Incidental Mutation 'R0541:Setd2'
ID 49919
Institutional Source Beutler Lab
Gene Symbol Setd2
Ensembl Gene ENSMUSG00000044791
Gene Name SET domain containing 2
Synonyms KMT3A, 4921524K10Rik
MMRRC Submission 038733-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.948) question?
Stock # R0541 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 110361665-110447701 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 110402741 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 1794 (V1794A)
Ref Sequence ENSEMBL: ENSMUSP00000116313 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000153838]
AlphaFold E9Q5F9
Predicted Effect probably damaging
Transcript: ENSMUST00000153838
AA Change: V1794A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000116313
Gene: ENSMUSG00000044791
AA Change: V1794A

DomainStartEndE-ValueType
low complexity region 19 34 N/A INTRINSIC
low complexity region 156 176 N/A INTRINSIC
low complexity region 185 207 N/A INTRINSIC
low complexity region 297 313 N/A INTRINSIC
low complexity region 392 419 N/A INTRINSIC
low complexity region 795 809 N/A INTRINSIC
low complexity region 867 883 N/A INTRINSIC
low complexity region 1015 1039 N/A INTRINSIC
low complexity region 1066 1077 N/A INTRINSIC
low complexity region 1384 1395 N/A INTRINSIC
AWS 1468 1523 8.39e-30 SMART
SET 1524 1647 3.07e-41 SMART
PostSET 1648 1664 1.27e-5 SMART
Blast:SET 1689 1714 2e-6 BLAST
low complexity region 1884 1909 N/A INTRINSIC
low complexity region 1956 1967 N/A INTRINSIC
coiled coil region 2090 2113 N/A INTRINSIC
low complexity region 2189 2211 N/A INTRINSIC
low complexity region 2248 2265 N/A INTRINSIC
WW 2363 2395 2.1e-11 SMART
Pfam:SRI 2440 2530 6e-30 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000196814
Predicted Effect probably benign
Transcript: ENSMUST00000197655
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198587
Predicted Effect unknown
Transcript: ENSMUST00000200460
AA Change: V17A
Meta Mutation Damage Score 0.1716 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.9%
Validation Efficiency 96% (64/67)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein belonging to a class of huntingtin interacting proteins characterized by WW motifs. This protein is a histone methyltransferase that is specific for lysine-36 of histone H3, and methylation of this residue is associated with active chromatin. This protein also contains a novel transcriptional activation domain and has been found associated with hyperphosphorylated RNA polymerase II. [provided by RefSeq, Aug 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired embryonic vascular remodeling in the embryo proper, yolk sac, and placenta that leads to death around E10.5. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik T C 7: 130,740,872 (GRCm39) M115V probably benign Het
4933415A04Rik TTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT TTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 11: 43,478,227 (GRCm39) probably null Het
Abca7 C T 10: 79,843,185 (GRCm39) A1220V probably benign Het
