Incidental Mutation 'R7373:Ehmt1'
ID 572199
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 045456-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7373 (G1)
Quality Score 102.008
Status Not validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation start codon destroyed
DNA Base Change (assembly) A to G at 24809585 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 1 (M1T)
Ref Sequence ENSEMBL: ENSMUSP00000119057 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000150379] [ENSMUST00000152161] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably null
Transcript: ENSMUST00000046227
AA Change: M1T

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: M1T

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 null
Transcript: ENSMUST00000091348
AA Change: M1T

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: M1T

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 null
Transcript: ENSMUST00000102938
AA Change: M1T

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: M1T

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 null
Transcript: ENSMUST00000114432
AA Change: M1T

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: M1T

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 null
Transcript: ENSMUST00000147147
AA Change: M1T

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: M1T

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 null
Transcript: ENSMUST00000150379
AA Change: M1T

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)
Predicted Effect probably null
Transcript: ENSMUST00000152161
AA Change: M1T

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000119854
Gene: ENSMUSG00000036893
AA Change: M1T

DomainStartEndE-ValueType
low complexity region 339 358 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000200655
AA Change: M1T
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 98% (57/58)
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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts2 G A 11: 50,686,262 (GRCm39) A1027T probably benign Het
Aldh7a1 G A 18: 56,675,389 (GRCm39) T260M possibly damaging Het
Anks3 T C 16: 4,773,735 (GRCm39) Y187C probably benign Het
Atp2c2 A T 8: 120,456,991 (GRCm39) I198F probably benign Het
Bsn T C 9: 107,990,683 (GRCm39) T1690A probably damaging Het
Catsper3 T C 13: 55,955,945 (GRCm39) I350T possibly damaging Het
Cdcp1 C T 9: 123,006,965 (GRCm39) R594H probably damaging Het
Cfap57 C T 4: 118,472,128 (GRCm39) V84I probably benign Het
Cldn1 G T 16: 26,179,606 (GRCm39) P154T probably damaging Het
Cntnap5a A T 1: 116,508,367 (GRCm39) N1293I probably benign Het
Cpsf4l C T 11: 113,590,657 (GRCm39) probably null Het
Crybg1 T C 10: 43,880,136 (GRCm39) T351A probably benign Het
Csmd1 T C 8: 16,042,713 (GRCm39) N2340S probably damaging Het
Dennd4a C A 9: 64,804,551 (GRCm39) Q1297K probably benign Het
Dll3 A G 7: 27,994,057 (GRCm39) V460A probably benign Het
Dnah8 T C 17: 30,986,939 (GRCm39) probably null Het
Dst G T 1: 34,227,472 (GRCm39) L1688F probably benign Het
Fasn A T 11: 120,704,802 (GRCm39) L1261Q possibly damaging Het
Fat1 A G 8: 45,479,702 (GRCm39) D2916G probably damaging Het
Fgfr3 C A 5: 33,885,034 (GRCm39) F49L probably benign Het
Hlx T C 1: 184,463,062 (GRCm39) T197A probably benign Het
Hormad1 A T 3: 95,483,628 (GRCm39) T147S probably damaging Het
Igf1r T A 7: 67,844,826 (GRCm39) Y866* probably null Het
Itgb8 A G 12: 119,166,210 (GRCm39) V107A probably benign Het
Kat2a C T 11: 100,599,392 (GRCm39) A533T probably benign Het
Kif20b T C 19: 34,913,071 (GRCm39) L328P probably damaging Het
Lims1 T C 10: 58,245,442 (GRCm39) F157S probably damaging Het
Lrp2 G T 2: 69,331,036 (GRCm39) H1673Q probably damaging Het
Lrrc46 C A 11: 96,929,706 (GRCm39) M43I probably benign Het
Lrrk2 T C 15: 91,584,207 (GRCm39) probably null Het
Meox2 A T 12: 37,158,797 (GRCm39) probably benign Het
Mff A G 1: 82,714,838 (GRCm39) probably null Het
Mfsd5 T A 15: 102,189,427 (GRCm39) F266L probably damaging Het
Miga2 A G 2: 30,272,083 (GRCm39) T468A probably damaging Het
Mmel1 T A 4: 154,973,665 (GRCm39) L316Q not run Het
Ndufa9 C A 6: 126,811,421 (GRCm39) G232C probably damaging Het
Obox2 A T 7: 15,131,145 (GRCm39) K84* probably null Het
Or4f58 T A 2: 111,851,787 (GRCm39) R137S probably benign Het
Or51a39 T A 7: 102,363,306 (GRCm39) I105F possibly damaging Het
Otogl G T 10: 107,737,112 (GRCm39) Q101K probably damaging Het
Pcnx2 C T 8: 126,534,766 (GRCm39) V1288M probably damaging Het
Pde10a T A 17: 9,161,824 (GRCm39) W220R probably benign Het
Recql5 T C 11: 115,819,198 (GRCm39) T123A possibly damaging Het
Rpl28 T C 7: 4,796,602 (GRCm39) V61A probably benign Het
Secisbp2l A T 2: 125,599,191 (GRCm39) M494K probably damaging Het
Sh3bgr G A 16: 96,007,035 (GRCm39) E2K unknown Het
Shcbp1l C A 1: 153,300,986 (GRCm39) T6K probably benign Het
Slc22a15 A C 3: 101,785,213 (GRCm39) L353R possibly damaging Het
Sqle T C 15: 59,189,658 (GRCm39) I100T probably benign Het
Tas2r106 A T 6: 131,655,317 (GRCm39) L178H probably damaging Het
Tll1 A T 8: 64,504,391 (GRCm39) N668K probably damaging Het
Tm7sf2 A G 19: 6,116,676 (GRCm39) S118P probably benign Het
Tmco5 G T 2: 116,717,226 (GRCm39) V169L probably benign Het
Trpv1 A G 11: 73,131,499 (GRCm39) K346E probably damaging Het
Ttk G A 9: 83,736,930 (GRCm39) R463H probably benign Het
Vmn2r120 G T 17: 57,816,406 (GRCm39) L650I probably benign Het
Vmn2r58 C T 7: 41,487,212 (GRCm39) C561Y probably damaging Het
Vmn2r-ps117 A T 17: 19,044,948 (GRCm39) Q455L probably benign Het
Zfr T A 15: 12,140,645 (GRCm39) S231T unknown 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
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'- AAAGATGGTGCCACGCTCTC -3'
(R):5'- GGTTGAATTTCAGCGCGCAG -3'

Sequencing Primer
(F):5'- AGTTGGCCCGGTCCACTTTG -3'
(R):5'- TGCTCACGCAGGCGCAGGA -3'
Posted On 2019-09-13