Incidental Mutation 'R8356:Ehmt1'
ID 660314
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 067870-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8356 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 24742781 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 466 (M466K)
Ref Sequence ENSEMBL: ENSMUSP00000119057 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably benign
Transcript: ENSMUST00000046227
AA Change: M466K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: M466K

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 benign
Transcript: ENSMUST00000091348
AA Change: M458K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: M458K

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 benign
Transcript: ENSMUST00000102938
AA Change: M459K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: M459K

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 benign
Transcript: ENSMUST00000114418
AA Change: M466K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: M466K

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 benign
Transcript: ENSMUST00000114432
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893

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 probably benign
Transcript: ENSMUST00000147147
AA Change: M466K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: M466K

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 benign
Transcript: ENSMUST00000150836
Predicted Effect probably benign
Transcript: ENSMUST00000152325
SMART Domains Protein: ENSMUSP00000123387
Gene: ENSMUSG00000036893

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 probably benign
Transcript: ENSMUST00000200655
Predicted Effect
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (58/58)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700069L16Rik T A 5: 113,861,868 (GRCm39) M1L unknown Het
Abcc9 A T 6: 142,536,096 (GRCm39) M1546K probably benign Het
Acbd3 T C 1: 180,553,881 (GRCm39) M72T probably benign Het
Adam6a T G 12: 113,509,757 (GRCm39) L710R probably benign Het
Aldh4a1 T C 4: 139,365,833 (GRCm39) S275P probably benign Het
Ap3d1 A T 10: 80,568,737 (GRCm39) L47Q probably damaging Het
Arhgap19 G A 19: 41,762,615 (GRCm39) R414C probably damaging Het
Ascc3 T C 10: 50,526,003 (GRCm39) S572P probably benign Het
Cdk10 G A 8: 123,955,096 (GRCm39) R78H probably benign Het
Celsr2 C T 3: 108,320,847 (GRCm39) R655H possibly damaging Het
Cntnap2 T A 6: 47,026,307 (GRCm39) H44Q probably benign Het
Cpped1 A T 16: 11,712,793 (GRCm39) C32* probably null Het
Ddi1 A G 9: 6,266,249 (GRCm39) V40A probably benign Het
Ddx50 T C 10: 62,457,287 (GRCm39) T588A probably benign Het
Degs2 A G 12: 108,658,223 (GRCm39) I252T possibly damaging Het
Dnah1 C T 14: 30,994,972 (GRCm39) V2762I probably benign Het
Dnah5 A G 15: 28,444,313 (GRCm39) D4037G probably benign Het
Dnah5 C T 15: 28,444,469 (GRCm39) A4089V probably null Het
Dthd1 A T 5: 63,007,081 (GRCm39) D594V probably damaging Het
Erich2 A T 2: 70,357,873 (GRCm39) probably null Het
Fam221b T C 4: 43,665,519 (GRCm39) D313G probably benign Het
Fbxl22 T C 9: 66,421,732 (GRCm39) D35G possibly damaging Het
Ggcx A G 6: 72,406,574 (GRCm39) E679G probably benign Het
Gm14295 A G 2: 176,501,307 (GRCm39) T266A probably benign Het
Hnrnpa1 A G 15: 103,150,529 (GRCm39) D160G probably null Het
Hnrnpul1 T C 7: 25,422,247 (GRCm39) probably benign Het
Hydin A G 8: 111,259,756 (GRCm39) E2576G possibly damaging Het
Ifit2 T A 19: 34,550,908 (GRCm39) C149* probably null Het
Il18rap T A 1: 40,564,084 (GRCm39) S67R probably benign Het
Kcnk4 T G 19: 6,903,668 (GRCm39) S294R probably benign Het
Kif21b A G 1: 136,100,683 (GRCm39) H1588R probably damaging Het
Klhl35 A T 7: 99,122,129 (GRCm39) S77C probably damaging Het
Lats2 A T 14: 57,934,867 (GRCm39) M228K probably damaging Het
Lrfn4 T C 19: 4,662,256 (GRCm39) D587G probably benign Het
Lrrd1 C A 5: 3,916,509 (GRCm39) T842K probably benign Het
Mafb G A 2: 160,208,125 (GRCm39) H158Y probably benign Het
Mapk8ip3 T A 17: 25,123,925 (GRCm39) E561D probably damaging Het
Mcemp1 A G 8: 3,717,542 (GRCm39) T158A probably damaging Het
Mst1r A T 9: 107,794,463 (GRCm39) E1214V probably damaging Het
Muc16 A G 9: 18,570,074 (GRCm39) I815T unknown Het
Ncoa6 T A 2: 155,248,172 (GRCm39) I1711L possibly damaging Het
Neo1 G A 9: 58,785,402 (GRCm39) T1408M probably damaging Het
Niban1 T A 1: 151,571,901 (GRCm39) V282D probably damaging Het
Nnt A C 13: 119,476,368 (GRCm39) F632C probably damaging Het
Nup210 G A 6: 91,051,330 (GRCm39) T351I probably benign Het
Or4f59 A G 2: 111,872,943 (GRCm39) S145P probably damaging Het
Or52e18 A G 7: 104,609,934 (GRCm39) S2P probably benign Het
P4ha1 C T 10: 59,191,185 (GRCm39) T364I probably damaging Het
Pcdhb11 T A 18: 37,555,252 (GRCm39) L194Q probably damaging Het
Pramel52-ps A G 5: 94,531,703 (GRCm39) K196E probably damaging Het
Rad51ap1 A G 6: 126,901,879 (GRCm39) probably null Het
Rbm11 G A 16: 75,397,694 (GRCm39) R208K probably benign Het
Rps6ka1 T A 4: 133,587,368 (GRCm39) Q535L possibly damaging Het
Slc26a3 A G 12: 31,516,505 (GRCm39) D621G probably benign Het
Sox10 T G 15: 79,040,652 (GRCm39) E296A probably damaging Het
St3gal4 A C 9: 34,964,438 (GRCm39) V188G probably damaging Het
Trim34a A T 7: 103,910,178 (GRCm39) I327F probably damaging Het
Ttc28 G A 5: 111,381,207 (GRCm39) D1240N probably benign Het
Zc2hc1c A G 12: 85,337,471 (GRCm39) E376G probably damaging Het
Zfp423 G A 8: 88,509,910 (GRCm39) P77S probably damaging Het
Zfp560 A T 9: 20,260,231 (GRCm39) S210R 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
R5134: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
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'- ATCAGGCTAACACGGAGAGC -3'
(R):5'- GAGAACTGGCCTCTAAATTAGAATG -3'

Sequencing Primer
(F):5'- CTAACACGGAGAGCTAGGCC -3'
(R):5'- GACAGCTTATGGGAGTAGATCTC -3'
Posted On 2021-01-18