Mutagenetix > Incidental Mutation

Incidental Mutation 'R8879:Ehmt1'

676740

Institutional Source

Beutler Lab

Gene Symbol

Ehmt1

Ensembl Gene

ENSMUSG00000036893

Gene Name

euchromatic histone methyltransferase 1

Synonyms

KMT1D, 9230102N17Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R8879 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

24789928-24919614 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 24836476 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 766 (M766L)

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: M718L

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: M718L

Domain	Start	End	E-Value	Type
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: M758L

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: M758L

Domain	Start	End	E-Value	Type
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: M759L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: M759L

Domain	Start	End	E-Value	Type
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: M718L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: M718L

Domain	Start	End	E-Value	Type
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: M713L

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: M713L

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000147147
AA Change: M766L

PolyPhen 2 Score 0.871 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: M766L

Domain	Start	End	E-Value	Type
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: M114L

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000141460
Gene: ENSMUSG00000036893
AA Change: M114L

Domain	Start	End	E-Value	Type
ANK	118	147	1.3e-7	SMART
ANK	151	182	2e-7	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000200655

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (69/69)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9130401M01Rik	C	T	15: 58,022,509	V326M	probably damaging	Het
Adap2	T	A	11: 80,156,959	H80Q	probably benign	Het
Ang4	T	C	14: 51,764,486	T2A	probably benign	Het
Arf2	T	C	11: 103,979,759		probably null	Het
B3gnt4	A	G	5: 123,511,148	D192G	probably damaging	Het
BC034090	T	C	1: 155,226,357	I54V	probably benign	Het
Catsper3	A	G	13: 55,804,895	T202A	probably benign	Het
Cenpe	T	A	3: 135,260,101	D2113E	probably damaging	Het
Clasp2	T	C	9: 113,773,705	V191A	probably benign	Het
Col5a1	G	T	2: 28,014,158	A1356S	unknown	Het
Cuzd1	A	G	7: 131,308,848	S573P	probably damaging	Het
Cyp1a2	C	A	9: 57,681,885	M215I	possibly damaging	Het
Dcaf17	T	A	2: 71,063,402	I122K	possibly damaging	Het
Dhcr24	A	G	4: 106,573,809	I232V	probably benign	Het
Dnah10	A	G	5: 124,818,117	E3570G	probably damaging	Het
