Incidental Mutation 'R5290:Setd2'
ID 424664
Institutional Source Beutler Lab
Gene Symbol Setd2
Ensembl Gene ENSMUSG00000044791
Gene Name SET domain containing 2
Synonyms KMT3A, 4921524K10Rik
MMRRC Submission 042873-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.948) question?
Stock # R5290 (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 110446899 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 2489 (V2489A)
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 probably damaging
Transcript: ENSMUST00000153838
AA Change: V2489A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000116313
Gene: ENSMUSG00000044791
AA Change: V2489A

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: V711A
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197894
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 0.4654 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 97% (70/72)
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110008E08Rik A T 16: 90,351,098 (GRCm39) noncoding transcript Het
2700049A03Rik C A 12: 71,235,565 (GRCm39) P1172T probably benign Het
Abi3bp T A 16: 56,462,838 (GRCm39) probably null Het
Apod T A 16: 31,129,884 (GRCm39) H24L probably damaging Het
Arfgef3 T C 10: 18,476,208 (GRCm39) E1537G probably damaging Het
B020004C17Rik T C 14: 57,254,036 (GRCm39) V53A possibly damaging Het
Ccdc113 C A 8: 96,267,424 (GRCm39) probably null Het
Cd7 T G 11: 120,928,936 (GRCm39) D105A probably damaging Het
Celsr3 C T 9: 108,720,357 (GRCm39) T2550M probably benign Het
Cibar1 T C 4: 12,171,195 (GRCm39) Q86R probably benign Het
Col6a5 C T 9: 105,823,282 (GRCm39) G25D unknown Het
Cps1 A G 1: 67,211,868 (GRCm39) M679V probably benign Het
Dnai4 A T 4: 102,906,730 (GRCm39) D694E probably benign Het
Dync1h1 A T 12: 110,581,502 (GRCm39) T316S probably benign Het
Edrf1 T C 7: 133,252,295 (GRCm39) Y449H probably damaging Het
Fkbpl G A 17: 34,864,303 (GRCm39) A24T probably benign Het
Flg2 A T 3: 93,127,873 (GRCm39) I2262L unknown Het
Flnc T C 6: 29,457,553 (GRCm39) L2417P probably damaging Het
Gabrp A T 11: 33,517,310 (GRCm39) Y121N probably damaging Het
Gdpd4 A G 7: 97,615,543 (GRCm39) T123A possibly damaging Het
Gpr162 C A 6: 124,838,232 (GRCm39) M139I probably benign Het
Greb1l G A 18: 10,542,427 (GRCm39) E1341K probably damaging Het
Gsn G A 2: 35,186,484 (GRCm39) S410N probably benign Het
Gtf2f2 T C 14: 76,135,089 (GRCm39) Y212C probably damaging Het
Hao2 C T 3: 98,784,493 (GRCm39) A291T probably damaging Het
Igkv1-133 A G 6: 67,702,563 (GRCm39) T94A possibly damaging Het
Irf2bp1 G A 7: 18,738,923 (GRCm39) A188T possibly damaging Het
Itpr1 T C 6: 108,383,106 (GRCm39) V1478A possibly damaging Het
Kdm5b T C 1: 134,549,837 (GRCm39) probably null Het
Kif5b A T 18: 6,234,882 (GRCm39) D49E probably damaging Het
Lmbr1l A G 15: 98,810,123 (GRCm39) W113R probably damaging Het
Lrp2 T C 2: 69,343,698 (GRCm39) D887G probably damaging Het
Lrrc14 T A 15: 76,598,143 (GRCm39) M291K probably benign Het
Lypd11 T C 7: 24,422,836 (GRCm39) E79G probably benign Het
Mgarp G A 3: 51,296,387 (GRCm39) A205V possibly damaging Het
Msl2 T C 9: 100,978,606 (GRCm39) probably null Het
Nfix G A 8: 85,440,406 (GRCm39) Q487* probably null Het
Notch4 T C 17: 34,784,263 (GRCm39) V22A probably benign Het
Npc1l1 T A 11: 6,172,221 (GRCm39) Q823L probably benign Het
Obox3 T C 7: 15,360,774 (GRCm39) K122E probably benign Het
Or10ab5 C T 7: 108,245,755 (GRCm39) M9I probably benign Het
Or2a12 A G 6: 42,904,972 (GRCm39) K269R probably damaging Het
Or8s10 T C 15: 98,336,213 (GRCm39) Y288H probably damaging Het
Plekhh3 T A 11: 101,057,397 (GRCm39) M287L possibly damaging Het
Prpf3 A T 3: 95,760,857 (GRCm39) I15K probably benign Het
Rpl12-ps1 G T 1: 36,997,423 (GRCm39) noncoding transcript Het
Rps8 G C 4: 117,012,352 (GRCm39) probably benign Het
Slfn10-ps T A 11: 82,919,851 (GRCm39) noncoding transcript Het
Smad2 C T 18: 76,395,795 (GRCm39) P78L probably damaging Het
Spen G A 4: 141,201,127 (GRCm39) T2500I probably damaging Het
Stmnd1 A G 13: 46,453,074 (GRCm39) D250G probably benign Het
Tjp2 T G 19: 24,108,568 (GRCm39) E181D probably benign Het
Tmem131l T C 3: 83,806,572 (GRCm39) D1478G probably benign Het
Trim72 G T 7: 127,609,176 (GRCm39) R326L probably benign Het
Ttn A T 2: 76,727,584 (GRCm39) probably benign Het
Vmn1r177 A T 7: 23,565,498 (GRCm39) M126K probably damaging Het
Vmn1r57 A G 7: 5,224,319 (GRCm39) I281M probably damaging Het
Vmn2r108 C A 17: 20,691,665 (GRCm39) R286L probably benign Het
Wdr25 T C 12: 108,863,968 (GRCm39) S38P probably benign Het
Zfp937 T A 2: 150,080,229 (GRCm39) Y86* probably null Het
Zfr2 CTCAGACTGGTGTCAGAC CTCAGAC 10: 81,082,544 (GRCm39) probably null Het
Zswim1 C T 2: 164,667,845 (GRCm39) H366Y 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
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
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'- CTCAGGAAGTATGGCTTATGTGC -3'
(R):5'- ATACTCCACTCTGGCCTGAG -3'

Sequencing Primer
(F):5'- GCTTATGTGCCAGATGCTAAG -3'
(R):5'- GCCTGAGGTCACTCTAGTTCAG -3'
Posted On 2016-08-04