Incidental Mutation 'IGL02740:Ehmt1'
ID 305885
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL02740
Quality Score
Status
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to A at 24705851 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000141460 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000152636]
AlphaFold Q5DW34
Predicted Effect probably benign
Transcript: ENSMUST00000046227
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893

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
SMART Domains Protein: ENSMUSP00000088906
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 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
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893

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
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893

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 noncoding transcript
Transcript: ENSMUST00000138805
Predicted Effect probably benign
Transcript: ENSMUST00000147147
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893

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: ENSMUST00000152636
SMART Domains Protein: ENSMUSP00000141460
Gene: ENSMUSG00000036893

DomainStartEndE-ValueType
ANK 118 147 1.3e-7 SMART
ANK 151 182 2e-7 SMART
Coding Region Coverage
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 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
Als2 C T 1: 59,209,078 (GRCm39) E1494K probably benign Het
Antxr2 A G 5: 98,178,251 (GRCm39) probably benign Het
Arhgap23 A C 11: 97,365,843 (GRCm39) K998Q probably damaging Het
Bap1 A G 14: 30,978,729 (GRCm39) N47D possibly damaging Het
Carmil1 A G 13: 24,278,501 (GRCm39) I156T probably damaging Het
Ccdc141 T C 2: 76,884,953 (GRCm39) T563A probably benign Het
Cct7 T C 6: 85,445,252 (GRCm39) F501S probably benign Het
Cd59b A G 2: 103,909,242 (GRCm39) I8V probably benign Het
Cep135 T C 5: 76,786,115 (GRCm39) probably null Het
Cep170 T G 1: 176,621,166 (GRCm39) T4P probably damaging Het
Chaf1a G T 17: 56,374,500 (GRCm39) G896W probably damaging Het
Cpt1b A T 15: 89,308,535 (GRCm39) L131Q probably damaging Het
Dcaf13 C T 15: 39,008,495 (GRCm39) R366* probably null Het
Ddr2 A T 1: 169,812,514 (GRCm39) N659K probably damaging Het
Dmrt2 C A 19: 25,655,837 (GRCm39) L479I possibly damaging Het
Dnah10 A G 5: 124,903,927 (GRCm39) probably benign Het
Dsg3 C T 18: 20,660,765 (GRCm39) T368M possibly damaging Het
Dspp C A 5: 104,325,104 (GRCm39) S489* probably null Het
Eed A C 7: 89,621,464 (GRCm39) V112G possibly damaging Het
Elavl3 T C 9: 21,947,675 (GRCm39) D89G probably benign Het
Ercc5 T C 1: 44,206,652 (GRCm39) S522P probably benign Het
Esrrg T C 1: 187,930,938 (GRCm39) L320P probably benign Het
Gadl1 T A 9: 115,835,629 (GRCm39) Y352* probably null Het
Gemin5 G A 11: 58,042,390 (GRCm39) A477V probably damaging Het
Gm3086 A T 12: 70,016,095 (GRCm39) probably benign Het
Gm8082 C T 14: 42,846,570 (GRCm39) probably benign Het
Gpr180 T C 14: 118,377,161 (GRCm39) L54P probably damaging Het
Gpsm1 G A 2: 26,230,585 (GRCm39) V512M probably benign Het
Ighv5-4 A G 12: 113,561,100 (GRCm39) S107P probably damaging Het
Irak4 T C 15: 94,464,925 (GRCm39) *460Q probably null Het
Nfkbiz G T 16: 55,638,317 (GRCm39) T381N probably benign Het
Or1e25 A T 11: 73,493,657 (GRCm39) N84Y probably benign Het
Or5d39 T A 2: 87,979,601 (GRCm39) H254L probably damaging Het
Or8b46 T C 9: 38,450,226 (GRCm39) F12L probably damaging Het
Or8g23 T C 9: 38,971,585 (GRCm39) I126V probably benign Het
Pou2f1 G A 1: 165,710,685 (GRCm39) Q523* probably null Het
Ptcra A G 17: 47,069,473 (GRCm39) S133P probably damaging Het
Ptgfrn A T 3: 100,980,253 (GRCm39) D362E possibly damaging Het
Rbm33 A T 5: 28,536,121 (GRCm39) D19V probably damaging Het
Rnf4 T A 5: 34,506,898 (GRCm39) V74D possibly damaging Het
Rprd1b A G 2: 157,889,899 (GRCm39) D7G probably damaging Het
Rrp1b A G 17: 32,278,305 (GRCm39) T659A probably damaging Het
Scaf11 T C 15: 96,316,883 (GRCm39) N894D probably benign Het
Scn1a G A 2: 66,155,106 (GRCm39) R618C probably damaging Het
Scn1a A T 2: 66,148,421 (GRCm39) D1041E probably benign Het
Slc43a1 G T 2: 84,690,094 (GRCm39) A424S probably damaging Het
Sprtn T C 8: 125,625,042 (GRCm39) L49P probably damaging Het
Sv2a G T 3: 96,092,723 (GRCm39) R141L possibly damaging Het
Thsd7b C T 1: 129,540,864 (GRCm39) S246F probably damaging Het
Tmem117 A T 15: 94,612,863 (GRCm39) D133V probably benign Het
Tnn A T 1: 159,968,347 (GRCm39) probably benign Het
Triobp G A 15: 78,850,889 (GRCm39) V348I probably benign Het
Trps1 A T 15: 50,709,935 (GRCm39) D134E probably damaging Het
Ttn T C 2: 76,598,162 (GRCm39) I19584V probably benign Het
Uqcrfs1 T C 13: 30,725,006 (GRCm39) H178R probably damaging Het
Ush2a A T 1: 188,380,585 (GRCm39) Q2298L possibly damaging Het
Vmn2r67 A G 7: 84,785,818 (GRCm39) I729T probably damaging Het
Vmn2r79 A T 7: 86,653,366 (GRCm39) M544L probably benign Het
Vps41 T A 13: 19,022,850 (GRCm39) L404Q probably damaging Het
Xrcc5 T G 1: 72,379,240 (GRCm39) probably null Het
Zfp735 A G 11: 73,601,412 (GRCm39) K119E possibly damaging 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
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
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
Posted On 2015-04-16