Incidental Mutation 'R7088:Nsd3'
ID 550010
Institutional Source Beutler Lab
Gene Symbol Nsd3
Ensembl Gene ENSMUSG00000054823
Gene Name nuclear receptor binding SET domain protein 3
Synonyms Whsc1l1, WHISTLE
MMRRC Submission 045182-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.303) question?
Stock # R7088 (G1)
Quality Score 225.009
Status Validated
Chromosome 8
Chromosomal Location 26091617-26209694 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 26156050 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 539 (I539T)
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 benign
Transcript: ENSMUST00000084026
AA Change: I539T

PolyPhen 2 Score 0.114 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000081040
Gene: ENSMUSG00000054823
AA Change: I539T

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 benign
Transcript: ENSMUST00000136107
AA Change: I539T

PolyPhen 2 Score 0.329 (Sensitivity: 0.90; Specificity: 0.89)
Predicted Effect probably benign
Transcript: ENSMUST00000139966
AA Change: I539T

PolyPhen 2 Score 0.114 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000122096
Gene: ENSMUSG00000054823
AA Change: I539T

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 benign
Transcript: ENSMUST00000142395
AA Change: I539T

PolyPhen 2 Score 0.114 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000117778
Gene: ENSMUSG00000054823
AA Change: I539T

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 benign
Transcript: ENSMUST00000143445
Predicted Effect probably benign
Transcript: ENSMUST00000146919
AA Change: I539T

PolyPhen 2 Score 0.397 (Sensitivity: 0.89; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000115470
Gene: ENSMUSG00000054823
AA Change: I539T

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 probably benign
Transcript: ENSMUST00000155861
AA Change: I539T

PolyPhen 2 Score 0.397 (Sensitivity: 0.89; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000117596
Gene: ENSMUSG00000054823
AA Change: I539T

