Incidental Mutation 'R5183:Ehmt1'
ID 397649
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 042762-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5183 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 24767509 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Threonine at position 135 (P135T)
Ref Sequence ENSEMBL: ENSMUSP00000143189 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000150379] [ENSMUST00000152161] [ENSMUST00000198923] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably damaging
Transcript: ENSMUST00000046227
AA Change: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: P259T

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: P258T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: P258T

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: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: P259T

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: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: P259T

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: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: P259T

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: P259T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: P259T

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: ENSMUST00000150379
AA Change: P261T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect probably damaging
Transcript: ENSMUST00000152161
AA Change: P258T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000119854
Gene: ENSMUSG00000036893
AA Change: P258T

DomainStartEndE-ValueType
low complexity region 339 358 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000198923
AA Change: P135T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000143189
Gene: ENSMUSG00000036893
AA Change: P135T

DomainStartEndE-ValueType
low complexity region 208 227 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000152325
AA Change: P7T
SMART Domains Protein: ENSMUSP00000123387
Gene: ENSMUSG00000036893
AA Change: P7T

DomainStartEndE-ValueType
low complexity region 89 108 N/A INTRINSIC
low complexity region 147 168 N/A INTRINSIC
low complexity region 189 201 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192397
Predicted Effect probably benign
Transcript: ENSMUST00000200655
Meta Mutation Damage Score 0.0852 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency 99% (73/74)
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930522L14Rik A T 5: 109,887,171 (GRCm39) D8E probably damaging Het
Abca3 T G 17: 24,593,427 (GRCm39) S275A probably benign Het
Adk A G 14: 21,290,599 (GRCm39) N155S probably damaging Het
Aqp11 T C 7: 97,386,963 (GRCm39) T78A probably benign Het
Arhgef40 T C 14: 52,241,556 (GRCm39) V1455A probably damaging Het
Asxl3 C G 18: 22,658,356 (GRCm39) A2122G possibly damaging Het
Cdan1 T A 2: 120,560,061 (GRCm39) I368F probably damaging Het
Cdc42bpg A G 19: 6,371,835 (GRCm39) probably benign Het
Celsr3 A G 9: 108,714,759 (GRCm39) D2013G probably damaging Het
Cep152 A G 2: 125,408,558 (GRCm39) V1332A probably damaging Het
Cftr T C 6: 18,299,832 (GRCm39) S1172P probably damaging Het
Commd2 A T 3: 57,554,235 (GRCm39) D155E probably benign Het
Coq7 T A 7: 118,127,490 (GRCm39) probably benign Het
Dnase2a T C 8: 85,636,207 (GRCm39) probably benign Het
Dnhd1 G A 7: 105,352,416 (GRCm39) R2523Q probably damaging Het
Dock6 C T 9: 21,752,899 (GRCm39) V305I probably benign Het
Fasn T C 11: 120,699,708 (GRCm39) Q2288R probably benign Het
Fat3 T A 9: 15,871,609 (GRCm39) N3594I probably damaging Het
Galnt10 T C 11: 57,660,414 (GRCm39) M284T probably damaging Het
