCTGTACACATTAGGG -3'

Posted On

2016-02-04