Incidental Mutation 'R5134:Ehmt1'
ID 396002
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 042722-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5134 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 24767509 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Threonine at position 135 (P135T)
Ref Sequence ENSEMBL: ENSMUSP00000143189 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000150379] [ENSMUST00000152161] [ENSMUST00000198923] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably damaging
Transcript: ENSMUST00000046227
AA Change: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: P259T

DomainStartEndE-ValueType
low complexity region 340 359 N/A INTRINSIC
low complexity region 398 419 N/A INTRINSIC
low complexity region 440 452 N/A INTRINSIC
ANK 722 751 2.02e-5 SMART
ANK 755 786 3.06e-5 SMART
ANK 788 818 1.69e-7 SMART
ANK 822 851 6.65e-6 SMART
ANK 855 884 7.71e-2 SMART
ANK 888 917 6.12e-5 SMART
ANK 921 954 7.29e2 SMART
PreSET 961 1060 1.05e-30 SMART
SET 1076 1199 2.24e-43 SMART
low complexity region 1216 1229 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000091348
AA Change: P258T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: P258T

DomainStartEndE-ValueType
low complexity region 333 352 N/A INTRINSIC
low complexity region 391 412 N/A INTRINSIC
low complexity region 433 445 N/A INTRINSIC
ANK 763 792 2.02e-5 SMART
ANK 796 827 3.06e-5 SMART
ANK 829 859 1.69e-7 SMART
ANK 863 892 6.65e-6 SMART
ANK 896 925 7.71e-2 SMART
ANK 929 958 6.12e-5 SMART
ANK 962 995 7.29e2 SMART
PreSET 1002 1101 1.05e-30 SMART
SET 1117 1240 2.24e-43 SMART
low complexity region 1257 1270 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000102938
AA Change: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: P259T

DomainStartEndE-ValueType
low complexity region 340 359 N/A INTRINSIC
low complexity region 398 419 N/A INTRINSIC
low complexity region 440 452 N/A INTRINSIC
ANK 770 799 2.02e-5 SMART
ANK 803 834 3.06e-5 SMART
ANK 836 866 1.69e-7 SMART
ANK 870 899 6.65e-6 SMART
ANK 903 932 7.71e-2 SMART
ANK 936 965 6.12e-5 SMART
ANK 969 1002 7.29e2 SMART
PreSET 1009 1108 1.05e-30 SMART
SET 1124 1247 2.24e-43 SMART
low complexity region 1264 1277 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000114418
AA Change: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: P259T

DomainStartEndE-ValueType
low complexity region 340 359 N/A INTRINSIC
low complexity region 398 419 N/A INTRINSIC
low complexity region 440 452 N/A INTRINSIC
ANK 722 751 2.02e-5 SMART
ANK 755 786 3.06e-5 SMART
ANK 788 818 1.69e-7 SMART
ANK 822 851 6.65e-6 SMART
ANK 855 884 7.71e-2 SMART
ANK 888 917 6.12e-5 SMART
ANK 921 954 7.29e2 SMART
PreSET 961 1060 1.05e-30 SMART
SET 1076 1199 2.24e-43 SMART
low complexity region 1216 1229 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000114432
AA Change: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: P259T

DomainStartEndE-ValueType
low complexity region 333 352 N/A INTRINSIC
low complexity region 391 412 N/A INTRINSIC
low complexity region 433 445 N/A INTRINSIC
ANK 717 746 2.02e-5 SMART
ANK 750 781 3.06e-5 SMART
ANK 783 813 1.69e-7 SMART
ANK 817 846 6.65e-6 SMART
ANK 850 879 7.71e-2 SMART
ANK 883 912 6.12e-5 SMART
ANK 916 949 7.29e2 SMART
PreSET 956 1055 1.05e-30 SMART
SET 1071 1194 2.24e-43 SMART
low complexity region 1211 1224 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139000
Predicted Effect probably damaging
Transcript: ENSMUST00000147147
AA Change: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: P259T

