Incidental Mutation 'R7678:Nsd3'
ID 592584
Institutional Source Beutler Lab
Gene Symbol Nsd3
Ensembl Gene ENSMUSG00000054823
Gene Name nuclear receptor binding SET domain protein 3
Synonyms Whsc1l1, WHISTLE
MMRRC Submission 045745-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.361) question?
Stock # R7678 (G1)
Quality Score 225.009
Status Validated
Chromosome 8
Chromosomal Location 26091617-26209694 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 26149833 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Aspartic acid at position 339 (E339D)
Ref Sequence ENSEMBL: ENSMUSP00000117596 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000084026] [ENSMUST00000136107] [ENSMUST00000139966] [ENSMUST00000142395] [ENSMUST00000143445] [ENSMUST00000146919] [ENSMUST00000155861]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000084026
AA Change: E339D

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000081040
Gene: ENSMUSG00000054823
AA Change: E339D

DomainStartEndE-ValueType
low complexity region 128 151 N/A INTRINSIC
low complexity region 193 225 N/A INTRINSIC
PWWP 278 341 1.6e-12 SMART
low complexity region 680 701 N/A INTRINSIC
PHD 713 756 4.49e-7 SMART
PHD 761 808 5.82e-1 SMART
PHD 809 861 3.06e0 SMART
PHD 874 963 1e-4 SMART
PWWP 968 1030 8.62e-18 SMART
AWS 1103 1154 2.61e-17 SMART
SET 1155 1278 2.17e-41 SMART
PostSET 1279 1295 2.63e-3 SMART
low complexity region 1309 1326 N/A INTRINSIC
PHD 1332 1375 4.32e-9 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000136107
AA Change: E339D

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)
Predicted Effect probably damaging
Transcript: ENSMUST00000139966
AA Change: E339D

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000122096
Gene: ENSMUSG00000054823
AA Change: E339D

DomainStartEndE-ValueType
low complexity region 128 151 N/A INTRINSIC
low complexity region 193 225 N/A INTRINSIC
PWWP 278 341 1.6e-12 SMART
low complexity region 680 701 N/A INTRINSIC
PHD 713 756 4.49e-7 SMART
PHD 761 808 5.82e-1 SMART
PHD 809 861 3.06e0 SMART
PHD 874 914 5.24e-8 SMART
PWWP 919 981 8.62e-18 SMART
AWS 1054 1105 2.61e-17 SMART
SET 1106 1229 2.17e-41 SMART
PostSET 1230 1246 2.63e-3 SMART
low complexity region 1260 1277 N/A INTRINSIC
PHD 1283 1326 4.32e-9 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000142395
AA Change: E339D

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000117778
Gene: ENSMUSG00000054823
AA Change: E339D

DomainStartEndE-ValueType
low complexity region 128 151 N/A INTRINSIC
low complexity region 193 225 N/A INTRINSIC
PWWP 278 341 1.6e-12 SMART
low complexity region 680 701 N/A INTRINSIC
PHD 713 756 4.49e-7 SMART
PHD 761 808 5.82e-1 SMART
PHD 809 861 3.06e0 SMART
PHD 874 963 1e-4 SMART
PWWP 968 1030 8.62e-18 SMART
AWS 1103 1154 2.61e-17 SMART
SET 1155 1278 2.17e-41 SMART
PostSET 1279 1295 2.63e-3 SMART
low complexity region 1309 1326 N/A INTRINSIC
PHD 1332 1375 4.32e-9 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000143445
AA Change: E339D

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
Predicted Effect possibly damaging
Transcript: ENSMUST00000146919
AA Change: E339D

PolyPhen 2 Score 0.818 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000115470
Gene: ENSMUSG00000054823
AA Change: E339D

DomainStartEndE-ValueType
low complexity region 128 151 N/A INTRINSIC
low complexity region 193 225 N/A INTRINSIC
Pfam:PWWP 278 388 1.6e-25 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000155861
AA Change: E339D

PolyPhen 2 Score 0.818 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000117596
Gene: ENSMUSG00000054823
AA Change: E339D

DomainStartEndE-ValueType
low complexity region 128 151 N/A INTRINSIC
low complexity region 193 225 N/A INTRINSIC
Pfam:PWWP 278 388 1.6e-25 PFAM
Meta Mutation Damage Score 0.1712 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency 99% (67/68)
MGI Phenotype FUNCTION: This gene encodes a member of the SET domain family of histone lysine N-methyltransferase proteins. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. It acts in opposition to the histone demethylase Jmjd1c. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2015]
Allele List at MGI

All alleles(5) : Gene trapped(5)

