Incidental Mutation 'R2069:Dnmt3l'
ID 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 10
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
PDB:2QRV|G 1 120 1e-38 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000131825
SMART Domains Protein: ENSMUSP00000119571
Gene: ENSMUSG00000000730

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 question?
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
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
AlleleSourceChrCoordTypePredicted EffectPPH 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