Incidental Mutation 'R1665:Ehmt1'
ID 187083
Institutional Source Beutler Lab
Gene Symbol Ehmt1
Ensembl Gene ENSMUSG00000036893
Gene Name euchromatic histone methyltransferase 1
Synonyms 9230102N17Rik, KMT1D
MMRRC Submission 039701-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1665 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 24680781-24809658 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 24767476 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 272 (S272P)
Ref Sequence ENSEMBL: ENSMUSP00000123187 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000198923] [ENSMUST00000152161] [ENSMUST00000150379] [ENSMUST00000200655]
AlphaFold Q5DW34
Predicted Effect probably damaging
Transcript: ENSMUST00000046227
AA Change: S270P

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: S270P

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: S269P

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: S269P

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: S270P

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: S270P

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: S270P

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: S270P

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: S270P

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: S270P

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: S270P

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: S270P

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: ENSMUST00000198923
AA Change: S146P

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000143189
Gene: ENSMUSG00000036893
AA Change: S146P

DomainStartEndE-ValueType
low complexity region 208 227 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000152161
AA Change: S269P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000119854
Gene: ENSMUSG00000036893
AA Change: S269P

DomainStartEndE-ValueType
low complexity region 339 358 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000152325
AA Change: S18P
SMART Domains Protein: ENSMUSP00000123387
Gene: ENSMUSG00000036893
AA Change: S18P

