Incidental Mutation 'IGL01403:Ehmt1'
ID 79699
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 # IGL01403
Quality Score
Status
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 24729638 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 633 (T633I)
Ref Sequence ENSEMBL: ENSMUSP00000088906 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000200655] [ENSMUST00000152636]
AlphaFold Q5DW34
Predicted Effect probably benign
Transcript: ENSMUST00000046227
AA Change: T593I

PolyPhen 2 Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: T593I

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 possibly damaging
Transcript: ENSMUST00000091348
AA Change: T633I

PolyPhen 2 Score 0.809 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: T633I

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: T634I

PolyPhen 2 Score 0.071 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: T634I

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: T593I

PolyPhen 2 Score 0.071 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: T593I

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
AA Change: T588I

PolyPhen 2 Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: T588I

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 possibly damaging
Transcript: ENSMUST00000147147
AA Change: T641I

PolyPhen 2 Score 0.660 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: T641I

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: ENSMUST00000200655
Predicted Effect probably benign
Transcript: ENSMUST00000150836
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 A T 12: 118,836,602 (GRCm39) L1103Q probably damaging Het
Adam12 T A 7: 133,521,339 (GRCm39) Q605L probably benign Het
Adk A G 14: 21,284,983 (GRCm39) K102R probably damaging Het
Afdn C T 17: 14,124,132 (GRCm39) P1761S probably damaging Het
Ascc1 A G 10: 59,848,280 (GRCm39) probably benign Het
Aspdh A G 7: 44,115,983 (GRCm39) probably null Het
Bbx T C 16: 50,022,876 (GRCm39) I753V probably benign Het
Ccdc33 T C 9: 58,024,668 (GRCm39) Y186C probably damaging Het
Ccdc78 T A 17: 26,007,218 (GRCm39) probably null Het
Ckmt1 T C 2: 121,193,447 (GRCm39) probably benign Het
Csf1r A G 18: 61,247,897 (GRCm39) T322A probably benign Het
Dnah7b T C 1: 46,155,460 (GRCm39) probably benign Het
Dr1 A G 5: 108,417,576 (GRCm39) N41D possibly damaging Het
Fgf7 T A 2: 125,877,860 (GRCm39) Y76N probably damaging Het
Hmcn1 A T 1: 150,468,848 (GRCm39) W5038R probably damaging Het
Ighv14-1 A G 12: 113,895,862 (GRCm39) V21A probably damaging Het
Igkv5-37 T A 6: 69,940,420 (GRCm39) I75F probably damaging Het
Inhbc T A 10: 127,205,968 (GRCm39) I100F probably damaging Het
Irs3 A G 5: 137,643,581 (GRCm39) F68L probably damaging Het
Itpr3 T A 17: 27,337,569 (GRCm39) C2460S probably damaging Het
Krt34 A G 11: 99,929,116 (GRCm39) C365R possibly damaging Het
Krt81 G A 15: 101,361,269 (GRCm39) H104Y probably benign Het
Ly6g A G 15: 75,030,497 (GRCm39) N82S probably damaging Het
Mrpl58 A T 11: 115,297,404 (GRCm39) I72F probably damaging Het
Myo9a G A 9: 59,778,846 (GRCm39) R1534H probably damaging Het
Npat T A 9: 53,466,429 (GRCm39) F239L probably benign Het
Nsd2 A G 5: 34,042,722 (GRCm39) probably benign Het
Nuggc T C 14: 65,860,635 (GRCm39) V427A probably benign Het
Or52b1 G A 7: 104,978,605 (GRCm39) R265C probably benign Het
Or5p55 A G 7: 107,566,828 (GRCm39) T75A possibly damaging Het
Pde4a A T 9: 21,116,412 (GRCm39) I467F probably damaging Het
Pkhd1l1 T A 15: 44,347,229 (GRCm39) C198* probably null Het
Pla2r1 A G 2: 60,254,632 (GRCm39) V1312A probably damaging Het
Pola2 T C 19: 6,009,121 (GRCm39) H79R probably benign Het
Potefam1 T C 2: 111,059,515 (GRCm39) probably benign Het
Pramel15 A T 4: 144,103,703 (GRCm39) M141K probably benign Het
Psen2 A T 1: 180,062,548 (GRCm39) probably benign Het
Rnf213 A G 11: 119,334,126 (GRCm39) K3112E probably damaging Het
Slc6a4 G T 11: 76,922,498 (GRCm39) V630L probably benign Het
Smg1 A T 7: 117,757,355 (GRCm39) probably benign Het
Tmc8 A G 11: 117,681,900 (GRCm39) T510A possibly damaging Het
Usp18 T A 6: 121,245,627 (GRCm39) H334Q possibly damaging Het
Vmn2r103 T C 17: 20,013,229 (GRCm39) Y117H probably benign Het
Vps13b T A 15: 35,709,625 (GRCm39) D1857E probably benign Het
Other mutations in Ehmt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00481:Ehmt1 APN 2 24,728,830 (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
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 2013-11-05