Incidental Mutation 'R9063:Setd1a'
ID 689090
Institutional Source Beutler Lab
Gene Symbol Setd1a
Ensembl Gene ENSMUSG00000042308
Gene Name SET domain containing 1A
Synonyms KMT2F
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9063 (G1)
Quality Score 225.009
Status Not validated
Chromosome 7
Chromosomal Location 127376561-127399294 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 127385558 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 755 (R755H)
Ref Sequence ENSEMBL: ENSMUSP00000047672 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047075] [ENSMUST00000047157] [ENSMUST00000126761] [ENSMUST00000144406] [ENSMUST00000154987]
AlphaFold E9PYH6
Predicted Effect possibly damaging
Transcript: ENSMUST00000047075
AA Change: R755H

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000047672
Gene: ENSMUSG00000042308
AA Change: R755H

DomainStartEndE-ValueType
RRM 95 168 7.6e-6 SMART
low complexity region 209 242 N/A INTRINSIC
low complexity region 278 295 N/A INTRINSIC
low complexity region 315 357 N/A INTRINSIC
low complexity region 427 487 N/A INTRINSIC
Blast:SET 488 976 N/A BLAST
low complexity region 977 1007 N/A INTRINSIC
low complexity region 1015 1079 N/A INTRINSIC
low complexity region 1087 1098 N/A INTRINSIC
low complexity region 1122 1152 N/A INTRINSIC
low complexity region 1157 1173 N/A INTRINSIC
Blast:SET 1193 1310 2e-24 BLAST
low complexity region 1311 1368 N/A INTRINSIC
low complexity region 1369 1396 N/A INTRINSIC
N-SET 1428 1567 6.75e-64 SMART
SET 1577 1700 3.22e-35 SMART
PostSET 1700 1716 1.16e-4 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000047157
AA Change: R755H

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000037600
Gene: ENSMUSG00000042308
AA Change: R755H

DomainStartEndE-ValueType
RRM 95 168 7.6e-6 SMART
low complexity region 209 242 N/A INTRINSIC
low complexity region 278 295 N/A INTRINSIC
low complexity region 315 357 N/A INTRINSIC
low complexity region 427 487 N/A INTRINSIC
Blast:SET 488 976 N/A BLAST
low complexity region 977 1007 N/A INTRINSIC
low complexity region 1015 1079 N/A INTRINSIC
low complexity region 1087 1098 N/A INTRINSIC
low complexity region 1122 1152 N/A INTRINSIC
low complexity region 1157 1173 N/A INTRINSIC
Blast:SET 1193 1310 2e-24 BLAST
low complexity region 1311 1368 N/A INTRINSIC
low complexity region 1369 1396 N/A INTRINSIC
N-SET 1428 1567 6.75e-64 SMART
SET 1577 1700 3.22e-35 SMART
PostSET 1700 1716 1.16e-4 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000126761
SMART Domains Protein: ENSMUSP00000120666
Gene: ENSMUSG00000042308

DomainStartEndE-ValueType
RRM 95 168 7.6e-6 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000144406
SMART Domains Protein: ENSMUSP00000115248
Gene: ENSMUSG00000042308

DomainStartEndE-ValueType
RRM 95 168 7.6e-6 SMART
low complexity region 209 242 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000154987
AA Change: R212H

