Incidental Mutation 'R7410:Ehmt1'
ID 574974
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 045491-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7410 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 24738080 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 508 (V508A)
Ref Sequence ENSEMBL: ENSMUSP00000119057 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably benign
Transcript: ENSMUST00000046227
AA Change: V508A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: V508A

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: V500A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: V500A

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: V501A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: V501A

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: V508A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: V508A

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: V455A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: V455A

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: V508A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: V508A

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
SMART Domains Protein: ENSMUSP00000123387
Gene: ENSMUSG00000036893
AA Change: V210A

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 probably benign
Transcript: ENSMUST00000200655
Predicted Effect
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210017I01Rik A G 3: 92,512,551 (GRCm39) S3P unknown Het
Adgrv1 A T 13: 81,711,738 (GRCm39) D1079E probably benign Het
Agbl5 A T 5: 31,048,032 (GRCm39) Y102F possibly damaging Het
Ankfy1 T C 11: 72,652,330 (GRCm39) L1094S probably damaging Het
Ankrd42 A T 7: 92,259,762 (GRCm39) V337E possibly damaging Het
Axl A G 7: 25,458,208 (GRCm39) L849P probably benign Het
Bmpr2 T C 1: 59,907,652 (GRCm39) I915T probably benign Het
Cables1 T A 18: 12,074,282 (GRCm39) F494L probably benign Het
Cacna1e A C 1: 154,347,980 (GRCm39) V927G probably benign Het
Cavin1 A T 11: 100,849,670 (GRCm39) V320E probably damaging Het
Cemip T G 7: 83,602,042 (GRCm39) S916R probably damaging Het
Cep57 G A 9: 13,729,980 (GRCm39) probably benign Het
Ces1d T C 8: 93,919,433 (GRCm39) N120D probably damaging Het
Cfap44 A T 16: 44,288,776 (GRCm39) S1509C probably damaging Het
Chga A G 12: 102,528,866 (GRCm39) D281G probably benign Het
Clstn2 A G 9: 97,423,920 (GRCm39) F282L probably benign Het
Cnot1 A T 8: 96,459,787 (GRCm39) V1855E possibly damaging Het
Cnr1 T A 4: 33,944,119 (GRCm39) V169D probably damaging Het
Cpd T A 11: 76,673,134 (GRCm39) H1337L probably damaging Het
Crabp2 T A 3: 87,859,585 (GRCm39) D78E probably damaging Het
Crat C T 2: 30,294,577 (GRCm39) R497Q probably benign Het
Cyp2ab1 G A 16: 20,135,475 (GRCm39) A9V probably benign Het
Cyp3a41b T C 5: 145,514,967 (GRCm39) D86G probably damaging Het
Dner T A 1: 84,563,332 (GRCm39) D96V probably damaging Het
Duox1 C A 2: 122,176,874 (GRCm39) T1465N probably damaging Het
Ehd3 T A 17: 74,112,428 (GRCm39) V64E probably benign Het
Ephb3 G A 16: 21,040,158 (GRCm39) V761I possibly damaging Het
Fam161b T C 12: 84,404,575 (GRCm39) Q35R probably benign Het
