Incidental Mutation 'R1800:Ehmt1'
ID 203006
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 039830-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1800 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 24774302 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 43 (S43R)
Ref Sequence ENSEMBL: ENSMUSP00000143189 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000152161] [ENSMUST00000198923] [ENSMUST00000150379] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably damaging
Transcript: ENSMUST00000046227
AA Change: S167R

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: S167R

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: S166R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: S166R

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: S167R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: S167R

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: S167R

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: S167R

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: S167R

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: S167R

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 probably damaging
Transcript: ENSMUST00000147147
AA Change: S167R

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: S167R

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 possibly damaging
Transcript: ENSMUST00000152161
AA Change: S166R

PolyPhen 2 Score 0.926 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000119854
Gene: ENSMUSG00000036893
AA Change: S166R

DomainStartEndE-ValueType
low complexity region 339 358 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000198923
AA Change: S43R

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000143189
Gene: ENSMUSG00000036893
AA Change: S43R

DomainStartEndE-ValueType
low complexity region 208 227 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000150379
AA Change: S169R

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
Predicted Effect probably benign
Transcript: ENSMUST00000200655
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.0%
  • 20x: 91.2%
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: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,772,479 (GRCm39) K556R probably damaging Het
4933406P04Rik A T 10: 20,186,893 (GRCm39) probably benign Het
Acmsd C A 1: 127,687,493 (GRCm39) Y258* probably null Het
Adgrf5 A T 17: 43,761,973 (GRCm39) I1223F probably damaging Het
Afp C T 5: 90,638,655 (GRCm39) P6S probably benign Het
Agap2 C A 10: 126,927,540 (GRCm39) H1120Q probably damaging Het
Angpt1 A G 15: 42,375,800 (GRCm39) V152A probably damaging Het
Ankrd1 A T 19: 36,096,759 (GRCm39) F23I probably damaging Het
Armc12 T C 17: 28,757,869 (GRCm39) S334P possibly damaging Het
Arnt2 C A 7: 83,924,583 (GRCm39) D415Y probably damaging Het
Cacna1s G T 1: 136,004,592 (GRCm39) V131L probably benign Het
Cacna2d2 T C 9: 107,404,632 (GRCm39) V1141A possibly damaging Het
Cfap61 T C 2: 145,884,542 (GRCm39) L580P probably damaging Het
Chga A T 12: 102,522,164 (GRCm39) S23C probably damaging Het
Chrna5 A G 9: 54,912,159 (GRCm39) T320A probably damaging Het
Col17a1 G T 19: 47,639,301 (GRCm39) N1081K possibly damaging Het
Cox7b2 A T 5: 71,600,406 (GRCm39) C51S possibly damaging Het
Cstdc3 T A 16: 36,132,895 (GRCm39) D57E probably damaging Het
Cwc22 A T 2: 77,759,797 (GRCm39) D83E possibly damaging Het
D130043K22Rik A C 13: 25,067,877 (GRCm39) D871A probably damaging Het
Dab2 A T 15: 6,464,948 (GRCm39) M361L probably benign Het
Dnah11 A C 12: 117,880,523 (GRCm39) Y3866D probably damaging Het
Dnmbp A G 19: 43,890,159 (GRCm39) I536T probably benign Het
Ercc5 T C 1: 44,212,540 (GRCm39) L666P probably benign Het
F5 A G 1: 164,010,403 (GRCm39) H378R probably damaging Het
Fat2 A T 11: 55,174,718 (GRCm39) N1998K probably damaging Het
Fbxo28 T C 1: 182,169,099 (GRCm39) D13G unknown Het
Fras1 T C 5: 96,857,741 (GRCm39) S2012P probably benign Het
Gm5624 T A 14: 44,799,302 (GRCm39) N41I probably damaging Het
Gm8104 A G 14: 42,959,028 (GRCm39) I73V possibly damaging Het
Gpr141b T C 13: 19,913,849 (GRCm39) noncoding transcript Het