Dnaja4	A	T	9: 54,714,704		probably benign	Het
Ehd1	A	G	19: 6,298,324	D444G	probably damaging	Het
Eno4	A	G	19: 58,970,722	I613M	probably benign	Het
Exoc3l	A	T	8: 105,290,549	M602K		Het
Fam107a	C	T	14: 8,301,352		probably null	Het
Frem3	A	T	8: 80,613,148	D690V	probably damaging	Het
Gm11639	T	C	11: 104,690,955	I41T	probably benign	Het
Gm19410	A	T	8: 35,771,868	D97V	probably damaging	Het
Grik5	T	A	7: 25,023,064	D540V	possibly damaging	Het
Hint1	T	A	11: 54,869,943	D69E	probably benign	Het
Krt13	T	C	11: 100,119,385	T257A	probably benign	Het
Lpin2	T	C	17: 71,242,754	L676P	probably damaging	Het
Lrguk	A	G	6: 34,029,683	E76G	probably benign	Het
Lrrc8a	A	G	2: 30,256,298	M375V	probably benign	Het
Lrrtm3	T	C	10: 64,089,238	Q50R	possibly damaging	Het
Mmrn1	T	A	6: 60,976,529	L598Q	probably damaging	Het
Mrs2	A	G	13: 25,001,784	I135T	probably damaging	Het
Neb	T	C	2: 52,235,580	D475G		Het
Notch2	A	G	3: 98,135,599	S1427G	possibly damaging	Het
Olfr118	C	A	17: 37,672,411	Y129*	probably null	Het
Olfr682-ps1	A	G	7: 105,126,686	V195A	probably benign	Het
Olfr694	A	T	7: 106,689,089	I214N	probably damaging	Het
Olfr816	A	G	10: 129,911,862	C139R	probably damaging	Het
Olfr952	A	C	9: 39,426,219	V284G	possibly damaging	Het
Opcml	T	C	9: 28,902,151	F246S	probably damaging	Het
Pdzd2	C	A	15: 12,402,319	V729F	probably damaging	Het
Pias2	C	T	18: 77,146,768	Q565*	probably null	Het
Pnp	T	A	14: 50,950,720		probably null	Het
Ptpn18	T	C	1: 34,463,130	S76P	probably benign	Het
Qtrt2	A	T	16: 43,863,197	L304Q	probably damaging	Het
Rad51ap2	A	T	12: 11,457,400	E441V	possibly damaging	Het
Ranbp2	T	A	10: 58,477,889	V1477E	probably benign	Het
Repin1	C	T	6: 48,597,433	T432I	possibly damaging	Het
Rest	G	A	5: 77,282,511	G926R	probably benign	Het
Rnft1	T	A	11: 86,486,690	F143L	possibly damaging	Het
Sema3e	A	T	5: 14,232,094	I415L	probably benign	Het
Slc10a1	T	A	12: 80,967,595	N117I	probably damaging	Het
Slc25a23	G	A	17: 57,059,709		probably benign	Het
Slc2a2	T	C	3: 28,713,802	S160P	possibly damaging	Het
Srrd	A	G	5: 112,338,456	V178A	possibly damaging	Het
Tmigd3	G	T	3: 105,921,961	G198C	probably benign	Het
Trbv29	G	A	6: 41,271,405	M1I	probably null	Het
Tril	A	G	6: 53,819,584	S218P	probably damaging	Het
Trip11	T	C	12: 101,862,598	K1749R	probably benign	Het
Ttc25	G	T	11: 100,566,926	E452*	probably null	Het
Ttn	A	G	2: 76,830,651	V12011A		Het
Ubr4	T	G	4: 139,410,518	F1093V	probably benign	Het
Urb2	C	A	8: 124,028,403	A283E	probably benign	Het
Usp43	T	A	11: 67,898,881		probably benign	Het
Vmn1r28	A	T	6: 58,265,684	I171F	probably benign	Het
Vps33a	G	A	5: 123,533,899	R469W	probably damaging	Het
Zfp202	G	A	9: 40,211,757	R605Q	probably damaging	Het
Zpbp2	A	T	11: 98,554,620	H158L	probably benign	Het