DomainStartEndE-ValueType
low complexity region 252 271 N/A INTRINSIC
low complexity region 310 331 N/A INTRINSIC
low complexity region 352 364 N/A INTRINSIC
ANK 634 663 2.02e-5 SMART
ANK 667 698 3.06e-5 SMART
ANK 700 730 1.69e-7 SMART
ANK 734 763 6.65e-6 SMART
ANK 767 796 7.71e-2 SMART
ANK 800 829 6.12e-5 SMART
ANK 833 866 7.29e2 SMART
PreSET 873 972 1.05e-30 SMART
SET 988 1111 2.24e-43 SMART
low complexity region 1128 1141 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000150379
AA Change: P261T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect probably damaging
Transcript: ENSMUST00000152161
AA Change: P258T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000119854
Gene: ENSMUSG00000036893
AA Change: P258T

DomainStartEndE-ValueType
low complexity region 339 358 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000198923
AA Change: P135T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000143189
Gene: ENSMUSG00000036893
AA Change: P135T

DomainStartEndE-ValueType
low complexity region 208 227 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000152325
AA Change: P7T
SMART Domains Protein: ENSMUSP00000123387
Gene: ENSMUSG00000036893
AA Change: P7T

DomainStartEndE-ValueType
low complexity region 89 108 N/A INTRINSIC
low complexity region 147 168 N/A INTRINSIC
low complexity region 189 201 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192397
Predicted Effect probably benign
Transcript: ENSMUST00000200655
Meta Mutation Damage Score 0.0852 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.5%
Validation Efficiency 96% (100/104)
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 histone methyltransferase that is part of the E2F6 complex, which represses transcription. The encoded protein methylates the Lys-9 position of histone H3, which tags it for transcriptional repression. This protein may be involved in the silencing of MYC- and E2F-responsive genes and therefore could play a role in the G0/G1 cell cycle transition. Defects in this gene are a cause of chromosome 9q subtelomeric deletion syndrome (9q-syndrome, also known as Kleefstra syndrome). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
PHENOTYPE: Nullizygous embryos die circa E9.5 showing delayed growth and incomplete somite formation and neural groove closure. Heterozygotes show behavioral deficits and synaptic dysfunction. Homozygotes with a H3K9me1-binding mutant form show delayed prenatal growth and bone ossification and postnatal death. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 89 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adarb1 T A 10: 77,161,679 (GRCm39) probably benign Het
Adrb3 A C 8: 27,717,798 (GRCm39) M217R probably damaging Het
Ank2 A T 3: 126,757,094 (GRCm39) N1054K possibly damaging Het
Aox4 A T 1: 58,275,835 (GRCm39) D389V probably benign Het
Aph1a G T 3: 95,802,843 (GRCm39) G148W probably damaging Het
Arsj A G 3: 126,231,803 (GRCm39) D183G probably benign Het
Atg2b A G 12: 105,641,209 (GRCm39) S76P probably damaging Het