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 0.0957 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 99% (77/78)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700020L24Rik G T 11: 83,331,232 (GRCm39) E48* probably null Het
Acaca T C 11: 84,169,783 (GRCm39) probably null Het
Albfm1 T A 5: 90,720,609 (GRCm39) L260* probably null Het
Alkbh3 A G 2: 93,835,097 (GRCm39) S83P possibly damaging Het
Ammecr1l T C 18: 31,904,872 (GRCm39) S38P probably benign Het
Armc10 T C 5: 21,858,390 (GRCm39) V145A probably damaging Het
BC048671 A G 6: 90,280,222 (GRCm39) K46R probably null Het
C2cd3 A G 7: 100,065,388 (GRCm39) T347A Het
C8b G T 4: 104,650,540 (GRCm39) E449D probably benign Het
Camk4 T C 18: 33,072,584 (GRCm39) S46P probably benign Het
Ccdc113 G A 8: 96,264,733 (GRCm39) R81H probably benign Het
Cd177 A T 7: 24,444,558 (GRCm39) C674* probably null Het
Cdc6 T A 11: 98,810,065 (GRCm39) V458D probably damaging Het
Cenpo C T 12: 4,265,307 (GRCm39) E238K probably benign Het
Ckap2 G T 8: 22,659,882 (GRCm39) P533Q possibly damaging Het
Cma1 T A 14: 56,181,273 (GRCm39) H44L probably damaging Het
Cmya5 A T 13: 93,228,372 (GRCm39) S2239T possibly damaging Het
Cntnap5b T A 1: 100,087,802 (GRCm39) I141N probably damaging Het
Col6a4 T A 9: 105,877,885 (GRCm39) T2031S possibly damaging Het
Cplane1 C T 15: 8,248,431 (GRCm39) T1660M probably benign Het
Cxcr5 T A 9: 44,424,683 (GRCm39) T325S possibly damaging Het
Dhx32 A T 7: 133,344,417 (GRCm39) L204Q probably damaging Het
Dse A G 10: 34,029,885 (GRCm39) Y402H probably damaging Het
Ecpas A T 4: 58,849,766 (GRCm39) L458I possibly damaging Het
Exoc6 G T 19: 37,565,458 (GRCm39) C178F probably damaging Het
Fam149a A G 8: 45,803,582 (GRCm39) V384A probably benign Het
Fcrl5 T C 3: 87,365,141 (GRCm39) *597Q probably null Het
Fer1l6 A G 15: 58,435,899 (GRCm39) K431E possibly damaging Het
Fmo3 T A 1: 162,796,434 (GRCm39) H46L probably benign Het
Gcm2 T C 13: 41,256,840 (GRCm39) D303G probably damaging Het
Gk2 T C 5: 97,603,534 (GRCm39) M435V probably damaging Het
Gli1 C A 10: 127,171,868 (GRCm39) M295I probably damaging Het
Gm11444 G T 11: 85,737,862 (GRCm39) H109Q Het
Gtpbp1 T A 15: 79,603,483 (GRCm39) D182E Het
Hnf4g A T 3: 3,713,185 (GRCm39) probably null Het
Hsf2 G A 10: 57,388,188 (GRCm39) R483H probably damaging Het
Kcnq4 C T 4: 120,561,596 (GRCm39) R491H probably damaging Het
Lama3 T C 18: 12,715,602 (GRCm39) V1686A possibly damaging Het
Larp6 A G 9: 60,631,638 (GRCm39) K137E probably damaging Het
Mboat1 T G 13: 30,379,772 (GRCm39) probably null Het
Mdh1 T C 11: 21,508,484 (GRCm39) Y286C probably damaging Het
Mga G T 2: 119,792,417 (GRCm39) K2607N probably damaging Het
Morf4l1 C A 9: 89,979,433 (GRCm39) V183F possibly damaging Het
Mroh4 G A 15: 74,497,993 (GRCm39) R196W probably benign Het
Muc16 C A 9: 18,503,976 (GRCm39) M6438I probably damaging Het
Myom3 A G 4: 135,530,589 (GRCm39) Y1167C probably damaging Het
Neurl3 T C 1: 36,308,302 (GRCm39) E170G possibly damaging Het
Nup155 T C 15: 8,186,177 (GRCm39) F1313S probably benign Het
Nxn A T 11: 76,153,974 (GRCm39) V287E possibly damaging Het
Or4a80 G A 2: 89,582,443 (GRCm39) T243I probably benign Het
Or7a38 A C 10: 78,753,593 (GRCm39) L306F probably benign Het
Or8c13 C A 9: 38,091,748 (GRCm39) V124F probably damaging Het
Pax6 A G 2: 105,526,753 (GRCm39) N220D probably benign Het
Pcdha11 G A 18: 37,138,470 (GRCm39) R33H probably benign Het
Pdzd8 A G 19: 59,333,389 (GRCm39) F211L probably damaging Het
Pear1 C A 3: 87,661,945 (GRCm39) V477F possibly damaging Het
Pex19 GTCTCTTGTCTCCGAAGGTGCTCTTGATGATTTCTCTTGTCTCCGAAGGTGCTCTTGATGATTTC GTCTCTTGTCTCCGAAGGTGCTCTTGATGATTTC 1: 171,956,150 (GRCm39) probably null Het
Pidd1 A T 7: 141,020,400 (GRCm39) V539E probably damaging Het
Ptprg A T 14: 12,207,365 (GRCm38) I878F probably damaging Het
Rabepk T C 2: 34,675,711 (GRCm39) T140A probably benign Het
Ranbp2 G T 10: 58,299,728 (GRCm39) R454L probably damaging Het
Rnf123 C T 9: 107,935,735 (GRCm39) R943Q probably null Het
Sash1 G A 10: 8,605,481 (GRCm39) R970* probably null Het
Serpinb2 C A 1: 107,452,422 (GRCm39) F333L probably damaging Het
Shank3 T A 15: 89,387,728 (GRCm39) probably null Het
Slc9a2 A C 1: 40,765,539 (GRCm39) I310L probably damaging Het
Strip2 T A 6: 29,920,532 (GRCm39) probably null Het
Thoc3 T C 13: 54,611,565 (GRCm39) T241A probably damaging Het
Tmem139 T A 6: 42,240,199 (GRCm39) V2E probably damaging Het
Usp24 G T 4: 106,244,743 (GRCm39) V1233F probably damaging Het
Vnn1 A G 10: 23,776,645 (GRCm39) Q332R probably benign Het
Wac T A 18: 7,921,455 (GRCm39) H530Q probably damaging Het
Wdr35 T A 12: 9,028,659 (GRCm39) N92K probably benign Het
Zbtb18 T G 1: 177,274,820 (GRCm39) L60R probably damaging Het
Zfp184 T A 13: 22,144,162 (GRCm39) C623S probably damaging Het
Zfp292 A G 4: 34,806,796 (GRCm39) Y2088H probably damaging Het
Zfp975 G T 7: 42,312,096 (GRCm39) S172R probably benign Het
Zswim2 G A 2: 83,746,071 (GRCm39) Q456* probably null 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
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
R7678:Nsd3 UTSW 8 26,149,833 (GRCm39) missense possibly damaging 0.82
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'- TACTTATCACCTGGACTTAAGGC -3'
(R):5'- AGTATGTCATTATGGCCTGCCTTC -3'

Sequencing Primer
(F):5'- GCAAATTACGGTCACGTTA -3'
(R):5'- CAATGAAACTTTCTTAGGAACCCCTG -3'
Posted On 2019-05-15