Incidental Mutation 'R7226:Ehmt1'
ID 562134
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 045298-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7226 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 24694794 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 1051 (D1051G)
Ref Sequence ENSEMBL: ENSMUSP00000119057 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000152636]
AlphaFold Q5DW34
Predicted Effect possibly damaging
Transcript: ENSMUST00000046227
AA Change: D1003G

PolyPhen 2 Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: D1003G

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: D1043G

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: D1043G

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 possibly damaging
Transcript: ENSMUST00000102938
AA Change: D1044G

PolyPhen 2 Score 0.935 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: D1044G

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 possibly damaging
Transcript: ENSMUST00000114418
AA Change: D1003G

PolyPhen 2 Score 0.935 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: D1003G

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: ENSMUST00000114432
AA Change: D998G

PolyPhen 2 Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: D998G

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: ENSMUST00000134775
Predicted Effect probably damaging
Transcript: ENSMUST00000147147
AA Change: D1051G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: D1051G

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
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700025B11Rik C T 15: 77,443,189 (GRCm39) V17I unknown Het
Acad8 T A 9: 26,889,726 (GRCm39) K323* probably null Het
Adam18 A T 8: 25,137,824 (GRCm39) C339S probably damaging Het
Anxa7 A G 14: 20,510,263 (GRCm39) F396L probably damaging Het
Ap2m1 T A 16: 20,358,201 (GRCm39) V73D probably damaging Het
Asic2 A T 11: 80,862,340 (GRCm39) I270N probably damaging Het
Atrn T G 2: 130,828,664 (GRCm39) C1070G probably damaging Het
Bag6 A G 17: 35,361,921 (GRCm39) N517S unknown Het
Bhmt1b A G 18: 87,775,590 (GRCm39) D371G possibly damaging Het
Bltp3b A T 10: 89,644,503 (GRCm39) Q1181L probably benign Het
Cavin1 A C 11: 100,861,284 (GRCm39) D3E probably benign Het
Cc2d2b T C 19: 40,779,751 (GRCm39) L571P unknown Het
Ccbe1 A T 18: 66,216,199 (GRCm39) C175S probably damaging Het
Cd19 A G 7: 126,013,995 (GRCm39) L5P unknown Het
Cd46 A G 1: 194,724,314 (GRCm39) S362P possibly damaging Het
Celf5 A G 10: 81,303,863 (GRCm39) S198P probably damaging Het
Cep170b A G 12: 112,704,359 (GRCm39) R706G possibly damaging Het
Chd3 G T 11: 69,260,037 (GRCm39) R61S unknown Het
Cpsf6 A C 10: 117,197,727 (GRCm39) W253G unknown Het
Cyp27a1 G A 1: 74,776,507 (GRCm39) G481D probably damaging Het
Ddr1 C T 17: 36,002,039 (GRCm39) D218N possibly damaging Het
Dhx34 A T 7: 15,932,801 (GRCm39) V1046D probably damaging Het
Dhx9 A T 1: 153,341,423 (GRCm39) D608E probably benign Het
Dnajc6 C A 4: 101,496,569 (GRCm39) A912E probably damaging Het
Fam217b C A 2: 178,062,996 (GRCm39) A320E probably benign Het
Farsa T A 8: 85,590,689 (GRCm39) I169N probably benign Het
Fbn2 A G 18: 58,170,142 (GRCm39) C2210R probably damaging Het
Fbxo3 T A 2: 103,880,642 (GRCm39) S251T probably benign Het
Fer1l6 C T 15: 58,462,384 (GRCm39) T813I probably benign Het
Ftl1-ps1 A T 13: 74,555,114 (GRCm39) E131V probably damaging Het
Gins3 T A 8: 96,364,499 (GRCm39) I83N probably damaging Het
Gja3 T C 14: 57,273,350 (GRCm39) T341A probably benign Het
Gja5 A G 3: 96,958,174 (GRCm39) Y77C probably damaging Het
Gm7247 A G 14: 51,602,808 (GRCm39) K48R probably damaging Het
Gsx2 C A 5: 75,236,621 (GRCm39) S67* probably null Het
H2-Q5 T A 17: 35,616,089 (GRCm39) L217Q Het
Impg2 T A 16: 56,087,467 (GRCm39) C1095* probably null Het
Itga7 G T 10: 128,776,801 (GRCm39) W222L probably damaging Het
Kdm2b T A 5: 123,059,512 (GRCm39) D530V possibly damaging Het
Klhdc8a A T 1: 132,230,344 (GRCm39) D153V probably damaging Het
Lin28a C T 4: 133,733,619 (GRCm39) G143S probably damaging Het
Memo1 A G 17: 74,509,338 (GRCm39) L227S probably damaging Het
Mettl27 T A 5: 134,964,657 (GRCm39) V138E probably damaging Het
Mov10 G T 3: 104,708,328 (GRCm39) L474I probably damaging Het
Nat10 T C 2: 103,557,098 (GRCm39) N852S probably benign Het
Nfkbie T C 17: 45,870,153 (GRCm39) V166A possibly damaging Het
Nktr T C 9: 121,575,599 (GRCm39) M369T probably damaging Het
Nlrp9a A T 7: 26,258,149 (GRCm39) N589I probably benign Het
Nrn1 G A 13: 36,914,577 (GRCm39) R8C probably benign Het
Nrsn1 A G 13: 25,437,451 (GRCm39) I159T probably damaging Het
Or1e29 A G 11: 73,667,503 (GRCm39) S217P possibly damaging Het
Or2h15 C T 17: 38,441,324 (GRCm39) G253D probably benign Het
Or5p61 A T 7: 107,758,164 (GRCm39) D305E probably benign Het
Or6c88 G A 10: 129,406,584 (GRCm39) G20D probably benign Het
Osbp T A 19: 11,956,031 (GRCm39) D385E probably benign Het
Pan3 T A 5: 147,463,802 (GRCm39) N547K probably damaging Het
Pip4p2 T A 4: 14,892,464 (GRCm39) D109E probably damaging Het
Pum1 C A 4: 130,499,292 (GRCm39) T1036K probably damaging Het
Rad54l2 C A 9: 106,590,671 (GRCm39) R485L probably damaging Het
Rps26 A T 10: 128,461,087 (GRCm39) F101I unknown Het
Sdsl T C 5: 120,598,702 (GRCm39) N138S probably benign Het
Slc28a2b C A 2: 122,353,013 (GRCm39) R453S probably benign Het
Slc39a6 A T 18: 24,717,084 (GRCm39) H649Q probably damaging Het
Snip1 T A 4: 124,965,273 (GRCm39) F226Y probably benign Het
Srrd T C 5: 112,485,322 (GRCm39) T334A unknown Het
St14 C T 9: 31,011,448 (GRCm39) D448N possibly damaging Het
Tmem270 T A 5: 134,930,538 (GRCm39) Q241L probably benign Het
Tubb4b T C 2: 25,114,180 (GRCm39) D41G probably benign Het
Usf3 T C 16: 44,040,368 (GRCm39) M1616T possibly damaging Het
Vmn2r95 A T 17: 18,672,245 (GRCm39) I733F possibly damaging Het
Zfp976 A T 7: 42,262,684 (GRCm39) C385* probably null 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
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'- TAGGGACACTTAGGGCCTTC -3'
(R):5'- CTGTCTTCCATGAGGCAGAAG -3'

Sequencing Primer
(F):5'- CTAGGAAAACTGGAGTCCTGCC -3'
(R):5'- TCTTCCATGAGGCAGAAGCTAAAG -3'
Posted On 2019-06-26