Atxn7l1 C A 12: 33,422,875 (GRCm39) N815K probably damaging Het
Cd3d A T 9: 44,896,296 (GRCm39) E28D probably damaging Het
Cir1 G A 2: 73,114,847 (GRCm39) R404* probably null Het
Cops8 A G 1: 90,538,724 (GRCm39) D51G probably damaging Het
Csgalnact1 T C 8: 68,913,623 (GRCm39) E194G probably benign Het
Cstf2t T A 19: 31,061,494 (GRCm39) D343E probably damaging Het
Ddx23 A T 15: 98,548,651 (GRCm39) D352E possibly damaging Het
Dhx34 G T 7: 15,952,175 (GRCm39) A150D possibly damaging Het
Dnal4 A T 15: 79,647,766 (GRCm39) V32E possibly damaging Het
Dvl3 G T 16: 20,343,357 (GRCm39) probably benign Het
Enpp2 C T 15: 54,762,726 (GRCm39) R174H probably damaging Het
Eps15 G A 4: 109,223,727 (GRCm39) probably benign Het
F10 T C 8: 13,105,698 (GRCm39) V421A probably damaging Het
Fabp3 C T 4: 130,206,180 (GRCm39) T57I probably benign Het
Fer1l6 A T 15: 58,512,003 (GRCm39) D1490V probably damaging Het
Fsd1l A G 4: 53,647,766 (GRCm39) K70E probably benign Het
Galnt12 G A 4: 47,113,818 (GRCm39) A79T probably damaging Het
Galnt17 A T 5: 130,992,873 (GRCm39) M347K probably damaging Het
Glyatl3 A G 17: 41,215,921 (GRCm39) V195A probably benign Het
Gm10770 A T 2: 150,021,480 (GRCm39) probably null Het
Gm5578 A T 6: 112,583,046 (GRCm39) noncoding transcript Het
Grn C A 11: 102,321,380 (GRCm39) probably benign Het
Gsk3b G A 16: 38,060,882 (GRCm39) R418H probably damaging Het
Hspa12b A G 2: 130,981,428 (GRCm39) E221G possibly damaging Het
Ighv1-50 T G 12: 115,083,653 (GRCm39) Q22H probably benign Het
Ipcef1 A G 10: 6,869,950 (GRCm39) I150T probably benign Het
Ipp T A 4: 116,372,654 (GRCm39) F228I possibly damaging Het
Itgb7 A G 15: 102,125,842 (GRCm39) C596R probably damaging Het
Kif27 T C 13: 58,438,904 (GRCm39) D1219G possibly damaging Het
Lats1 T A 10: 7,567,575 (GRCm39) D115E probably benign Het
Lpcat3 A G 6: 124,679,493 (GRCm39) N331S probably benign Het
Lrpprc A T 17: 85,058,684 (GRCm39) N725K probably benign Het
Lss T G 10: 76,382,070 (GRCm39) probably benign Het
Mfsd6 T C 1: 52,747,515 (GRCm39) Y450C possibly damaging Het
Mmp21 A T 7: 133,280,742 (GRCm39) V76E probably benign Het
Mtmr11 A T 3: 96,077,223 (GRCm39) Y527F probably damaging Het
Nat10 A T 2: 103,573,638 (GRCm39) F327I probably benign Het
Nfkbiz A T 16: 55,638,863 (GRCm39) M199K probably damaging Het
Nuak1 A G 10: 84,210,214 (GRCm39) Y625H probably benign Het
Odf1 A G 15: 38,226,393 (GRCm39) T98A possibly damaging Het
Oprl1 T A 2: 181,360,403 (GRCm39) I153N probably damaging Het
Or10g3b T C 14: 52,587,248 (GRCm39) N85S probably benign Het
Or1j4 A T 2: 36,740,488 (GRCm39) L143F probably benign Het
Or4x13 T A 2: 90,231,107 (GRCm39) M34K probably benign Het
Osbpl8 T A 10: 111,124,554 (GRCm39) D705E probably benign Het
Otud4 G A 8: 80,382,318 (GRCm39) V176I probably damaging Het
Paics T C 5: 77,104,669 (GRCm39) probably benign Het
Pax5 A G 4: 44,710,407 (GRCm39) M1T probably null Het
Pck1 A T 2: 172,995,282 (GRCm39) N34I probably benign Het
Pde8b T C 13: 95,223,250 (GRCm39) I335V probably benign Het
Piezo2 A G 18: 63,207,691 (GRCm39) V1440A probably damaging Het
