Incidental Mutation 'R2108:Ehmt1'
ID 232225
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 040112-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2108 (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 24727630 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 735 (S735T)
Ref Sequence ENSEMBL: ENSMUSP00000088906 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000152636] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably damaging
Transcript: ENSMUST00000046227
AA Change: S695T

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: S695T

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: ENSMUST00000091348
AA Change: S735T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: S735T

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 damaging
Transcript: ENSMUST00000102938
AA Change: S736T

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: S736T

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 damaging
Transcript: ENSMUST00000114418
AA Change: S695T

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: S695T

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: S690T

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: S690T

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: S743T

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: S743T

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 damaging
Transcript: ENSMUST00000152636
AA Change: S91T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000141460
Gene: ENSMUSG00000036893
AA Change: S91T

DomainStartEndE-ValueType
ANK 118 147 1.3e-7 SMART
ANK 151 182 2e-7 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000150836
Predicted Effect probably benign
Transcript: ENSMUST00000200655
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
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: 93 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd10 A G 16: 45,552,303 (GRCm39) M190T probably benign Het
Abhd5 A G 9: 122,207,005 (GRCm39) Y250C probably damaging Het
Ace2 A G X: 162,923,728 (GRCm39) N24S probably benign Het
Adamtsl2 A G 2: 26,985,570 (GRCm39) M485V probably benign Het
Adamtsl4 G T 3: 95,588,357 (GRCm39) P577H probably damaging Het
Akap8l C T 17: 32,551,457 (GRCm39) R511H probably damaging Het
Apc T C 18: 34,402,282 (GRCm39) Y141H probably damaging Het
Arsi A T 18: 61,049,443 (GRCm39) T109S possibly damaging Het
Asb3 G A 11: 31,031,355 (GRCm39) probably null Het
Atm T C 9: 53,355,297 (GRCm39) D2899G probably damaging Het
Bcas3 G A 11: 85,348,704 (GRCm39) V199I probably damaging Het
Bub1 T C 2: 127,661,255 (GRCm39) K279E probably damaging Het
C3 A T 17: 57,530,974 (GRCm39) probably null Het
Cabcoco1 T C 10: 68,267,153 (GRCm39) K185E probably benign Het
Cadm2 A T 16: 66,528,357 (GRCm39) I326N probably benign Het
Ccr3 T C 9: 123,829,336 (GRCm39) S224P possibly damaging Het
Cdhr4 A G 9: 107,874,843 (GRCm39) T638A probably damaging Het
Cfap46 T C 7: 139,263,677 (GRCm39) I4V probably benign Het
Csf2rb2 A T 15: 78,176,744 (GRCm39) V216E probably damaging Het
Csmd3 A T 15: 47,868,257 (GRCm39) D754E possibly damaging Het
Dnaaf1 T C 8: 120,309,471 (GRCm39) probably null Het
Dnah11 A C 12: 117,984,088 (GRCm39) Y2466D probably damaging Het
Dtx2 C T 5: 136,059,431 (GRCm39) S493F probably damaging Het
E2f7 T C 10: 110,616,763 (GRCm39) Y668H probably benign Het
Eomes T C 9: 118,307,920 (GRCm39) F65L probably benign Het
Ercc6l2 T C 13: 64,019,802 (GRCm39) probably benign Het
Fbrsl1 A T 5: 110,526,300 (GRCm39) L439Q probably damaging Het
Fyco1 C T 9: 123,626,581 (GRCm39) probably null Het
Gfm2 A G 13: 97,291,950 (GRCm39) T229A probably benign Het
Gm7735 G A 16: 88,966,433 (GRCm39) G19D unknown Het
Gnpda1 T C 18: 38,466,243 (GRCm39) probably null Het
Gpr6 T A 10: 40,946,649 (GRCm39) Y311F possibly damaging Het
Gprc6a A T 10: 51,491,304 (GRCm39) V744E probably damaging Het