Adamts19 G A 18: 59,060,372 (GRCm39) probably null Het
Agbl1 G A 7: 76,058,993 (GRCm39) V194M probably benign Het
Arhgap20 G T 9: 51,760,963 (GRCm39) S902I probably damaging Het
Atp11b T G 3: 35,861,093 (GRCm39) D193E probably damaging Het
B3gntl1 A T 11: 121,535,430 (GRCm39) probably benign Het
C2cd2 T C 16: 97,723,496 (GRCm39) E7G possibly damaging Het
Camta2 A G 11: 70,572,447 (GRCm39) L259P probably benign Het
Ccni T C 5: 93,335,563 (GRCm39) N192D probably benign Het
Cgnl1 A G 9: 71,558,535 (GRCm39) I946T possibly damaging Het
Chil3 T C 3: 106,068,548 (GRCm39) probably null Het
Cntn5 A G 9: 9,673,407 (GRCm39) probably benign Het
Cpn2 C T 16: 30,078,169 (GRCm39) G511S possibly damaging Het
Dagla C A 19: 10,232,170 (GRCm39) probably null Het
Dcc T C 18: 71,392,086 (GRCm39) N1440S probably damaging Het
Drosha T A 15: 12,907,474 (GRCm39) N1069K probably benign Het
Edc4 A G 8: 106,616,060 (GRCm39) T812A probably benign Het
Eml4 A G 17: 83,747,471 (GRCm39) I238V probably benign Het
Ep400 T C 5: 110,852,882 (GRCm39) T1288A unknown Het
Fastkd1 A C 2: 69,532,750 (GRCm39) L539R probably damaging Het
Fbln7 G A 2: 128,719,454 (GRCm39) probably benign Het
Fbxo39 A G 11: 72,209,297 (GRCm39) I386V probably benign Het
Gm17430 T C 18: 9,726,267 (GRCm39) K135R probably damaging Het
Gm3646 T A 1: 39,843,483 (GRCm39) T8S unknown Het
Gtsf1 A T 15: 103,329,619 (GRCm39) V100E possibly damaging Het
Helz2 A G 2: 180,876,618 (GRCm39) F1292S possibly damaging Het
Igf2bp3 G A 6: 49,084,401 (GRCm39) probably benign Het
Ip6k2 T G 9: 108,681,826 (GRCm39) D252E probably damaging Het
Iqck T A 7: 118,514,817 (GRCm39) L232Q probably damaging Het
Kif18b A G 11: 102,806,001 (GRCm39) V186A probably damaging Het
Klhl6 T A 16: 19,768,197 (GRCm39) probably null Het
Lao1 C T 4: 118,820,999 (GRCm39) T75I probably benign Het
Lyst T C 13: 13,855,878 (GRCm39) F2400L probably benign Het
Map3k9 A T 12: 81,780,997 (GRCm39) S388T possibly damaging Het
Mmp11 G T 10: 75,762,767 (GRCm39) H229N probably damaging Het
Myh7 T G 14: 55,212,158 (GRCm39) I1529L probably benign Het
Nckap5 G T 1: 126,623,459 (GRCm39) D11E possibly damaging Het
Ncoa1 A T 12: 4,373,033 (GRCm39) F123I probably damaging Het
Nelfb A T 2: 25,093,992 (GRCm39) D385E probably benign Het
Obscn C T 11: 58,972,810 (GRCm39) V2288M probably damaging Het
Or2f1b A G 6: 42,739,154 (GRCm39) H56R probably damaging Het
Or4d6 C T 19: 12,086,884 (GRCm39) V9M possibly damaging Het
Or52x1 A T 7: 104,853,367 (GRCm39) M61K probably damaging Het
Or5b12b A G 19: 12,861,458 (GRCm39) Y71C probably damaging Het
Otog T A 7: 45,918,673 (GRCm39) probably benign Het
Oxa1l A G 14: 54,605,646 (GRCm39) E375G possibly damaging Het
Pan2 T A 10: 128,144,091 (GRCm39) I129K possibly damaging Het
Parp1 A G 1: 180,426,616 (GRCm39) I919M probably benign Het
Pnpla7 T C 2: 24,885,305 (GRCm39) Y174H probably damaging Het
Polr3b T C 10: 84,473,928 (GRCm39) F169S probably damaging Het
Rab10 T C 12: 3,314,743 (GRCm39) D45G probably damaging Het
Reln A G 5: 22,185,107 (GRCm39) S1537P possibly damaging Het