Other mutations in this stock
Total: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam22 C A 5: 8,137,750 (GRCm39) probably null Het
Ank1 A G 8: 23,607,074 (GRCm39) D1325G probably damaging Het
Asxl1 T C 2: 153,242,572 (GRCm39) S1042P probably damaging Het
Bpifb1 C T 2: 154,044,649 (GRCm39) H39Y possibly damaging Het
Capn13 C A 17: 73,622,300 (GRCm39) M663I probably damaging Het
Cemip2 C A 19: 21,775,480 (GRCm39) T241K probably damaging Het
Clec2g A G 6: 128,956,400 (GRCm39) E72G probably damaging Het
Col12a1 T A 9: 79,558,768 (GRCm39) Y1899F probably damaging Het
Ctbp2 A G 7: 132,616,353 (GRCm39) V194A probably benign Het
Cttnbp2 G T 6: 18,382,809 (GRCm39) L1320I probably damaging Het
E2f2 T A 4: 135,920,137 (GRCm39) L374* probably null Het
Echdc3 C T 2: 6,217,687 (GRCm39) G29S probably benign Het
Ecm1 A G 3: 95,643,494 (GRCm39) S269P probably damaging Het
Elmo2 G A 2: 165,133,664 (GRCm39) P775S unknown Het
Eno3 T A 11: 70,549,993 (GRCm39) probably null Het
Faf1 G A 4: 109,687,061 (GRCm39) R267K probably benign Het
Fam162a G A 16: 35,870,307 (GRCm39) probably benign Het
Fam178b T A 1: 36,603,532 (GRCm39) D473V probably damaging Het
Fat2 G A 11: 55,173,156 (GRCm39) T2519I probably damaging Het
Foxc2 A G 8: 121,844,834 (GRCm39) Y494C probably damaging Het
Gcnt2 C A 13: 41,107,195 (GRCm39) Q355K probably benign Het
Glg1 G T 8: 111,905,497 (GRCm39) H595N probably benign Het
Gm9913 A T 2: 125,348,480 (GRCm39) H97L unknown Het
Hbegf T A 18: 36,640,601 (GRCm39) N152I possibly damaging Het
Hipk1 G A 3: 103,667,866 (GRCm39) T567I probably damaging Het
Idh3a C T 9: 54,502,453 (GRCm39) P78S probably damaging Het
Igsf10 A T 3: 59,226,761 (GRCm39) M2304K possibly damaging Het
Inf2 A G 12: 112,573,428 (GRCm39) T723A unknown Het
Itpr2 A T 6: 146,089,048 (GRCm39) F2220Y probably benign Het
Kpnb1 C T 11: 97,059,999 (GRCm39) R557Q probably damaging Het
Lefty1 A G 1: 180,764,325 (GRCm39) D155G probably damaging Het
Lrp1 A G 10: 127,409,922 (GRCm39) C1554R probably damaging Het
Lrrc10 A G 10: 116,881,662 (GRCm39) D112G probably benign Het
Med12l A G 3: 58,984,141 (GRCm39) E439G probably damaging Het
Ms4a7 A T 19: 11,301,868 (GRCm39) F185Y probably benign Het
Mtmr6 T A 14: 60,527,101 (GRCm39) M234K probably damaging Het
Myh7b C A 2: 155,459,698 (GRCm39) probably null Het
Myo1d T C 11: 80,567,719 (GRCm39) M254V possibly damaging Het
Nbas T C 12: 13,465,662 (GRCm39) V1368A probably damaging Het
Nbeal1 G C 1: 60,276,310 (GRCm39) V684L probably benign Het
Neb A G 2: 52,096,714 (GRCm39) V4999A probably damaging Het
Npbwr1 G T 1: 5,986,927 (GRCm39) Q196K probably benign Het
Oog4 CAA CA 4: 143,164,022 (GRCm39) probably null Het
Or11g1 T C 14: 50,651,471 (GRCm39) F157L probably damaging Het
Or6c206 A G 10: 129,096,937 (GRCm39) S36G probably damaging Het
Or7d11 T C 9: 19,965,901 (GRCm39) N168S probably damaging Het
Plxna1 C T 6: 89,308,882 (GRCm39) V1199M probably damaging Het
Ppfibp2 T A 7: 107,315,873 (GRCm39) M285K probably damaging Het
Ppip5k1 A G 2: 121,168,142 (GRCm39) Y704H probably damaging Het
Ptpn18 G A 1: 34,512,445 (GRCm39) D417N possibly damaging Het
Sbspon T C 1: 15,929,282 (GRCm39) M170V probably benign Het
Scfd2 A C 5: 74,619,297 (GRCm39) F440V probably benign Het
Slc22a19 T A 19: 7,688,302 (GRCm39) D86V possibly damaging Het
