Incidental Mutation 'R9460:Ehmt1'
ID 714790
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9460 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 24728791 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 703 (V703A)
Ref Sequence ENSEMBL: ENSMUSP00000119057 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000152636] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably benign
Transcript: ENSMUST00000046227
AA Change: V655A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: V655A

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: ENSMUST00000091348
AA Change: V695A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: V695A

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: V696A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: V696A

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: V655A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: V655A

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: V650A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: V650A

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: ENSMUST00000147147
AA Change: V703A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: V703A

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: ENSMUST00000150836
Predicted Effect probably benign
Transcript: ENSMUST00000152636
AA Change: V51A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000141460
Gene: ENSMUSG00000036893
AA Change: V51A

DomainStartEndE-ValueType
ANK 118 147 1.3e-7 SMART
ANK 151 182 2e-7 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000200655
Meta Mutation Damage Score 0.0846 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 100% (56/56)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsbg3 C T 17: 57,183,316 (GRCm39) T19I probably damaging Het
Alg1 T A 16: 5,060,425 (GRCm39) M382K probably damaging Het
Arhgap17 A G 7: 122,879,286 (GRCm39) S822P unknown Het
Bend7 A C 2: 4,749,302 (GRCm39) T140P probably benign Het
C1rb T G 6: 124,557,865 (GRCm39) D667E probably benign Het
Carmil1 A G 13: 24,253,750 (GRCm39) C794R probably damaging Het
Cd36 T C 5: 18,000,608 (GRCm39) D365G probably null Het
Cep164 T C 9: 45,685,282 (GRCm39) N825S probably benign Het
Cp T C 3: 20,018,566 (GRCm39) L90P Het
Cpeb2 C T 5: 43,390,769 (GRCm39) probably benign Het
Cramp1 A G 17: 25,222,281 (GRCm39) S146P probably damaging Het
Csmd3 A T 15: 47,617,130 (GRCm39) D1019E Het
Cyp2d10 T A 15: 82,289,470 (GRCm39) D214V probably benign Het
Dcaf17 G C 2: 70,917,695 (GRCm39) V406L possibly damaging Het
Ermp1 A C 19: 29,609,916 (GRCm39) V293G probably benign Het
Fancd2os C A 6: 113,574,569 (GRCm39) V146F probably benign Het
Galnt12 C T 4: 47,117,983 (GRCm39) T426I probably damaging Het
Gm11011 T A 2: 169,429,289 (GRCm39) T44S unknown Het
Gm2832 C T 14: 41,000,843 (GRCm39) T27I Het
Klhl32 A G 4: 24,649,866 (GRCm39) V310A probably benign Het
Kntc1 T A 5: 123,941,378 (GRCm39) C1728* probably null Het
Lama2 T A 10: 27,298,475 (GRCm39) N207I probably damaging Het
Lpar5 A G 6: 125,058,234 (GRCm39) probably benign Het
Map3k8 T C 18: 4,349,277 (GRCm39) I14V probably benign Het
Marf1 A T 16: 13,947,526 (GRCm39) V1151E probably damaging Het
Me1 G A 9: 86,495,685 (GRCm39) A274V probably damaging Het
Mybpc1 A T 10: 88,372,197 (GRCm39) I797N probably damaging Het
Myo15a T A 11: 60,372,566 (GRCm39) probably null Het
N4bp2 A T 5: 65,963,886 (GRCm39) D645V probably benign Het
Nlrp4f G T 13: 65,342,006 (GRCm39) D546E possibly damaging Het
Npc1 T C 18: 12,346,398 (GRCm39) D266G possibly damaging Het
Or4a81 G A 2: 89,618,778 (GRCm39) S306L probably benign Het
Or8k16 A G 2: 85,520,359 (GRCm39) I195M probably benign Het
Pcdha12 C T 18: 37,153,574 (GRCm39) R98W probably damaging Het
Peg10 GC GCTCC 6: 4,756,452 (GRCm39) probably benign Het
Pigr T C 1: 130,772,403 (GRCm39) I207T probably damaging Het
Plxnc1 T A 10: 94,700,895 (GRCm39) E596D probably benign Het
Polr1e C T 4: 45,018,691 (GRCm39) P7L probably benign Het
Ppp5c G T 7: 16,741,137 (GRCm39) Y313* probably null Het
Sacs C A 14: 61,441,611 (GRCm39) T1219K probably benign Het
Scn3a A G 2: 65,300,535 (GRCm39) V1277A probably damaging Het
Serinc5 G T 13: 92,844,607 (GRCm39) A450S possibly damaging Het
Serinc5 T C 13: 92,844,619 (GRCm39) C454R probably benign Het
Slc12a6 G A 2: 112,183,280 (GRCm39) V771I probably benign Het
Slc4a1ap T C 5: 31,685,463 (GRCm39) I247T probably benign Het
Snx10 T A 6: 51,565,888 (GRCm39) S184R probably damaging Het
Tgm2 A T 2: 157,971,241 (GRCm39) probably null Het
Thap1 CAGCATCTGCTCGGAGCA CAGCA 8: 26,650,884 (GRCm39) probably null Het
Thsd7b T C 1: 130,090,674 (GRCm39) probably null Het
Tiam2 G A 17: 3,487,585 (GRCm39) G702E probably damaging Het
Tmco4 T A 4: 138,747,387 (GRCm39) V212D probably damaging Het
Usp48 G A 4: 137,340,996 (GRCm39) G332E probably benign Het
Vipas39 A G 12: 87,288,021 (GRCm39) L482P probably damaging Het
Vmn1r5 T A 6: 56,962,829 (GRCm39) M168K Het
Vps13c T C 9: 67,837,904 (GRCm39) L1818S possibly damaging Het
Vwa2 A G 19: 56,886,388 (GRCm39) I152V probably benign Het
Zfp180 G A 7: 23,804,399 (GRCm39) G273R probably damaging Het
Zpld2 G A 4: 133,929,312 (GRCm39) P331L 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
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
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'- GGAAACTACTAAGAATCCCTGGG -3'
(R):5'- TAGACTGCTTGTTGAGTCTACTC -3'

Sequencing Primer
(F):5'- GGAAGACCATGACTCTAAGCTGTCTC -3'
(R):5'- AGTCTACTCAGAGGCAGCCTG -3'
Posted On 2022-06-15