Sema6d T A 2: 124,507,197 (GRCm39) S1045T probably benign Het
Spidr T A 16: 15,733,229 (GRCm39) I589F probably damaging Het
Stmn4 A C 14: 66,595,388 (GRCm39) I165L probably benign Het
Stx5a T C 19: 8,727,301 (GRCm39) M177T probably damaging Het
Tll1 T C 8: 64,491,486 (GRCm39) probably null Het
Tmem192 T C 8: 65,416,912 (GRCm39) Y168H probably damaging Het
Ttc21a C T 9: 119,785,892 (GRCm39) probably benign Het
Ush2a A G 1: 188,446,663 (GRCm39) probably benign Het
Vezf1 A G 11: 87,972,403 (GRCm39) M255V possibly damaging Het
Vmn2r25 A G 6: 123,816,786 (GRCm39) F265S probably damaging Het
Vps13a A G 19: 16,681,941 (GRCm39) S1021P probably benign Het
Wfdc16 T C 2: 164,477,773 (GRCm39) E92G possibly damaging Het
Zkscan2 T C 7: 123,079,423 (GRCm39) T845A possibly damaging Het
Other mutations in Setd2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00722:Setd2 APN 9 110,380,204 (GRCm39) missense possibly damaging 0.94
IGL01023:Setd2 APN 9 110,376,581 (GRCm39) nonsense probably null
IGL01063:Setd2 APN 9 110,402,741 (GRCm39) missense probably damaging 1.00
IGL01745:Setd2 APN 9 110,423,779 (GRCm39) missense probably damaging 0.99
IGL01911:Setd2 APN 9 110,446,499 (GRCm39) splice site probably null
IGL01955:Setd2 APN 9 110,378,386 (GRCm39) missense probably benign 0.38
IGL02023:Setd2 APN 9 110,423,704 (GRCm39) missense probably benign 0.06
IGL02080:Setd2 APN 9 110,376,518 (GRCm39) splice site probably null
IGL02412:Setd2 APN 9 110,379,842 (GRCm39) missense probably benign 0.00
IGL02519:Setd2 APN 9 110,382,184 (GRCm39) missense probably damaging 0.97
IGL02631:Setd2 APN 9 110,379,644 (GRCm39) missense possibly damaging 0.80
IGL02754:Setd2 APN 9 110,379,124 (GRCm39) missense possibly damaging 0.77
IGL02828:Setd2 APN 9 110,390,282 (GRCm39) missense probably benign 0.31
IGL03033:Setd2 APN 9 110,380,343 (GRCm39) missense possibly damaging 0.96
IGL03140:Setd2 APN 9 110,444,020 (GRCm39) critical splice donor site probably null
IGL03378:Setd2 APN 9 110,382,220 (GRCm39) missense unknown
American_samoa UTSW 9 110,396,826 (GRCm39) nonsense probably null
slingshot UTSW 9 110,378,575 (GRCm39) missense probably benign 0.00
P0028:Setd2 UTSW 9 110,403,022 (GRCm39) missense probably benign 0.00
PIT4544001:Setd2 UTSW 9 110,380,232 (GRCm39) missense probably damaging 1.00
R0058:Setd2 UTSW 9 110,423,494 (GRCm39) missense probably damaging 0.98
R0058:Setd2 UTSW 9 110,423,494 (GRCm39) missense probably damaging 0.98
R0167:Setd2 UTSW 9 110,402,850 (GRCm39) missense probably damaging 1.00
R0408:Setd2 UTSW 9 110,423,310 (GRCm39) missense probably damaging 1.00
R0452:Setd2 UTSW 9 110,382,168 (GRCm39) splice site probably null
R0947:Setd2 UTSW 9 110,377,579 (GRCm39) missense possibly damaging 0.87
R1249:Setd2 UTSW 9 110,402,948 (GRCm39) missense probably damaging 0.99
R1294:Setd2 UTSW 9 110,378,575 (GRCm39) missense probably benign 0.00
R1518:Setd2 UTSW 9 110,431,306 (GRCm39) missense probably damaging 0.98
R1585:Setd2 UTSW 9 110,380,464 (GRCm39) missense unknown