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 damaging
Transcript: ENSMUST00000150379
AA Change: S272P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192397
Predicted Effect probably benign
Transcript: ENSMUST00000200655
Meta Mutation Damage Score 0.0713 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.0%
Validation Efficiency 100% (87/87)
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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca3 G A 17: 24,596,816 (GRCm39) G423E probably damaging Het
Acox3 A T 5: 35,760,371 (GRCm39) H429L probably damaging Het
Afg1l T A 10: 42,302,573 (GRCm39) K142N probably damaging Het
Aldh1a7 T C 19: 20,704,825 (GRCm39) I18V probably benign Het
Angel2 T C 1: 190,669,664 (GRCm39) Y115H probably damaging Het
Bsg T G 10: 79,547,352 (GRCm39) N261K probably damaging Het
C2cd2l A T 9: 44,228,072 (GRCm39) V83E probably benign Het
Caml C A 13: 55,779,784 (GRCm39) L286I probably benign Het
Ccdc125 A G 13: 100,830,081 (GRCm39) I284V probably benign Het
Ces2a G A 8: 105,464,187 (GRCm39) probably benign Het
Cfap61 T C 2: 145,877,239 (GRCm39) probably null Het
Creg2 C T 1: 39,662,372 (GRCm39) W253* probably null Het
Csmd3 T C 15: 47,560,185 (GRCm39) T2293A probably damaging Het
Cttnbp2 A T 6: 18,434,982 (GRCm39) I292K probably benign Het
Dab2ip T A 2: 35,610,290 (GRCm39) M770K probably damaging Het
Dct T A 14: 118,271,663 (GRCm39) D389V probably damaging Het
Dnah17 A T 11: 118,012,321 (GRCm39) probably benign Het
Dnah6 T C 6: 73,101,761 (GRCm39) E1921G probably benign Het
Efcab3 A G 11: 104,611,940 (GRCm39) K594R probably benign Het
Ero1b T C 13: 12,594,142 (GRCm39) probably null Het
Fnip2 A G 3: 79,422,456 (GRCm39) F108S probably benign Het
Foxb1 G A 9: 69,667,104 (GRCm39) A142V probably damaging Het
Fras1 A T 5: 96,746,768 (GRCm39) S613C probably damaging Het
Gm7276 C A 18: 77,273,266 (GRCm39) probably benign Het
Gnb4 A C 3: 32,644,188 (GRCm39) L152* probably null Het
H1f7 G T 15: 98,154,796 (GRCm39) Q118K probably benign Het
Hdac7 A G 15: 97,704,406 (GRCm39) L119P probably damaging Het
Hsd17b4 G A 18: 50,293,282 (GRCm39) E274K probably benign Het
Htr4 T C 18: 62,545,305 (GRCm39) I30T probably damaging Het
Ikzf2 T A 1: 69,577,973 (GRCm39) Y512F probably damaging Het
Itga10 C T 3: 96,559,054 (GRCm39) probably benign Het
Klhl22 C A 16: 17,594,352 (GRCm39) D160E probably benign Het
Kpna6 T A 4: 129,551,264 (GRCm39) R80S probably benign Het
Lclat1 A G 17: 73,494,999 (GRCm39) E142G probably damaging Het
Lrig3 T C 10: 125,833,570 (GRCm39) Y349H probably benign Het
Lsmem1 GTACATACATACATACATACATACATACA GTACATACATACATACATACATACATACATACA 12: 40,235,260 (GRCm39) probably null Het
Map1b T A 13: 99,568,437 (GRCm39) N1428I unknown Het
Map3k19 T A 1: 127,745,393 (GRCm39) T1354S possibly damaging Het
Med13l T A 5: 118,887,813 (GRCm39) W1696R probably damaging Het
Mfn1 T G 3: 32,588,471 (GRCm39) V66G probably benign Het
Mllt10 A T 2: 18,213,601 (GRCm39) Q459L possibly damaging Het
Morc2a G A 11: 3,625,885 (GRCm39) V162M probably benign Het
Muc15 C T 2: 110,564,243 (GRCm39) Q260* probably null Het
Nfkb1 T C 3: 135,300,718 (GRCm39) H616R probably damaging Het
Nr2c1 T A 10: 94,024,045 (GRCm39) W417R probably damaging Het
Or10a2 T C 7: 106,673,481 (GRCm39) S149P probably damaging Het
Or13a26 G T 7: 140,284,707 (GRCm39) C181F probably damaging Het
Or4g16 T C 2: 111,137,116 (GRCm39) C189R probably damaging Het
Or4k39 T C 2: 111,239,098 (GRCm39) Y113H probably damaging Het
Or5b121 A T 19: 13,507,202 (GRCm39) H99L probably damaging Het
Or8c10 C T 9: 38,278,862 (GRCm39) H7Y probably benign Het
Pde10a A G 17: 9,117,702 (GRCm39) D26G probably damaging Het
Pi15 G T 1: 17,691,726 (GRCm39) C176F probably damaging Het
Pou2f2 T A 7: 24,792,149 (GRCm39) T569S possibly damaging Het
Prf1 A C 10: 61,138,666 (GRCm39) E208A probably benign Het
Prkd1 G A 12: 50,441,709 (GRCm39) H277Y probably damaging Het
Rc3h1 T A 1: 160,786,993 (GRCm39) V796E probably benign Het
Rgl1 T C 1: 152,409,326 (GRCm39) Y503C probably damaging Het
Ripk3 T A 14: 56,023,808 (GRCm39) H1L probably benign Het
Ryr1 C T 7: 28,735,503 (GRCm39) D4064N probably damaging Het
Sec63 T A 10: 42,674,724 (GRCm39) probably null Het
Slco1a4 T G 6: 141,785,303 (GRCm39) M96L possibly damaging Het
Slit3 A T 11: 35,125,733 (GRCm39) R137S possibly damaging Het
Smad1 T C 8: 80,098,658 (GRCm39) E52G probably damaging Het
Srd5a2 A T 17: 74,328,476 (GRCm39) W201R probably damaging Het
Steap1 A T 5: 5,786,498 (GRCm39) L313Q probably damaging Het
Syt2 C A 1: 134,675,358 (GRCm39) A403D probably damaging Het
Tax1bp1 T A 6: 52,713,897 (GRCm39) S225R probably benign Het
Thap3 C T 4: 152,070,161 (GRCm39) V78M probably damaging Het
Thoc5 A G 11: 4,869,792 (GRCm39) K446R probably benign Het
Timmdc1 A C 16: 38,331,079 (GRCm39) probably null Het
Tm6sf2 G T 8: 70,531,580 (GRCm39) probably benign Het
Tmem126b G T 7: 90,125,179 (GRCm39) A2E probably damaging Het
Trim9 T A 12: 70,301,887 (GRCm39) R584W probably damaging Het
Ttn C A 2: 76,661,200 (GRCm39) probably benign Het
Vmn1r25 A T 6: 57,955,446 (GRCm39) I281N probably damaging Het
Wdr59 A G 8: 112,205,994 (GRCm39) F553S probably damaging Het
Zc3h4 A G 7: 16,163,505 (GRCm39) M575V unknown Het
Zfp53 A G 17: 21,729,766 (GRCm39) T600A probably damaging Het
Zic5 A G 14: 122,696,939 (GRCm39) S559P 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
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
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'- CCAGCACCTCACTGAGATTCACTG -3'
(R):5'- ACCTGATCCAGCAGAGGATGGTAG -3'

Sequencing Primer
(F):5'- CACTCGTATCTCGTAAGATTTCAG -3'
(R):5'- TCTATTCCTATGGTTCACGAGTTAG -3'
Posted On 2014-05-09