Gatm A T 2: 122,425,984 (GRCm39) F422L probably benign Het
Glrp1 A T 1: 88,437,574 (GRCm39) I12N unknown Het
Gm5455 T A 13: 110,441,962 (GRCm39) noncoding transcript Het
Gpam C T 19: 55,071,659 (GRCm39) E361K probably damaging Het
Gps2 A G 11: 69,806,023 (GRCm39) T126A probably benign Het
Grn C A 11: 102,321,380 (GRCm39) probably benign Het
Gsg1 T A 6: 135,218,368 (GRCm39) Q176L probably damaging Het
Htra1 C T 7: 130,585,446 (GRCm39) A412V possibly damaging Het
Icosl C T 10: 77,905,319 (GRCm39) probably benign Het
Iqgap1 T C 7: 80,372,813 (GRCm39) T1509A probably damaging Het
Irag2 A G 6: 145,083,946 (GRCm39) E37G probably benign Het
Itgad T C 7: 127,797,395 (GRCm39) probably null Het
Kdm5a C A 6: 120,406,977 (GRCm39) probably benign Het
Kidins220 T C 12: 25,101,125 (GRCm39) L1017S probably benign Het
Lrrc37 T C 11: 103,433,947 (GRCm39) Y898C probably damaging Het
Man2b1 T A 8: 85,822,413 (GRCm39) S804R probably damaging Het
Miip A T 4: 147,947,526 (GRCm39) F211L probably damaging Het
Moxd1 T G 10: 24,155,445 (GRCm39) probably null Het
Moxd1 T G 10: 24,163,034 (GRCm39) Y499D probably damaging Het
Mrpl45 T C 11: 97,207,577 (GRCm39) I24T probably benign Het
Msh2 C A 17: 88,030,841 (GRCm39) A906E probably benign Het
Mthfr T A 4: 148,135,817 (GRCm39) probably null Het
Muc5b T A 7: 141,404,547 (GRCm39) D827E unknown Het
Myo1g G C 11: 6,458,243 (GRCm39) L866V probably damaging Het
Myo3a A T 2: 22,468,170 (GRCm39) M475L probably benign Het
Ncoa2 A C 1: 13,244,590 (GRCm39) L703V probably damaging Het
Ncoa4-ps A C 12: 119,225,023 (GRCm39) noncoding transcript Het
Nme6 T A 9: 109,670,557 (GRCm39) Y69* probably null Het
Nwd1 T A 8: 73,397,714 (GRCm39) M651K probably benign Het
Or4k15c A C 14: 50,322,003 (GRCm39) I45S probably damaging Het
Orc2 A T 1: 58,513,977 (GRCm39) S298R possibly damaging Het
Oscp1 A T 4: 125,981,522 (GRCm39) E328V probably damaging Het
Pan2 T C 10: 128,153,838 (GRCm39) V1003A probably damaging Het
Pik3r4 T C 9: 105,559,507 (GRCm39) V1200A possibly damaging Het
Prl T C 13: 27,241,579 (GRCm39) probably benign Het
Ptprk T C 10: 28,351,232 (GRCm39) V575A probably benign Het
Rflna A T 5: 125,088,469 (GRCm39) S139C probably damaging Het
Robo1 T C 16: 72,539,038 (GRCm39) F27S probably benign Het
Secisbp2 T C 13: 51,819,460 (GRCm39) S347P probably benign Het
Shmt1 A G 11: 60,688,308 (GRCm39) probably benign Het
Slc27a3 A G 3: 90,296,477 (GRCm39) probably null Het
Slc6a5 T C 7: 49,585,957 (GRCm39) V425A probably damaging Het
Slc8a3 A G 12: 81,361,265 (GRCm39) V518A possibly damaging Het
Slco1a4 A T 6: 141,785,357 (GRCm39) Y78N probably damaging Het
Stt3b A T 9: 115,095,211 (GRCm39) H273Q probably damaging Het
Tle6 T A 10: 81,428,635 (GRCm39) N431I probably damaging Het
Trim34b C A 7: 103,979,118 (GRCm39) Q122K possibly damaging Het
Trio C A 15: 27,902,686 (GRCm39) R258S probably benign Het
Ttc7 A T 17: 87,600,306 (GRCm39) D23V probably damaging Het
Ttn A T 2: 76,810,525 (GRCm39) M1K probably null Het
Ufsp2 T C 8: 46,447,126 (GRCm39) V391A probably benign Het
Vps13c T C 9: 67,815,334 (GRCm39) L990S probably damaging Het
Zfp108 G T 7: 23,960,163 (GRCm39) K251N probably benign Het
Zfp618 G A 4: 63,017,519 (GRCm39) M234I 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
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
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'- TCAGGAGAACAAAATCAGTGCC -3'
(R):5'- GGATGCGCTTTATTCCATTCAC -3'

Sequencing Primer
(F):5'- TCAGTGCCATAAAGTCTTAAGGGC -3'
(R):5'- ACCATCTACTTCTGCAGTCATC -3'
Posted On 2016-07-06