R1647:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R1649:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R1651:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R1652:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R1673:Setd2 UTSW 9 110,433,248 (GRCm39) missense probably damaging 0.97
R1703:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R1706:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R1709:Setd2 UTSW 9 110,378,925 (GRCm39) missense probably benign 0.00
R1752:Setd2 UTSW 9 110,423,673 (GRCm39) missense probably damaging 1.00
R1796:Setd2 UTSW 9 110,446,884 (GRCm39) critical splice acceptor site probably null
R1796:Setd2 UTSW 9 110,379,413 (GRCm39) missense probably benign 0.01
R1812:Setd2 UTSW 9 110,379,170 (GRCm39) missense probably damaging 0.99
R1884:Setd2 UTSW 9 110,385,486 (GRCm39) critical splice donor site probably null
R2024:Setd2 UTSW 9 110,378,201 (GRCm39) missense possibly damaging 0.65
R2051:Setd2 UTSW 9 110,379,958 (GRCm39) missense probably benign
R2117:Setd2 UTSW 9 110,433,212 (GRCm39) frame shift probably null
R2120:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R2124:Setd2 UTSW 9 110,378,932 (GRCm39) missense probably benign 0.12
R2172:Setd2 UTSW 9 110,378,912 (GRCm39) missense probably benign 0.10
R2179:Setd2 UTSW 9 110,423,756 (GRCm39) nonsense probably null
R2262:Setd2 UTSW 9 110,390,311 (GRCm39) intron probably benign
R2411:Setd2 UTSW 9 110,379,497 (GRCm39) missense possibly damaging 0.46
R2413:Setd2 UTSW 9 110,376,572 (GRCm39) missense probably damaging 1.00
R2419:Setd2 UTSW 9 110,378,065 (GRCm39) missense possibly damaging 0.48
R2424:Setd2 UTSW 9 110,446,590 (GRCm39) missense probably benign 0.37
R3757:Setd2 UTSW 9 110,402,753 (GRCm39) missense probably damaging 0.99
R3765:Setd2 UTSW 9 110,423,314 (GRCm39) missense probably damaging 1.00
R3796:Setd2 UTSW 9 110,378,639 (GRCm39) missense probably benign 0.00
R3797:Setd2 UTSW 9 110,378,639 (GRCm39) missense probably benign 0.00
R3799:Setd2 UTSW 9 110,378,639 (GRCm39) missense probably benign 0.00
R3899:Setd2 UTSW 9 110,421,586 (GRCm39) missense probably damaging 1.00
R3900:Setd2 UTSW 9 110,421,586 (GRCm39) missense probably damaging 1.00
R3913:Setd2 UTSW 9 110,380,114 (GRCm39) missense probably damaging 0.99
R4010:Setd2 UTSW 9 110,428,263 (GRCm39) missense probably null 1.00
R4580:Setd2 UTSW 9 110,403,311 (GRCm39) missense probably benign 0.06
R4614:Setd2 UTSW 9 110,398,881 (GRCm39) critical splice donor site probably null
R4651:Setd2 UTSW 9 110,423,200 (GRCm39) missense possibly damaging 0.53
R4652:Setd2 UTSW 9 110,423,200 (GRCm39) missense possibly damaging 0.53
R4855:Setd2 UTSW 9 110,401,022 (GRCm39) missense probably benign 0.02
R4970:Setd2 UTSW 9 110,377,226 (GRCm39) missense probably benign 0.28
R5112:Setd2 UTSW 9 110,377,226 (GRCm39) missense probably benign 0.28
R5123:Setd2 UTSW 9 110,446,595 (GRCm39) missense possibly damaging 0.76
R5140:Setd2 UTSW 9 110,380,197 (GRCm39) missense probably benign 0.00
R5202:Setd2 UTSW 9 110,380,298 (GRCm39) missense probably damaging 1.00
R5290:Setd2 UTSW 9 110,446,899 (GRCm39) missense probably damaging 1.00