Gpr68 G A 12: 100,845,167 (GRCm39) P126S probably damaging Het
Gucy1a2 A T 9: 3,582,685 (GRCm39) T156S possibly damaging Het
Hacl1 T A 14: 31,336,221 (GRCm39) Y429F probably damaging Het
Haus3 A C 5: 34,320,916 (GRCm39) L510R probably damaging Het
Helq C T 5: 100,921,990 (GRCm39) G738D probably benign Het
Hsd3b2 G C 3: 98,619,553 (GRCm39) P131A probably damaging Het
Il22ra1 G T 4: 135,475,471 (GRCm39) C247F probably benign Het
Ivl T C 3: 92,479,891 (GRCm39) E58G unknown Het
Kcnk9 G T 15: 72,417,948 (GRCm39) Q61K probably benign Het
Kremen1 CGGG CGGGGGG 11: 5,151,791 (GRCm39) probably benign Het
Loxhd1 G T 18: 77,490,198 (GRCm39) A1314S probably damaging Het
Lratd1 T C 12: 14,200,226 (GRCm39) Y167C probably damaging Het
Lrba A G 3: 86,259,175 (GRCm39) I1397V probably benign Het
Lrig3 T A 10: 125,832,920 (GRCm39) probably null Het
Lrrc36 A G 8: 106,176,397 (GRCm39) D378G probably damaging Het
Lrrc49 G A 9: 60,505,474 (GRCm39) T527I probably damaging Het
Map4k4 C A 1: 40,062,620 (GRCm39) T1195K probably damaging Het
Mrps33 G A 6: 39,779,429 (GRCm39) R89C probably damaging Het
Mtor T C 4: 148,547,349 (GRCm39) V444A probably benign Het
Myh2 A G 11: 67,079,764 (GRCm39) E1046G probably damaging Het
Myo15b G T 11: 115,771,335 (GRCm39) probably null Het
Myo5c T C 9: 75,153,446 (GRCm39) Y111H probably damaging Het
Ncoa4-ps A T 12: 119,225,506 (GRCm39) noncoding transcript Het
Ndufv2 G C 17: 66,390,481 (GRCm39) T163R probably damaging Het
Nf1 A G 11: 79,444,794 (GRCm39) N373S possibly damaging Het
Nwd2 A G 5: 63,962,917 (GRCm39) M834V probably benign Het
Ogfod2 T C 5: 124,253,019 (GRCm39) V343A probably damaging Het
Or11g2 C T 14: 50,856,143 (GRCm39) L155F probably benign Het
Or11j4 C A 14: 50,630,786 (GRCm39) S191* probably null Het
Or3a1b A T 11: 74,012,234 (GRCm39) T40S probably benign Het
Or4c115 T A 2: 88,928,050 (GRCm39) T74S probably benign Het
Or51ag1 T C 7: 103,155,248 (GRCm39) I302V possibly damaging Het
Or52ab2 T A 7: 102,969,621 (GRCm39) M1K probably null Het
Or8g34 A T 9: 39,373,410 (GRCm39) I228F probably damaging Het
Parp1 T A 1: 180,428,091 (GRCm39) probably null Het
Ppp3ca A T 3: 136,640,792 (GRCm39) I448F probably damaging Het
Prss44 T C 9: 110,646,272 (GRCm39) V333A probably damaging Het
Pxk C T 14: 8,151,507 (GRCm38) R441* probably null Het
Rars1 A C 11: 35,716,822 (GRCm39) D231E probably benign Het
Rfc1 T C 5: 65,421,722 (GRCm39) Y1059C probably damaging Het
Rilpl1 T A 5: 124,652,719 (GRCm39) I2F probably damaging Het
Sarm1 G T 11: 78,381,820 (GRCm39) A221E possibly damaging Het
Serpina3f A G 12: 104,183,665 (GRCm39) T176A probably damaging Het
Slc22a20 T C 19: 6,035,695 (GRCm39) E131G probably benign Het
Slc26a11 T C 11: 119,263,979 (GRCm39) V343A probably damaging Het
Slc2a4 A G 11: 69,837,133 (GRCm39) I9T probably benign Het
Slc39a6 G T 18: 24,718,259 (GRCm39) D599E probably damaging Het
Slc5a6 G T 5: 31,198,020 (GRCm39) S285* probably null Het
Spata9 A G 13: 76,125,760 (GRCm39) H81R probably benign Het
St7l A G 3: 104,826,812 (GRCm39) E436G probably damaging Het
Tecrl A G 5: 83,427,077 (GRCm39) I357T probably damaging Het
Thop1 C T 10: 80,909,043 (GRCm39) R25C probably damaging Het
Tmprss12 A G 15: 100,190,428 (GRCm39) E266G probably benign Het
Tpgs1 T A 10: 79,511,344 (GRCm39) V162D possibly damaging Het
Trpa1 C T 1: 14,944,648 (GRCm39) R1032Q probably benign Het
Tspan12 A G 6: 21,795,699 (GRCm39) Y164H probably damaging Het
Ubr4 T C 4: 139,135,274 (GRCm39) Y869H probably damaging Het
Vmn1r21 A G 6: 57,820,799 (GRCm39) I215T probably benign Het
Zan A T 5: 137,384,713 (GRCm39) S5104T unknown Het
Zfp318 T C 17: 46,722,980 (GRCm39) V1661A probably benign Het
Zfp365 C T 10: 67,724,772 (GRCm39) R372K probably 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
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
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
Predicted Primers PCR Primer
(F):5'- ACCTGGCTTTGCTGTTCATATG -3'
(R):5'- CACAGCTGACGACTTCATGC -3'

Sequencing Primer
(F):5'- AGCTACTTATTGATGACTACTGCC -3'
(R):5'- TGACGACTTCATGCAGACATCTG -3'
Posted On 2014-06-23