Other mutations in Ehmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00481:Ehmt1	APN	2	24838818	missense	possibly damaging	0.81
IGL01403:Ehmt1	APN	2	24839626	missense	possibly damaging	0.81
IGL01636:Ehmt1	APN	2	24839608	missense	probably damaging	0.97
IGL01804:Ehmt1	APN	2	24791954	missense	probably damaging	1.00
IGL01836:Ehmt1	APN	2	24863220	splice site	probably null
IGL02740:Ehmt1	APN	2	24815839	splice site	probably benign
IGL02750:Ehmt1	APN	2	24863869	missense	probably damaging	1.00
IGL03026:Ehmt1	APN	2	24852734	missense	probably benign
IGL02799:Ehmt1	UTSW	2	24815806	missense	probably damaging	1.00
R0908:Ehmt1	UTSW	2	24804888	missense	probably damaging	1.00
R1275:Ehmt1	UTSW	2	24886995	critical splice donor site	probably null
R1665:Ehmt1	UTSW	2	24877464	missense	probably damaging	1.00
R1707:Ehmt1	UTSW	2	24805138	missense	probably benign
R1800:Ehmt1	UTSW	2	24884290	missense	probably damaging	0.99
R2108:Ehmt1	UTSW	2	24837618	missense	probably damaging	1.00
R2113:Ehmt1	UTSW	2	24804003	missense	probably damaging	1.00
R2393:Ehmt1	UTSW	2	24806217	missense	probably damaging	1.00
R2570:Ehmt1	UTSW	2	24815741	missense	probably damaging	1.00
R3923:Ehmt1	UTSW	2	24884335	splice site	probably null
R4646:Ehmt1	UTSW	2	24891684	missense	probably null	0.01
R4924:Ehmt1	UTSW	2	24839722	missense	probably damaging	0.97
R4989:Ehmt1	UTSW	2	24877497	missense	probably damaging	1.00
R5040:Ehmt1	UTSW	2	24884304	missense	probably benign	0.19
R5110:Ehmt1	UTSW	2	24852790	missense	probably benign	0.01
R5133:Ehmt1	UTSW	2	24877497	missense	probably damaging	1.00
R5134:Ehmt1	UTSW	2	24877497	missense	probably damaging	1.00
R5161:Ehmt1	UTSW	2	24858195	missense	possibly damaging	0.71
R5162:Ehmt1	UTSW	2	24877497	missense	probably damaging	1.00
R5183:Ehmt1	UTSW	2	24877497	missense	probably damaging	1.00
R5184:Ehmt1	UTSW	2	24877497	missense	probably damaging	1.00
R5208:Ehmt1	UTSW	2	24801533	missense	probably benign	0.34
R5309:Ehmt1	UTSW	2	24884195	missense	probably damaging	1.00
R5312:Ehmt1	UTSW	2	24884195	missense	probably damaging	1.00
R5837:Ehmt1	UTSW	2	24863914	missense	probably damaging	0.98
R5968:Ehmt1	UTSW	2	24836457	missense	probably damaging	0.99
R6539:Ehmt1	UTSW	2	24804767	missense	probably damaging	1.00
R6646:Ehmt1	UTSW	2	24806310	missense	probably damaging	0.99
R7065:Ehmt1	UTSW	2	24840697	missense	probably damaging	1.00
R7226:Ehmt1	UTSW	2	24804782	missense	probably damaging	1.00
R7361:Ehmt1	UTSW	2	24856701	missense	possibly damaging	0.94
R7373:Ehmt1	UTSW	2	24919573	start codon destroyed	probably null	0.03
R7410:Ehmt1	UTSW	2	24848068	missense	probably benign
R7418:Ehmt1	UTSW	2	24884634	missense	probably benign	0.02
R7633:Ehmt1	UTSW	2	24815780	missense	possibly damaging	0.68
R7716:Ehmt1	UTSW	2	24884499	missense	probably damaging	0.99
R7916:Ehmt1	UTSW	2	24856696	missense	probably damaging	1.00
R8112:Ehmt1	UTSW	2	24863384	missense	probably damaging	1.00
R8356:Ehmt1	UTSW	2	24852769	missense	probably benign
R9133:Ehmt1	UTSW	2	24839623	missense	possibly damaging	0.66
R9217:Ehmt1	UTSW	2	24839566	missense	probably benign	0.11
R9248:Ehmt1	UTSW	2	24848065	missense	possibly damaging	0.67
R9365:Ehmt1	UTSW	2	24838710	missense	probably damaging	1.00
R9439:Ehmt1	UTSW	2	24825018	missense	probably damaging	0.99
R9460:Ehmt1	UTSW	2	24838779	missense	probably benign
R9684:Ehmt1	UTSW	2	24863317	missense	possibly damaging	0.82
X0062:Ehmt1	UTSW	2	24863836	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTCTAACAGAGGCAAGTGTCAG -3'
(R):5'- ACAAGTGGGTCTGACTCCTG -3'

Sequencing Primer
(F):5'- TGTCAGGATAAACAGTAGAAGCACTC -3'
(R):5'- TGACTCCTGCCTGCAGACAG -3'

Posted On

2021-07-15