R5560:Setd2 UTSW 9 110,378,907 (GRCm39) nonsense probably null
R5604:Setd2 UTSW 9 110,433,284 (GRCm39) missense probably damaging 0.99
R5678:Setd2 UTSW 9 110,431,254 (GRCm39) missense probably damaging 0.99
R5708:Setd2 UTSW 9 110,377,891 (GRCm39) missense possibly damaging 0.59
R5763:Setd2 UTSW 9 110,385,343 (GRCm39) splice site probably null
R5814:Setd2 UTSW 9 110,396,826 (GRCm39) nonsense probably null
R5924:Setd2 UTSW 9 110,403,112 (GRCm39) missense probably benign 0.23
R6244:Setd2 UTSW 9 110,377,733 (GRCm39) missense probably damaging 1.00
R6313:Setd2 UTSW 9 110,385,434 (GRCm39) missense unknown
R6431:Setd2 UTSW 9 110,379,453 (GRCm39) missense possibly damaging 0.65
R6526:Setd2 UTSW 9 110,361,785 (GRCm39) missense probably benign 0.33
R6579:Setd2 UTSW 9 110,378,846 (GRCm39) missense possibly damaging 0.87
R6996:Setd2 UTSW 9 110,379,640 (GRCm39) missense probably damaging 0.99
R7012:Setd2 UTSW 9 110,376,751 (GRCm39) missense probably damaging 0.97
R7105:Setd2 UTSW 9 110,377,328 (GRCm39) missense probably damaging 1.00
R7134:Setd2 UTSW 9 110,377,865 (GRCm39) missense possibly damaging 0.87
R7222:Setd2 UTSW 9 110,380,530 (GRCm39) missense
R7359:Setd2 UTSW 9 110,392,012 (GRCm39) missense
R7492:Setd2 UTSW 9 110,423,700 (GRCm39) missense
R7643:Setd2 UTSW 9 110,396,908 (GRCm39) splice site probably null
R7869:Setd2 UTSW 9 110,379,082 (GRCm39) nonsense probably null
R7903:Setd2 UTSW 9 110,446,905 (GRCm39) missense
R8004:Setd2 UTSW 9 110,421,613 (GRCm39) missense
R8017:Setd2 UTSW 9 110,431,255 (GRCm39) missense
R8019:Setd2 UTSW 9 110,431,255 (GRCm39) missense
R8366:Setd2 UTSW 9 110,377,816 (GRCm39) missense probably damaging 1.00
R8460:Setd2 UTSW 9 110,423,338 (GRCm39) missense
R8498:Setd2 UTSW 9 110,378,989 (GRCm39) missense probably damaging 0.99
R8725:Setd2 UTSW 9 110,402,912 (GRCm39) missense
R8870:Setd2 UTSW 9 110,423,321 (GRCm39) missense
R8878:Setd2 UTSW 9 110,421,467 (GRCm39) missense probably benign
R9132:Setd2 UTSW 9 110,374,385 (GRCm39) critical splice donor site probably null
R9159:Setd2 UTSW 9 110,374,385 (GRCm39) critical splice donor site probably null
R9198:Setd2 UTSW 9 110,378,168 (GRCm39) missense possibly damaging 0.77
R9277:Setd2 UTSW 9 110,379,619 (GRCm39) missense probably damaging 1.00
R9326:Setd2 UTSW 9 110,378,671 (GRCm39) missense probably benign 0.00
R9558:Setd2 UTSW 9 110,376,628 (GRCm39) missense probably damaging 0.99
R9664:Setd2 UTSW 9 110,377,570 (GRCm39) missense probably damaging 1.00
R9673:Setd2 UTSW 9 110,378,138 (GRCm39) missense probably damaging 1.00
RF009:Setd2 UTSW 9 110,379,779 (GRCm39) missense probably damaging 1.00
Z1176:Setd2 UTSW 9 110,376,343 (GRCm39) missense probably damaging 0.99
Z1176:Setd2 UTSW 9 110,361,794 (GRCm39) missense possibly damaging 0.85
Z1176:Setd2 UTSW 9 110,376,647 (GRCm39) missense probably damaging 0.97
Z1177:Setd2 UTSW 9 110,376,544 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCACACTTAGTGGCATGGGTAGGC -3'
(R):5'- TCTCAACTTTGGACTCGCACAGC -3'

Sequencing Primer
(F):5'- CATGGGTAGGCATTATGTCATTAC -3'
(R):5'- CAGTGACAGTCTCTAACTGATCAAGG -3'
Posted On 2013-06-12