Smg5 A G 3: 88,261,202 (GRCm39) N685S possibly damaging Het
Spata46 A G 1: 170,139,333 (GRCm39) R111G possibly damaging Het
Sry A T Y: 2,663,248 (GRCm39) D137E possibly damaging Het
Tbkbp1 T C 11: 97,040,309 (GRCm39) D35G probably damaging Het
Tcf20 A T 15: 82,735,766 (GRCm39) V1895D possibly damaging Het
Tfap4 G T 16: 4,369,630 (GRCm39) Q112K possibly damaging Het
Trmt10c T A 16: 55,855,302 (GRCm39) D111V probably benign Het
Unc80 T C 1: 66,688,881 (GRCm39) I2415T probably benign Het
Vmn2r107 A T 17: 20,576,901 (GRCm39) M300L probably benign Het
Vmn2r5 A T 3: 64,416,943 (GRCm39) F72I probably benign Het
Vmn2r53 T A 7: 12,332,425 (GRCm39) H408L probably benign Het
Zan C T 5: 137,461,802 (GRCm39) V1126M unknown Het
Zfp493 A T 13: 67,927,814 (GRCm39) probably benign Het
Zfp618 C A 4: 63,004,858 (GRCm39) A86E probably benign Het
Other mutations in Nsd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00435:Nsd3 APN 8 26,166,728 (GRCm39) missense probably benign 0.40
IGL00718:Nsd3 APN 8 26,196,562 (GRCm39) missense probably damaging 0.97
IGL00727:Nsd3 APN 8 26,131,174 (GRCm39) missense probably damaging 1.00
IGL01324:Nsd3 APN 8 26,152,836 (GRCm39) missense probably damaging 1.00
IGL01614:Nsd3 APN 8 26,156,095 (GRCm39) missense possibly damaging 0.65
IGL01834:Nsd3 APN 8 26,130,668 (GRCm39) missense probably damaging 1.00
IGL02066:Nsd3 APN 8 26,203,515 (GRCm39) missense probably damaging 1.00
IGL02229:Nsd3 APN 8 26,200,775 (GRCm39) missense probably damaging 0.98
IGL02481:Nsd3 APN 8 26,181,143 (GRCm39) missense probably damaging 1.00
IGL02686:Nsd3 APN 8 26,156,086 (GRCm39) missense probably damaging 0.96
IGL03394:Nsd3 APN 8 26,165,765 (GRCm39) splice site probably benign
Pine UTSW 8 26,169,952 (GRCm39) missense possibly damaging 0.87
D3080:Nsd3 UTSW 8 26,203,572 (GRCm39) missense possibly damaging 0.77
IGL02802:Nsd3 UTSW 8 26,130,922 (GRCm39) missense probably damaging 1.00
R0136:Nsd3 UTSW 8 26,149,870 (GRCm39) nonsense probably null
R0195:Nsd3 UTSW 8 26,170,709 (GRCm39) missense probably damaging 1.00
R0207:Nsd3 UTSW 8 26,173,273 (GRCm39) missense probably benign 0.02
R0471:Nsd3 UTSW 8 26,138,450 (GRCm39) splice site probably benign
R0511:Nsd3 UTSW 8 26,168,732 (GRCm39) missense possibly damaging 0.81
R0524:Nsd3 UTSW 8 26,190,605 (GRCm39) missense possibly damaging 0.90
R0581:Nsd3 UTSW 8 26,200,718 (GRCm39) missense probably damaging 1.00
R0589:Nsd3 UTSW 8 26,131,303 (GRCm39) missense probably damaging 1.00
R0645:Nsd3 UTSW 8 26,199,096 (GRCm39) missense probably benign 0.08
R0664:Nsd3 UTSW 8 26,204,267 (GRCm39) missense probably damaging 0.97
R0738:Nsd3 UTSW 8 26,168,725 (GRCm39) splice site probably null
R1148:Nsd3 UTSW 8 26,203,407 (GRCm39) missense probably benign 0.09
R1148:Nsd3 UTSW 8 26,203,407 (GRCm39) missense probably benign 0.09
R1265:Nsd3 UTSW 8 26,172,578 (GRCm39) missense probably benign
R1298:Nsd3 UTSW 8 26,169,952 (GRCm39) missense possibly damaging 0.87
R1424:Nsd3 UTSW 8 26,190,594 (GRCm39) missense probably damaging 1.00
R1493:Nsd3 UTSW 8 26,203,407 (GRCm39) missense probably benign 0.09
R1528:Nsd3 UTSW 8 26,188,795 (GRCm39) missense probably damaging 1.00
R2051:Nsd3 UTSW 8 26,181,116 (GRCm39) missense probably damaging 0.99
R2199:Nsd3 UTSW 8 26,156,073 (GRCm39) missense probably damaging 0.99