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily. [provided by RefSeq, Dec 2016]
PHENOTYPE: Animals homozygous for this allele were dead by E7.5 [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110004F10Rik T G 7: 115,703,660 (GRCm39) S178A probably benign Het
Add3 T C 19: 53,222,302 (GRCm39) L303P probably damaging Het
Agr2 T A 12: 36,053,898 (GRCm39) *176K probably null Het
Apobr C T 7: 126,185,920 (GRCm39) T477I probably benign Het
Cdca7l G A 12: 117,838,536 (GRCm39) V336M probably damaging Het
Cep63 T G 9: 102,496,227 (GRCm39) H18P unknown Het
Copa A G 1: 171,944,529 (GRCm39) D838G probably benign Het
Cspg4 G T 9: 56,795,687 (GRCm39) V1141L probably benign Het
D930020B18Rik A G 10: 121,497,002 (GRCm39) T146A probably benign Het
Dapk1 A T 13: 60,866,264 (GRCm39) I206L probably benign Het
Emsy C T 7: 98,295,684 (GRCm39) D73N probably damaging Het
Esr2 A T 12: 76,168,590 (GRCm39) Y540N probably benign Het
Exoc7 C A 11: 116,180,101 (GRCm39) V668L probably benign Het
Fcgbp C T 7: 27,791,277 (GRCm39) T846I probably damaging Het
Fhod3 A G 18: 25,153,772 (GRCm39) E418G probably damaging Het
Fryl G A 5: 73,238,346 (GRCm39) R1467C possibly damaging Het
Gas2l3 A G 10: 89,249,558 (GRCm39) I520T probably benign Het
Gfod1 A G 13: 43,354,280 (GRCm39) C232R probably benign Het
Gpr61 T C 3: 108,057,555 (GRCm39) R369G probably benign Het
Hk1 T C 10: 62,122,429 (GRCm39) Y423C probably damaging Het
Itpr3 G A 17: 27,337,651 (GRCm39) probably benign Het
Jmy T C 13: 93,635,580 (GRCm39) R79G probably benign Het
Kcnn4 T A 7: 24,076,934 (GRCm39) V161E probably damaging Het
Kif15 T A 9: 122,833,706 (GRCm39) I1040N probably damaging Het
Kif2b A G 11: 91,466,654 (GRCm39) L543S probably damaging Het
Kpna2 A G 11: 106,883,489 (GRCm39) I81T probably benign Het
Krt12 A G 11: 99,307,757 (GRCm39) S444P probably benign Het
Lmnb2 C T 10: 80,742,005 (GRCm39) V29M probably benign Het
Lmod2 T C 6: 24,603,364 (GRCm39) V113A probably benign Het
Lrp1b T C 2: 41,231,838 (GRCm39) T1211A Het
Lrrc8d T C 5: 105,961,959 (GRCm39) S790P probably damaging Het
Map3k4 A G 17: 12,482,878 (GRCm39) V613A probably damaging Het
Marveld2 T C 13: 100,748,653 (GRCm39) N142S probably benign Het
Mgll G A 6: 88,802,690 (GRCm39) V282I possibly damaging Het
Mief2 G A 11: 60,622,314 (GRCm39) E295K probably damaging Het
Mmrn2 A T 14: 34,120,567 (GRCm39) H479L probably benign Het
Myh15 T A 16: 48,913,118 (GRCm39) N358K probably benign Het
Mzf1 T G 7: 12,787,005 (GRCm39) K101Q probably damaging Het
Ncbp3 T A 11: 72,964,253 (GRCm39) L401Q probably damaging Het
Nck2 T C 1: 43,593,503 (GRCm39) C237R possibly damaging Het
Nlrp9a T G 7: 26,273,291 (GRCm39) N976K possibly damaging Het
Nol11 A G 11: 107,064,240 (GRCm39) V524A probably benign Het
Nol11 T C 11: 107,069,857 (GRCm39) Y331C possibly damaging Het
Nsmf A T 2: 24,952,622 (GRCm39) H149L probably benign Het
Olfm3 T C 3: 114,914,582 (GRCm39) V231A probably benign Het
Or1l4b A T 2: 37,036,646 (GRCm39) M141L probably benign Het
Or51a6 A G 7: 102,604,446 (GRCm39) S121P probably benign Het
Or55b4 T C 7: 102,133,931 (GRCm39) Y132C probably damaging Het
Pcdhgb5 T A 18: 37,864,739 (GRCm39) F178Y probably damaging Het
Plk2 T A 13: 110,532,920 (GRCm39) S160R possibly damaging Het
Plk5 C G 10: 80,193,830 (GRCm39) R40G probably damaging Het
