Incidental Mutation 'R2393:Ehmt1'
ID 247845
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 040361-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2393 (G1)
Quality Score 126
Status Validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 24696229 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glycine at position 953 (V953G)
Ref Sequence ENSEMBL: ENSMUSP00000119057 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000152636]
AlphaFold Q5DW34
Predicted Effect probably damaging
Transcript: ENSMUST00000046227
AA Change: V905G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: V905G

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: V945G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: V945G

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: V946G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: V946G

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: V905G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: V905G

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: V900G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: V900G

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 unknown
Transcript: ENSMUST00000134775
AA Change: V46G
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138805
Predicted Effect probably damaging
Transcript: ENSMUST00000147147
AA Change: V953G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: V953G

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 noncoding transcript
Transcript: ENSMUST00000144672
Predicted Effect probably benign
Transcript: ENSMUST00000152636
SMART Domains Protein: ENSMUSP00000141460
Gene: ENSMUSG00000036893

DomainStartEndE-ValueType
ANK 118 147 1.3e-7 SMART
ANK 151 182 2e-7 SMART
Meta Mutation Damage Score 0.6213 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.7%
Validation Efficiency 100% (54/54)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 T A 11: 9,225,057 (GRCm39) L512* probably null Het
Adam4 A T 12: 81,467,485 (GRCm39) F379I probably benign Het
Ano6 C G 15: 95,863,906 (GRCm39) probably benign Het
Apc2 A G 10: 80,148,903 (GRCm39) E1319G possibly damaging Het
Arfgef3 A G 10: 18,473,535 (GRCm39) V1588A possibly damaging Het
Arl8a T A 1: 135,080,604 (GRCm39) V93E probably damaging Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Cd200r2 T A 16: 44,729,630 (GRCm39) I95N probably damaging Het
Cd209d A G 8: 3,928,436 (GRCm39) probably null Het
Cep290 A G 10: 100,397,100 (GRCm39) probably null Het
Chd2 G T 7: 73,157,631 (GRCm39) D171E possibly damaging Het
Chrna7 G A 7: 62,748,994 (GRCm39) A496V probably damaging Het
Col9a2 C G 4: 120,911,455 (GRCm39) R599G probably damaging Het
Colgalt1 C G 8: 72,076,385 (GRCm39) T612S probably benign Het
Copg2 T C 6: 30,787,893 (GRCm39) K602E probably benign Het
Crtc1 T A 8: 70,840,808 (GRCm39) T473S probably benign Het
Ctbp2 A T 7: 132,625,290 (GRCm39) probably null Het
Edem1 T G 6: 108,829,504 (GRCm39) M541R probably damaging Het
Fabp3 C T 4: 130,206,180 (GRCm39) T57I probably benign Het
Fgfr2 T C 7: 129,828,968 (GRCm39) probably null Het
Focad A G 4: 88,039,567 (GRCm39) D10G probably damaging Het
Gfus G T 15: 75,798,200 (GRCm39) L191I probably damaging Het
Gm5901 G T 7: 105,026,996 (GRCm39) V255F possibly damaging Het
Hsp90aa1 T C 12: 110,659,840 (GRCm39) N416S probably damaging Het
Hspb1 T C 5: 135,917,950 (GRCm39) F142L probably benign Het
Il17re C T 6: 113,439,314 (GRCm39) H75Y possibly damaging Het
Kctd3 A G 1: 188,713,568 (GRCm39) I389T probably damaging Het
Lhx6 T C 2: 35,981,402 (GRCm39) D63G probably benign Het
Mepe A G 5: 104,485,327 (GRCm39) T156A possibly damaging Het
Met A G 6: 17,534,197 (GRCm39) Y680C probably damaging Het
Mrgpra3 T C 7: 47,239,365 (GRCm39) Y187C possibly damaging Het
Mst1 T G 9: 107,960,151 (GRCm39) probably null Het
Myh13 T A 11: 67,231,184 (GRCm39) S394T possibly damaging Het
Nbeal1 T A 1: 60,290,529 (GRCm39) V1042E probably damaging Het
Ndrg4 T A 8: 96,432,839 (GRCm39) Y15* probably null Het
Neurl4 G A 11: 69,797,900 (GRCm39) R720H probably damaging Het
Nfkbia A G 12: 55,537,455 (GRCm39) probably benign Het
Nwd1 T A 8: 73,389,055 (GRCm39) M202K probably benign Het
Or10d4 G T 9: 39,580,569 (GRCm39) C72F possibly damaging Het
Or2av9 T A 11: 58,381,546 (GRCm39) I12F probably benign Het
Pate2 T C 9: 35,581,036 (GRCm39) probably benign Het
Pibf1 A G 14: 99,480,368 (GRCm39) T715A probably benign Het
Pitpnm1 T C 19: 4,160,935 (GRCm39) L858P probably benign Het
Pla2g3 A C 11: 3,443,115 (GRCm39) S483R probably benign Het
Rad51ap2 T A 12: 11,507,798 (GRCm39) D573E probably damaging Het
Rho T C 6: 115,912,352 (GRCm39) probably benign Het
Rpl39l A T 16: 9,992,328 (GRCm39) *52L probably null Het
Slco1a5 T A 6: 142,194,501 (GRCm39) R381W possibly damaging Het
Spns3 T A 11: 72,441,059 (GRCm39) probably benign Het
Srgap2 A G 1: 131,259,872 (GRCm39) S493P probably benign Het
Tecpr2 T C 12: 110,892,836 (GRCm39) S293P probably damaging Het
Ttn C T 2: 76,583,211 (GRCm39) V20815M probably benign Het
Ushbp1 T C 8: 71,847,132 (GRCm39) I167V probably benign Het
Wdr81 C T 11: 75,340,231 (GRCm39) A1296T probably damaging Het
Zmym2 A G 14: 57,158,180 (GRCm39) Y573C 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
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
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'- TTCAACTAAGAATGTGGGTGGG -3'
(R):5'- GCCAGAAACCATCTTCACTGGG -3'

Sequencing Primer
(F):5'- ACTAAGAATGTGGGTGGGTTTGTTTG -3'
(R):5'- AGAAACCATCTTCACTGGGTTCTC -3'
Posted On 2014-11-11