Prr23a4 T C 9: 98,785,793 (GRCm39) S153P probably benign Het
Ptpre T A 7: 135,253,821 (GRCm39) F83Y probably damaging Het
Pwwp3a T C 10: 80,068,702 (GRCm39) L282P probably benign Het
Rassf6 T A 5: 90,752,225 (GRCm39) probably null Het
Rilp A T 11: 75,403,534 (GRCm39) L325F probably damaging Het
Rpf1 A G 3: 146,212,293 (GRCm39) L349S probably damaging Het
Rprd2 G C 3: 95,672,632 (GRCm39) R924G probably benign Het
Rps6kc1 T A 1: 190,505,845 (GRCm39) D1039V probably damaging Het
Rufy3 G A 5: 88,793,426 (GRCm39) V579I probably benign Het
Serpinc1 A G 1: 160,825,140 (GRCm39) probably null Het
Siae T G 9: 37,557,816 (GRCm39) I541S possibly damaging Het
St14 T G 9: 31,006,879 (GRCm39) D649A probably benign Het
Stab2 A G 10: 86,707,674 (GRCm39) probably null Het
Sun3 T C 11: 8,988,287 (GRCm39) T12A probably benign Het
Tdrd6 A G 17: 43,937,101 (GRCm39) Y1316H probably damaging Het
Thbs3 CAGAAG CAG 3: 89,130,409 (GRCm39) probably benign Het
Tmem161b C A 13: 84,442,887 (GRCm39) T269K possibly damaging Het
Trav14-3 T A 14: 54,000,701 (GRCm39) S17T unknown Het
Trmu T A 15: 85,780,556 (GRCm39) probably null Het
Ttn T A 2: 76,537,586 (GRCm39) T26454S possibly damaging Het
Ubr3 T C 2: 69,850,790 (GRCm39) probably benign Het
Unc5b A T 10: 60,610,879 (GRCm39) V376E probably benign Het
Usp3 T C 9: 66,449,814 (GRCm39) S166G possibly damaging Het
Vldlr C A 19: 27,216,212 (GRCm39) C344* probably null Het
Vmn1r17 A G 6: 57,337,828 (GRCm39) V130A probably benign Het
Wdfy3 A C 5: 102,091,969 (GRCm39) Y457D probably damaging Het
Zbtb2 T C 10: 4,319,267 (GRCm39) Y253C possibly damaging Het
Zfp687 A C 3: 94,917,697 (GRCm39) F692V probably damaging Het
Zfp758 A G 17: 22,594,386 (GRCm39) K291E probably damaging Het
Zfp799 A T 17: 33,039,415 (GRCm39) C284S probably damaging Het
Zp1 C A 19: 10,897,926 (GRCm39) C5F probably benign Het
Other mutations in Ehmt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00481:Ehmt1 APN 2 24,728,830 (GRCm39) missense possibly damaging 0.81
IGL01403:Ehmt1 APN 2 24,729,638 (GRCm39) missense possibly damaging 0.81
IGL01636:Ehmt1 APN 2 24,729,620 (GRCm39) missense probably damaging 0.97
IGL01804:Ehmt1 APN 2 24,681,966 (GRCm39) missense probably damaging 1.00
IGL01836:Ehmt1 APN 2 24,753,232 (GRCm39) splice site probably null
IGL02740:Ehmt1 APN 2 24,705,851 (GRCm39) splice site probably benign
IGL02750:Ehmt1 APN 2 24,753,881 (GRCm39) missense probably damaging 1.00
IGL03026:Ehmt1 APN 2 24,742,746 (GRCm39) missense probably benign
IGL02799:Ehmt1 UTSW 2 24,705,818 (GRCm39) missense probably damaging 1.00
R0908:Ehmt1 UTSW 2 24,694,900 (GRCm39) missense probably damaging 1.00
R1275:Ehmt1 UTSW 2 24,777,007 (GRCm39) critical splice donor site probably null
R1665:Ehmt1 UTSW 2 24,767,476 (GRCm39) missense probably damaging 1.00
R1707:Ehmt1 UTSW 2 24,695,150 (GRCm39) missense probably benign
R1800:Ehmt1 UTSW 2 24,774,302 (GRCm39) missense probably damaging 0.99
R2108:Ehmt1 UTSW 2 24,727,630 (GRCm39) missense probably damaging 1.00