Fam186a T A 15: 99,844,826 (GRCm39) K473* probably null Het
Fam227b A T 2: 125,960,983 (GRCm39) D215E probably damaging Het
Fkbp15 C A 4: 62,258,536 (GRCm39) D144Y probably damaging Het
Galt T C 4: 41,757,707 (GRCm39) I259T possibly damaging Het
Gbp11 G A 5: 105,491,774 (GRCm39) P8S probably damaging Het
Gfap A T 11: 102,783,963 (GRCm39) M339K probably damaging Het
Gm14443 C T 2: 175,011,069 (GRCm39) R459Q possibly damaging Het
Grip1 A G 10: 119,855,925 (GRCm39) N632S probably benign Het
H4c18 G A 13: 22,016,211 (GRCm39) R40W probably damaging Het
Hcar1 T G 5: 124,017,161 (GRCm39) I177L possibly damaging Het
Ighv1-37 A G 12: 114,860,099 (GRCm39) V37A probably damaging Het
Ilf3 T A 9: 21,311,100 (GRCm39) F657L unknown Het
Ints2 T G 11: 86,124,052 (GRCm39) T579P probably benign Het
Iqgap1 G T 7: 80,372,778 (GRCm39) Y1520* probably null Het
Kdm4a T C 4: 118,001,115 (GRCm39) H884R possibly damaging Het
Krtap19-1 A T 16: 88,666,132 (GRCm39) Y52N unknown Het
Lama5 A T 2: 179,844,183 (GRCm39) probably null Het
Lrrc72 T C 12: 36,272,803 (GRCm39) N89D probably damaging Het
Med13l A G 5: 118,698,897 (GRCm39) D16G possibly damaging Het
Mefv A G 16: 3,533,545 (GRCm39) L242P probably damaging Het
Mob3c T C 4: 115,688,784 (GRCm39) Y106H probably damaging Het
Nlrp1a A G 11: 71,014,683 (GRCm39) I189T probably damaging Het
Nudt7 T C 8: 114,860,559 (GRCm39) probably benign Het
Or13p10 T C 4: 118,523,629 (GRCm39) L305P probably benign Het
Or4f7 T A 2: 111,644,271 (GRCm39) I267L probably benign Het
Pappa A G 4: 65,253,956 (GRCm39) T1537A probably damaging Het
Pik3r4 T A 9: 105,527,790 (GRCm39) V381E probably damaging Het
Pkd1 T A 17: 24,794,855 (GRCm39) Y2181N probably damaging Het
Pmel G T 10: 128,552,353 (GRCm39) V396F probably benign Het
Prdm9 A G 17: 15,765,259 (GRCm39) I507T possibly damaging Het
Psme4 C T 11: 30,765,279 (GRCm39) Q549* probably null Het
Ptprg T A 14: 11,962,657 (GRCm38) W152R probably damaging Het
Ptprm A C 17: 67,000,561 (GRCm39) V1141G probably damaging Het
Rapgef5 G A 12: 117,685,063 (GRCm39) V505M probably damaging Het
Rnf213 T A 11: 119,325,877 (GRCm39) M1558K Het
Slc35a1 A G 4: 34,675,034 (GRCm39) V168A probably benign Het
Srebf1 T C 11: 60,096,693 (GRCm39) T347A probably benign Het
Stard9 T A 2: 120,531,978 (GRCm39) V2745D probably benign Het
Taar7e A T 10: 23,914,424 (GRCm39) T305S probably benign Het
Tie1 T C 4: 118,337,074 (GRCm39) S551G probably benign Het
Tmc5 T A 7: 118,222,820 (GRCm39) Y173* probably null Het
Tns2 T A 15: 102,018,961 (GRCm39) V384D probably damaging Het
Tubgcp4 T A 2: 121,014,890 (GRCm39) Y267N probably damaging Het
Vmn1r53 A G 6: 90,200,700 (GRCm39) V208A probably damaging Het
Vwa8 A C 14: 79,219,674 (GRCm39) probably null Het
Wdfy4 T C 14: 32,696,191 (GRCm39) D2784G Het
Zfp712 A C 13: 67,189,400 (GRCm39) S376A probably benign Het
Znrf3 C T 11: 5,238,955 (GRCm39) C232Y unknown 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
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'- GAAGATGACAGTTCTTGTTGCC -3'
(R):5'- GATGAACTTGCAGCCTGTCC -3'

Sequencing Primer
(F):5'- ACAGTTCTTGTTGCCATTTTAAGG -3'
(R):5'- GAACTTGCAGCCTGTCCTATGAC -3'
Posted On 2019-10-07