Ppp1cc A G 5: 122,306,279 (GRCm39) N33D probably benign Het
Ptpn23 T C 9: 110,218,693 (GRCm39) E499G possibly damaging Het
Pwp1 A G 10: 85,720,431 (GRCm39) H356R probably benign Het
Rbsn G T 6: 92,171,000 (GRCm39) T307K probably benign Het
Rnf19a G A 15: 36,265,615 (GRCm39) Q161* probably null Het
Scin T C 12: 40,134,336 (GRCm39) D236G possibly damaging Het
Sik3 C T 9: 46,123,735 (GRCm39) T1178I probably benign Het
Slc49a3 A G 5: 108,590,103 (GRCm39) L433P probably damaging Het
Tex26 C T 5: 149,393,826 (GRCm39) R272C probably damaging Het
Trim60 T A 8: 65,453,465 (GRCm39) K261N possibly damaging Het
Tspan9 A G 6: 127,944,072 (GRCm39) I76T probably damaging Het
Ttn T A 2: 76,588,833 (GRCm39) Y21412F probably damaging Het
Ttn A T 2: 76,710,907 (GRCm39) I8409N unknown Het
Unc80 T C 1: 66,645,816 (GRCm39) probably null Het
Ush2a A T 1: 187,995,457 (GRCm39) Q76L probably benign Het
Usp1 G A 4: 98,819,389 (GRCm39) V284I probably benign Het
Usp31 A G 7: 121,306,466 (GRCm39) V4A probably benign Het
Vmn2r88 G A 14: 51,648,329 (GRCm39) probably benign Het
Zfp959 G A 17: 56,204,221 (GRCm39) R86K probably benign Het
Other mutations in Setd1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02508:Setd1a APN 7 127,396,870 (GRCm39) unclassified probably benign
IGL02657:Setd1a APN 7 127,394,997 (GRCm39) unclassified probably benign
IGL02792:Setd1a APN 7 127,390,522 (GRCm39) missense unknown
IGL02876:Setd1a APN 7 127,377,673 (GRCm39) splice site probably benign
IGL02967:Setd1a APN 7 127,384,349 (GRCm39) unclassified probably benign
IGL03090:Setd1a APN 7 127,385,672 (GRCm39) missense possibly damaging 0.83
IGL03238:Setd1a APN 7 127,384,718 (GRCm39) missense possibly damaging 0.86
FR4449:Setd1a UTSW 7 127,384,498 (GRCm39) unclassified probably benign
FR4548:Setd1a UTSW 7 127,384,485 (GRCm39) unclassified probably benign
FR4548:Setd1a UTSW 7 127,384,479 (GRCm39) unclassified probably benign
FR4589:Setd1a UTSW 7 127,384,469 (GRCm39) unclassified probably benign
FR4737:Setd1a UTSW 7 127,384,484 (GRCm39) unclassified probably benign
FR4976:Setd1a UTSW 7 127,384,488 (GRCm39) unclassified probably benign
FR4976:Setd1a UTSW 7 127,384,479 (GRCm39) unclassified probably benign
R0367:Setd1a UTSW 7 127,387,358 (GRCm39) splice site probably benign
R0411:Setd1a UTSW 7 127,395,223 (GRCm39) unclassified probably benign
R0416:Setd1a UTSW 7 127,384,469 (GRCm39) unclassified probably benign
R0470:Setd1a UTSW 7 127,384,229 (GRCm39) unclassified probably benign
R0645:Setd1a UTSW 7 127,386,382 (GRCm39) missense probably damaging 0.96
R0667:Setd1a UTSW 7 127,385,765 (GRCm39) missense probably damaging 0.99
R1251:Setd1a UTSW 7 127,396,596 (GRCm39) unclassified probably benign
R1465:Setd1a UTSW 7 127,387,512 (GRCm39) unclassified probably benign
R1465:Setd1a UTSW 7 127,387,512 (GRCm39) unclassified probably benign
R1660:Setd1a UTSW 7 127,395,841 (GRCm39) unclassified probably benign
R1730:Setd1a UTSW 7 127,384,296 (GRCm39) nonsense probably null
R1760:Setd1a UTSW 7 127,385,062 (GRCm39) missense possibly damaging 0.68
R1783:Setd1a UTSW 7 127,384,296 (GRCm39) nonsense probably null
R2149:Setd1a UTSW 7 127,385,690 (GRCm39) missense possibly damaging 0.75
R2159:Setd1a UTSW 7 127,384,661 (GRCm39) missense possibly damaging 0.91