R2113:Ehmt1 UTSW 2 24,694,015 (GRCm39) missense probably damaging 1.00
R2393:Ehmt1 UTSW 2 24,696,229 (GRCm39) missense probably damaging 1.00
R2570:Ehmt1 UTSW 2 24,705,753 (GRCm39) missense probably damaging 1.00
R3923:Ehmt1 UTSW 2 24,774,347 (GRCm39) splice site probably null
R4646:Ehmt1 UTSW 2 24,781,696 (GRCm39) missense probably null 0.01
R4924:Ehmt1 UTSW 2 24,729,734 (GRCm39) missense probably damaging 0.97
R4989:Ehmt1 UTSW 2 24,767,509 (GRCm39) missense probably damaging 1.00
R5040:Ehmt1 UTSW 2 24,774,316 (GRCm39) missense probably benign 0.19
R5110:Ehmt1 UTSW 2 24,742,802 (GRCm39) missense probably benign 0.01
R5133:Ehmt1 UTSW 2 24,767,509 (GRCm39) missense probably damaging 1.00
R5161:Ehmt1 UTSW 2 24,748,207 (GRCm39) missense possibly damaging 0.71
R5162:Ehmt1 UTSW 2 24,767,509 (GRCm39) missense probably damaging 1.00
R5183:Ehmt1 UTSW 2 24,767,509 (GRCm39) missense probably damaging 1.00
R5184:Ehmt1 UTSW 2 24,767,509 (GRCm39) missense probably damaging 1.00
R5208:Ehmt1 UTSW 2 24,691,545 (GRCm39) missense probably benign 0.34
R5309:Ehmt1 UTSW 2 24,774,207 (GRCm39) missense probably damaging 1.00
R5312:Ehmt1 UTSW 2 24,774,207 (GRCm39) missense probably damaging 1.00
R5837:Ehmt1 UTSW 2 24,753,926 (GRCm39) missense probably damaging 0.98
R5968:Ehmt1 UTSW 2 24,726,469 (GRCm39) missense probably damaging 0.99
R6539:Ehmt1 UTSW 2 24,694,779 (GRCm39) missense probably damaging 1.00
R6646:Ehmt1 UTSW 2 24,696,322 (GRCm39) missense probably damaging 0.99
R7065:Ehmt1 UTSW 2 24,730,709 (GRCm39) missense probably damaging 1.00
R7226:Ehmt1 UTSW 2 24,694,794 (GRCm39) missense probably damaging 1.00
R7361:Ehmt1 UTSW 2 24,746,713 (GRCm39) missense possibly damaging 0.94
R7373:Ehmt1 UTSW 2 24,809,585 (GRCm39) start codon destroyed probably null 0.03
R7410:Ehmt1 UTSW 2 24,738,080 (GRCm39) missense probably benign
R7418:Ehmt1 UTSW 2 24,774,646 (GRCm39) missense probably benign 0.02
R7633:Ehmt1 UTSW 2 24,705,792 (GRCm39) missense possibly damaging 0.68
R7716:Ehmt1 UTSW 2 24,774,511 (GRCm39) missense probably damaging 0.99
R7916:Ehmt1 UTSW 2 24,746,708 (GRCm39) missense probably damaging 1.00
R8112:Ehmt1 UTSW 2 24,753,396 (GRCm39) missense probably damaging 1.00
R8356:Ehmt1 UTSW 2 24,742,781 (GRCm39) missense probably benign
R8879:Ehmt1 UTSW 2 24,726,488 (GRCm39) missense possibly damaging 0.87
R9133:Ehmt1 UTSW 2 24,729,635 (GRCm39) missense possibly damaging 0.66
R9217:Ehmt1 UTSW 2 24,729,578 (GRCm39) missense probably benign 0.11
R9248:Ehmt1 UTSW 2 24,738,077 (GRCm39) missense possibly damaging 0.67
R9365:Ehmt1 UTSW 2 24,728,722 (GRCm39) missense probably damaging 1.00
R9439:Ehmt1 UTSW 2 24,715,030 (GRCm39) missense probably damaging 0.99
R9460:Ehmt1 UTSW 2 24,728,791 (GRCm39) missense probably benign
R9684:Ehmt1 UTSW 2 24,753,329 (GRCm39) missense possibly damaging 0.82
X0062:Ehmt1 UTSW 2 24,753,848 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCAGGAGAACAAAATCAGTGCC -3'
(R):5'- GGATGCGCTTTATTCCATTCAC -3'

Sequencing Primer
(F):5'- TCAGTGCCATAAAGTCTTAAGGGC -3'
(R):5'- ACCATCTACTTCTGCAGTCATC -3'
Posted On 2016-06-21