Incidental Mutation 'R5123:Setd2'
ID 393403
Institutional Source Beutler Lab
Gene Symbol Setd2
Ensembl Gene ENSMUSG00000044791
Gene Name SET domain containing 2
Synonyms KMT3A, 4921524K10Rik
MMRRC Submission 042711-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.948) question?
Stock # R5123 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 110361665-110447701 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 110446595 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 2482 (A2482S)
Ref Sequence ENSEMBL: ENSMUSP00000116313 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035069] [ENSMUST00000153838] [ENSMUST00000196735] [ENSMUST00000196876] [ENSMUST00000197399]
AlphaFold E9Q5F9
Predicted Effect probably benign
Transcript: ENSMUST00000035069
SMART Domains Protein: ENSMUSP00000035069
Gene: ENSMUSG00000032491

DomainStartEndE-ValueType
transmembrane domain 52 74 N/A INTRINSIC
Pfam:Death 143 222 1.7e-18 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000153838
AA Change: A2482S

PolyPhen 2 Score 0.760 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000116313
Gene: ENSMUSG00000044791
AA Change: A2482S

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: ENSMUST00000196735
SMART Domains Protein: ENSMUSP00000143785
Gene: ENSMUSG00000032491

DomainStartEndE-ValueType
transmembrane domain 52 74 N/A INTRINSIC
Pfam:Death 143 200 2.1e-9 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000196814
Predicted Effect probably benign
Transcript: ENSMUST00000196876
SMART Domains Protein: ENSMUSP00000142925
Gene: ENSMUSG00000032491

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197260
Predicted Effect unknown
Transcript: ENSMUST00000200460
AA Change: A704S
Predicted Effect probably benign
Transcript: ENSMUST00000197399
SMART Domains Protein: ENSMUSP00000142572
Gene: ENSMUSG00000044791

DomainStartEndE-ValueType
WW 7 39 2.1e-11 SMART
Meta Mutation Damage Score 0.4701 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.5%
Validation Efficiency 98% (53/54)
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca3 G A 17: 24,603,434 (GRCm39) G542D possibly damaging Het
Adh6b A G 3: 138,063,450 (GRCm39) Y343C probably damaging Het
Adsl T A 15: 80,836,495 (GRCm39) probably null Het
Apob T A 12: 8,057,630 (GRCm39) probably null Het
Atp6ap1l T A 13: 91,047,017 (GRCm39) probably benign Het
Cacnb3 A G 15: 98,537,750 (GRCm39) D74G probably damaging Het
Cfap251 A G 5: 123,411,696 (GRCm39) probably benign Het
Clca3a2 T A 3: 144,512,104 (GRCm39) D544V probably damaging Het
Col3a1 G A 1: 45,372,756 (GRCm39) probably benign Het
D7Ertd443e A G 7: 133,951,397 (GRCm39) probably null Het
Dscam T C 16: 96,573,637 (GRCm39) D775G probably damaging Het
Eif2b3 T A 4: 116,879,408 (GRCm39) M16K probably damaging Het
Eml5 T C 12: 98,840,771 (GRCm39) Y281C probably damaging Het
Epha2 T A 4: 141,036,176 (GRCm39) L204Q possibly damaging Het
Filip1l A C 16: 57,391,025 (GRCm39) I538L possibly damaging Het
Gcnt2 T A 13: 41,071,831 (GRCm39) V158D probably damaging Het
Gnaq A G 19: 16,309,449 (GRCm39) N162S probably benign Het
Haus5 A T 7: 30,353,651 (GRCm39) N575K probably benign Het
Hjurp A T 1: 88,202,772 (GRCm39) Y71N possibly damaging Het
Igsf5 A G 16: 96,174,279 (GRCm39) D103G probably damaging Het
Myo10 A G 15: 25,726,569 (GRCm39) D297G possibly damaging Het
Net1 C T 13: 3,936,623 (GRCm39) R314H probably damaging Het
Or4b1c C A 2: 90,126,512 (GRCm39) R231L probably benign Het
Or4k51 T A 2: 111,584,897 (GRCm39) V101D probably damaging Het
Pcsk4 C A 10: 80,157,979 (GRCm39) Q586H probably null Het
Pramel11 A T 4: 143,623,706 (GRCm39) M156K probably benign Het
Prss1 A G 6: 41,440,131 (GRCm39) D156G possibly damaging Het
Rnf133 A T 6: 23,649,259 (GRCm39) N266K probably damaging Het
Sgo2a A T 1: 58,055,726 (GRCm39) S637C probably damaging Het
Slc2a5 C A 4: 150,224,262 (GRCm39) S290* probably null Het
Spata6 T G 4: 111,625,992 (GRCm39) H120Q possibly damaging Het
Stk11 G A 10: 79,963,775 (GRCm39) V194I probably damaging Het
Tkt T C 14: 30,287,603 (GRCm39) V199A probably benign Het
Traf3 G A 12: 111,209,952 (GRCm39) V183M possibly damaging Het
Trappc11 T C 8: 47,966,437 (GRCm39) Y483C probably damaging Het
Trappc9 T C 15: 72,785,215 (GRCm39) probably benign Het
Trim59 T C 3: 68,945,067 (GRCm39) H91R probably benign Het
Ttc21a A G 9: 119,781,278 (GRCm39) S484G probably benign Het
Usp13 A T 3: 32,969,947 (GRCm39) H691L probably benign Het
Vmn1r238 T C 18: 3,123,243 (GRCm39) Y57C probably benign Het
Vmn2r111 T A 17: 22,790,124 (GRCm39) Q294L possibly damaging Het
Vmn2r17 A G 5: 109,575,774 (GRCm39) D215G possibly damaging Het
Zfp280b A G 10: 75,875,183 (GRCm39) D354G probably benign Het
Zfp607a A G 7: 27,578,523 (GRCm39) H531R probably damaging Het
Zfp74 A T 7: 29,634,158 (GRCm39) C517S probably 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
R0541:Setd2 UTSW 9 110,402,741 (GRCm39) missense probably damaging 1.00
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
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'- TGCATCTCATTGGCTTCCTAGG -3'
(R):5'- CACAGGAGAAACCGAGCTTTC -3'

Sequencing Primer
(F):5'- ATTGTTGGCCTAGACAGCAGC -3'
(R):5'- GGAGAAACCGAGCTTTCAAAGTCTC -3'
Posted On 2016-06-15