Mutagenetix > Incidental Mutations

Incidental Mutation 'R5183:Ehmt1'

397649

Institutional Source

Beutler Lab

Gene Symbol

Ehmt1

Ensembl Gene

ENSMUSG00000036893

Gene Name

euchromatic histone methyltransferase 1

Synonyms

KMT1D, 9230102N17Rik

MMRRC Submission

042762-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R5183 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24789928-24919614 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 24877497 bp

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]

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

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 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

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 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

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 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

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 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

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

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

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 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

Domain	Start	End	E-Value	Type
low complexity region	339	358	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000152325
AA Change: P7T

SMART Domains

Protein: ENSMUSP00000123387
Gene: ENSMUSG00000036893
AA Change: P7T

Domain	Start	End	E-Value	Type
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 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

Domain	Start	End	E-Value	Type
low complexity region	208	227	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000200655

Meta Mutation Damage Score

0.0852

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522L14Rik	A	T	5: 109,739,305	D8E	probably damaging	Het
Abca3	T	G	17: 24,374,453	S275A	probably benign	Het
Adk	A	G	14: 21,240,531	N155S	probably damaging	Het
Aqp11	T	C	7: 97,737,756	T78A	probably benign	Het
Arhgef40	T	C	14: 52,004,099	V1455A	probably damaging	Het
Asxl3	C	G	18: 22,525,299	A2122G	possibly damaging	Het
Cdan1	T	A	2: 120,729,580	I368F	probably damaging	Het
Cdc42bpg	A	G	19: 6,321,805		probably benign	Het
Celsr3	A	G	9: 108,837,560	D2013G	probably damaging	Het
Cep152	A	G	2: 125,566,638	V1332A	probably damaging	Het
Cftr	T	C	6: 18,299,833	S1172P	probably damaging	Het
Commd2	A	T	3: 57,646,814	D155E	probably benign	Het
Coq7	T	A	7: 118,528,267		probably benign	Het
Dnase2a	T	C	8: 84,909,578		probably benign	Het
Dnhd1	G	A	7: 105,703,209	R2523Q	probably damaging	Het
Dock6	C	T	9: 21,841,603	V305I	probably benign	Het
Fasn	T	C	11: 120,808,882	Q2288R	probably benign	Het
Fat3	T	A	9: 15,960,313	N3594I	probably damaging	Het
Galnt10	T	C	11: 57,769,588	M284T	probably damaging	Het
Gatm	A	T	2: 122,595,503	F422L	probably benign	Het
Glrp1	A	T	1: 88,509,852	I12N	unknown	Het
Gm5455	T	A	13: 110,305,428		noncoding transcript	Het
Gm6768	A	C	12: 119,261,288		noncoding transcript	Het
Gm884	T	C	11: 103,543,121	Y898C	probably damaging	Het
Gpam	C	T	19: 55,083,227	E361K	probably damaging	Het
Gps2	A	G	11: 69,915,197	T126A	probably benign	Het
Grn	C	A	11: 102,430,554		probably benign	Het
Gsg1	T	A	6: 135,241,370	Q176L	probably damaging	Het
Htra1	C	T	7: 130,983,716	A412V	possibly damaging	Het
Icosl	C	T	10: 78,069,485		probably benign	Het
Iqgap1	T	C	7: 80,723,065	T1509A	probably damaging	Het
Itgad	T	C	7: 128,198,223		probably null	Het
Kdm5a	C	A	6: 120,430,016		probably benign	Het
Kidins220	T	C	12: 25,051,126	L1017S	probably benign	Het
Lrmp	A	G	6: 145,138,220	E37G	probably benign	Het
Man2b1	T	A	8: 85,095,784	S804R	probably damaging	Het
Miip	A	T	4: 147,863,069	F211L	probably damaging	Het
Moxd1	T	G	10: 24,279,547		probably null	Het
Moxd1	T	G	10: 24,287,136	Y499D	probably damaging	Het
Mrpl45	T	C	11: 97,316,751	I24T	probably benign	Het
Msh2	C	A	17: 87,723,413	A906E	probably benign	Het
Mthfr	T	A	4: 148,051,360		probably null	Het
Muc5b	T	A	7: 141,850,810	D827E	unknown	Het
Myo1g	G	C	11: 6,508,243	L866V	probably damaging	Het
Myo3a	A	T	2: 22,578,158	M475L	probably benign	Het
Ncoa2	A	C	1: 13,174,366	L703V	probably damaging	Het
Nme6	T	A	9: 109,841,489	Y69*	probably null	Het
Nwd1	T	A	8: 72,671,086	M651K	probably benign	Het
Olfr726	A	C	14: 50,084,546	I45S	probably damaging	Het
Orc2	A	T	1: 58,474,818	S298R	possibly damaging	Het
Oscp1	A	T	4: 126,087,729	E328V	probably damaging	Het
Pan2	T	C	10: 128,317,969	V1003A	probably damaging	Het
Pik3r4	T	C	9: 105,682,308	V1200A	possibly damaging	Het
Prl	T	C	13: 27,057,596		probably benign	Het
Ptprk	T	C	10: 28,475,236	V575A	probably benign	Het
Rflna	A	T	5: 125,011,405	S139C	probably damaging	Het
Robo1	T	C	16: 72,742,150	F27S	probably benign	Het
Secisbp2	T	C	13: 51,665,424	S347P	probably benign	Het
Shmt1	A	G	11: 60,797,482		probably benign	Het
Slc27a3	A	G	3: 90,389,170		probably null	Het
Slc6a5	T	C	7: 49,936,209	V425A	probably damaging	Het
Slc8a3	A	G	12: 81,314,491	V518A	possibly damaging	Het
Slco1a4	A	T	6: 141,839,631	Y78N	probably damaging	Het
Stt3b	A	T	9: 115,266,143	H273Q	probably damaging	Het
Tle6	T	A	10: 81,592,801	N431I	probably damaging	Het
Trim34b	C	A	7: 104,329,911	Q122K	possibly damaging	Het
Trio	C	A	15: 27,902,600	R258S	probably benign	Het
Ttc7	A	T	17: 87,292,878	D23V	probably damaging	Het
Ttn	A	T	2: 76,980,181	M1K	probably null	Het
Ufsp2	T	C	8: 45,994,089	V391A	probably benign	Het
Vps13c	T	C	9: 67,908,052	L990S	probably damaging	Het
Zfp108	G	T	7: 24,260,738	K251N	probably benign	Het
Zfp618	G	A	4: 63,099,282	M234I	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
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
X0062:Ehmt1	UTSW	2	24863836	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