Grin3a C T 4: 49,665,510 (GRCm39) D1042N possibly damaging Het
Gstm3 A G 3: 107,873,450 (GRCm39) C174R probably damaging Het
Hectd4 A G 5: 121,471,487 (GRCm39) E2670G possibly damaging Het
Hsd3b6 A T 3: 98,713,503 (GRCm39) Y265* probably null Het
Hus1 T A 11: 8,961,110 (GRCm39) M1L probably null Het
Idi2l G A 13: 8,991,764 (GRCm39) P221S possibly damaging Het
Ifi213 T G 1: 173,396,668 (GRCm39) probably null Het
Igf2r A C 17: 12,917,138 (GRCm39) N1587K probably benign Het
Ints1 A T 5: 139,753,505 (GRCm39) V709E probably damaging Het
Ints8 C A 4: 11,235,552 (GRCm39) R359L probably damaging Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Lrp1b C T 2: 41,000,769 (GRCm39) E2152K probably damaging Het
Lrp2 A T 2: 69,336,968 (GRCm39) V1268D possibly damaging Het
Mpo T C 11: 87,686,901 (GRCm39) Y177H probably damaging Het
Mpp4 G A 1: 59,182,941 (GRCm39) P322L possibly damaging Het
Mprip A G 11: 59,660,717 (GRCm39) K2166R probably damaging Het
Myo15a T C 11: 60,382,636 (GRCm39) Y1544H probably damaging Het
Neu1 G A 17: 35,153,374 (GRCm39) R299Q probably benign Het
Nfxl1 C A 5: 72,671,675 (GRCm39) probably null Het
Nrp2 T A 1: 62,783,436 (GRCm39) I179N probably damaging Het
Nup153 A G 13: 46,846,986 (GRCm39) probably null Het
Or1j4 C A 2: 36,740,355 (GRCm39) A99E possibly damaging Het
Or2g7 G T 17: 38,378,746 (GRCm39) R228L possibly damaging Het
Or5p54 A T 7: 107,554,709 (GRCm39) H287L probably benign Het
Or6c6c A T 10: 129,541,490 (GRCm39) I248L probably benign Het
Or8g27 A T 9: 39,129,318 (GRCm39) I222F probably damaging Het
P2ry12 A T 3: 59,124,774 (GRCm39) D300E probably damaging Het
Pkhd1 C A 1: 20,623,798 (GRCm39) G766* probably null Het
Plagl1 A C 10: 13,004,391 (GRCm39) probably benign Het
Prkcq A T 2: 11,237,380 (GRCm39) Y53F probably damaging Het
Psg18 T C 7: 18,084,799 (GRCm39) E99G probably damaging Het
Ptprz1 T A 6: 23,033,476 (GRCm39) H1921Q probably damaging Het
Rcc1l A G 5: 134,184,629 (GRCm39) V391A probably benign Het
Sdr42e1 C T 8: 118,391,763 (GRCm39) V11I probably damaging Het
Slc12a3 C A 8: 95,067,158 (GRCm39) N404K probably damaging Het
Slc38a4 T C 15: 96,906,878 (GRCm39) M287V probably benign Het
Slc6a8 A T X: 72,720,492 (GRCm39) I96F possibly damaging Het
Smyd2 A G 1: 189,629,623 (GRCm39) S136P probably damaging Het
Sox11 A G 12: 27,391,702 (GRCm39) Y236H probably damaging Het
Tbc1d2 G A 4: 46,637,652 (GRCm39) P198L possibly damaging Het
Tcof1 G T 18: 60,968,845 (GRCm39) A256E probably damaging Het
Tenm4 A G 7: 96,555,497 (GRCm39) Y2726C probably damaging Het
Tnfsf14 T A 17: 57,497,867 (GRCm39) R122W probably damaging Het
Tril T C 6: 53,796,068 (GRCm39) T385A probably damaging Het
Trrap A G 5: 144,762,684 (GRCm39) T2386A probably benign Het
Tspear T A 10: 77,706,253 (GRCm39) L341H possibly damaging Het
Uba7 A G 9: 107,856,487 (GRCm39) M595V probably benign Het
Usp43 GC G 11: 67,746,566 (GRCm39) probably null Het
Utrn C A 10: 12,312,108 (GRCm39) D616Y probably damaging Het
Vmn2r69 T C 7: 85,059,404 (GRCm39) I502V probably benign Het
Vps13d C A 4: 144,801,617 (GRCm39) G419C probably damaging Het
Zbtb25 A T 12: 76,396,880 (GRCm39) M114K probably benign Het
Zcchc4 A G 5: 52,953,474 (GRCm39) Y161C probably damaging Het
Zfp292 A T 4: 34,808,593 (GRCm39) F1484I possibly damaging Het
Zfp326 A G 5: 106,062,646 (GRCm39) probably benign Het
Zfp395 T A 14: 65,630,565 (GRCm39) S372T probably benign Het
Zfp423 T A 8: 88,507,806 (GRCm39) E825V possibly damaging Het
Zfp445 A T 9: 122,681,305 (GRCm39) Y879N probably benign Het
Zfp451 A G 1: 33,818,248 (GRCm39) I77T possibly damaging Het
Zfp85 A T 13: 67,897,003 (GRCm39) S356R probably benign 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
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'- TAGAGATGCACAGAGGACATTTCTAG -3'
(R):5'- CTGAAGACAGTTGCTTGGGG -3'

Sequencing Primer
(F):5'- TGCACAGAGGACATTTCTAGTGTCAG -3'
(R):5'- GCAGTGCCTCAGGGATTTAAAC -3'
Posted On 2014-09-18