R2303:Setd1a UTSW 7 127,398,327 (GRCm39) unclassified probably benign
R2679:Setd1a UTSW 7 127,394,896 (GRCm39) unclassified probably benign
R3428:Setd1a UTSW 7 127,384,493 (GRCm39) unclassified probably benign
R4108:Setd1a UTSW 7 127,398,374 (GRCm39) unclassified probably benign
R4227:Setd1a UTSW 7 127,395,819 (GRCm39) unclassified probably benign
R4438:Setd1a UTSW 7 127,384,903 (GRCm39) missense possibly damaging 0.83
R4730:Setd1a UTSW 7 127,396,502 (GRCm39) unclassified probably benign
R4869:Setd1a UTSW 7 127,396,776 (GRCm39) unclassified probably benign
R4892:Setd1a UTSW 7 127,377,696 (GRCm39) missense probably damaging 0.99
R5152:Setd1a UTSW 7 127,383,197 (GRCm39) missense probably benign
R5502:Setd1a UTSW 7 127,396,420 (GRCm39) critical splice donor site probably null
R5527:Setd1a UTSW 7 127,384,801 (GRCm39) missense probably damaging 0.99
R6189:Setd1a UTSW 7 127,377,455 (GRCm39) splice site probably null
R6250:Setd1a UTSW 7 127,390,471 (GRCm39) missense unknown
R7131:Setd1a UTSW 7 127,395,590 (GRCm39) small deletion probably benign
R7988:Setd1a UTSW 7 127,385,366 (GRCm39) missense probably benign 0.02
R8029:Setd1a UTSW 7 127,385,386 (GRCm39) missense probably benign 0.08
R8079:Setd1a UTSW 7 127,384,225 (GRCm39) missense unknown
R8171:Setd1a UTSW 7 127,390,399 (GRCm39) missense unknown
R8175:Setd1a UTSW 7 127,395,415 (GRCm39) missense unknown
R8286:Setd1a UTSW 7 127,385,356 (GRCm39) missense possibly damaging 0.96
R8327:Setd1a UTSW 7 127,390,669 (GRCm39) missense unknown
R8460:Setd1a UTSW 7 127,383,292 (GRCm39) missense unknown
R8547:Setd1a UTSW 7 127,395,676 (GRCm39) unclassified probably benign
R8699:Setd1a UTSW 7 127,385,774 (GRCm39) missense possibly damaging 0.53
R8822:Setd1a UTSW 7 127,385,332 (GRCm39) missense possibly damaging 0.86
R8968:Setd1a UTSW 7 127,385,279 (GRCm39) missense possibly damaging 0.93
R9178:Setd1a UTSW 7 127,385,590 (GRCm39) missense possibly damaging 0.93
R9672:Setd1a UTSW 7 127,385,237 (GRCm39) missense possibly damaging 0.96
R9700:Setd1a UTSW 7 127,385,752 (GRCm39) missense possibly damaging 0.53
RF001:Setd1a UTSW 7 127,384,486 (GRCm39) unclassified probably benign
RF008:Setd1a UTSW 7 127,384,486 (GRCm39) unclassified probably benign
RF011:Setd1a UTSW 7 127,384,515 (GRCm39) unclassified probably benign
RF014:Setd1a UTSW 7 127,384,518 (GRCm39) unclassified probably benign
RF030:Setd1a UTSW 7 127,384,483 (GRCm39) unclassified probably benign
RF030:Setd1a UTSW 7 127,384,473 (GRCm39) unclassified probably benign
RF031:Setd1a UTSW 7 127,384,483 (GRCm39) unclassified probably benign
RF036:Setd1a UTSW 7 127,384,472 (GRCm39) unclassified probably benign
RF041:Setd1a UTSW 7 127,384,504 (GRCm39) unclassified probably benign
RF052:Setd1a UTSW 7 127,384,529 (GRCm39) unclassified probably benign
RF055:Setd1a UTSW 7 127,384,471 (GRCm39) unclassified probably benign
RF056:Setd1a UTSW 7 127,384,500 (GRCm39) unclassified probably benign
RF056:Setd1a UTSW 7 127,384,475 (GRCm39) unclassified probably benign
RF058:Setd1a UTSW 7 127,384,490 (GRCm39) unclassified probably benign
Z1176:Setd1a UTSW 7 127,398,266 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- ATGTCCTTCCAGATGCAGAC -3'
(R):5'- TAAGGTCTCGCTGCATAATGC -3'

Sequencing Primer
(F):5'- TGCAGACCCAGATGTTAACACGG -3'
(R):5'- TCATCTCTTGGACAAGGGTAGCC -3'
Posted On 2021-11-19