R3414:Nsd3 UTSW 8 26,190,047 (GRCm39) missense probably damaging 1.00
R3522:Nsd3 UTSW 8 26,196,642 (GRCm39) missense probably benign
R3623:Nsd3 UTSW 8 26,152,835 (GRCm39) missense probably damaging 0.98
R3624:Nsd3 UTSW 8 26,152,835 (GRCm39) missense probably damaging 0.98
R3798:Nsd3 UTSW 8 26,188,873 (GRCm39) missense probably damaging 1.00
R4345:Nsd3 UTSW 8 26,131,333 (GRCm39) missense probably benign 0.04
R4370:Nsd3 UTSW 8 26,138,524 (GRCm39) missense probably benign 0.13
R4421:Nsd3 UTSW 8 26,131,288 (GRCm39) missense probably damaging 0.99
R4583:Nsd3 UTSW 8 26,200,703 (GRCm39) missense probably benign 0.20
R4664:Nsd3 UTSW 8 26,188,894 (GRCm39) missense probably damaging 1.00
R4741:Nsd3 UTSW 8 26,163,382 (GRCm39) missense probably damaging 1.00
R4876:Nsd3 UTSW 8 26,181,161 (GRCm39) missense possibly damaging 0.94
R4888:Nsd3 UTSW 8 26,188,939 (GRCm39) missense probably damaging 1.00
R5000:Nsd3 UTSW 8 26,172,593 (GRCm39) missense probably damaging 1.00
R5132:Nsd3 UTSW 8 26,168,855 (GRCm39) missense possibly damaging 0.73
R5632:Nsd3 UTSW 8 26,169,985 (GRCm39) missense probably benign 0.00
R5760:Nsd3 UTSW 8 26,149,772 (GRCm39) missense probably damaging 1.00
R5778:Nsd3 UTSW 8 26,149,834 (GRCm39) missense probably damaging 1.00
R5779:Nsd3 UTSW 8 26,172,685 (GRCm39) nonsense probably null
R5860:Nsd3 UTSW 8 26,156,107 (GRCm39) missense probably damaging 0.98
R5911:Nsd3 UTSW 8 26,156,092 (GRCm39) missense probably damaging 1.00
R6168:Nsd3 UTSW 8 26,181,188 (GRCm39) missense probably null 1.00
R6467:Nsd3 UTSW 8 26,130,646 (GRCm39) missense probably damaging 1.00
R6490:Nsd3 UTSW 8 26,204,212 (GRCm39) missense probably damaging 1.00
R6519:Nsd3 UTSW 8 26,152,955 (GRCm39) missense probably damaging 1.00
R6554:Nsd3 UTSW 8 26,152,891 (GRCm39) missense probably damaging 0.99
R7038:Nsd3 UTSW 8 26,131,279 (GRCm39) missense probably damaging 1.00
R7088:Nsd3 UTSW 8 26,156,050 (GRCm39) missense probably benign 0.40
R7244:Nsd3 UTSW 8 26,156,055 (GRCm39) missense probably damaging 0.96
R7308:Nsd3 UTSW 8 26,130,740 (GRCm39) missense probably damaging 1.00
R7717:Nsd3 UTSW 8 26,172,578 (GRCm39) missense probably benign
R8064:Nsd3 UTSW 8 26,190,698 (GRCm39) nonsense probably null
R8242:Nsd3 UTSW 8 26,196,567 (GRCm39) nonsense probably null
R8312:Nsd3 UTSW 8 26,153,268 (GRCm39) missense probably damaging 1.00
R8547:Nsd3 UTSW 8 26,184,811 (GRCm39) missense probably damaging 1.00
R8954:Nsd3 UTSW 8 26,163,394 (GRCm39) missense probably damaging 1.00
R8995:Nsd3 UTSW 8 26,131,169 (GRCm39) missense probably damaging 1.00
R9026:Nsd3 UTSW 8 26,172,576 (GRCm39) missense probably benign 0.10
R9281:Nsd3 UTSW 8 26,152,961 (GRCm39) missense probably benign 0.00
R9320:Nsd3 UTSW 8 26,199,088 (GRCm39) critical splice acceptor site probably null
R9563:Nsd3 UTSW 8 26,204,230 (GRCm39) missense
R9703:Nsd3 UTSW 8 26,131,228 (GRCm39) missense probably benign 0.00
X0026:Nsd3 UTSW 8 26,190,621 (GRCm39) missense probably damaging 1.00
Z1088:Nsd3 UTSW 8 26,131,018 (GRCm39) small deletion probably benign
Predicted Primers PCR Primer
(F):5'- GAATGATTTGATCAGTGTTTGCCTC -3'
(R):5'- TCTTGGCAGTACTACAATGTTGC -3'

Sequencing Primer
(F):5'- GATCAGTGTTTGCCTCTTAAAAGTTC -3'
(R):5'- GGCCTGGAACTTGCTATATACAGC -3'
Posted On 2019-11-12