Mutagenetix > Incidental Mutations

Incidental Mutation 'R5309:Ehmt1'

404688

Institutional Source

Beutler Lab

Gene Symbol

Ehmt1

Ensembl Gene

ENSMUSG00000036893

Gene Name

euchromatic histone methyltransferase 1

Synonyms

KMT1D, 9230102N17Rik

MMRRC Submission

042892-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R5309 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24789928-24919614 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 24884195 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 201 (V201A)

Ref Sequence

ENSEMBL: ENSMUSP00000123187 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046227] [ENSMUST00000091348] [ENSMUST00000102938] [ENSMUST00000114418] [ENSMUST00000114432] [ENSMUST00000147147] [ENSMUST00000150379] [ENSMUST00000152161] [ENSMUST00000198923] [ENSMUST00000200655]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000046227
AA Change: V199A

PolyPhen 2 Score 0.859 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000046077
Gene: ENSMUSG00000036893
AA Change: V199A

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

possibly damaging
Transcript: ENSMUST00000091348
AA Change: V198A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000088906
Gene: ENSMUSG00000036893
AA Change: V198A

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

possibly damaging
Transcript: ENSMUST00000102938
AA Change: V199A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000100002
Gene: ENSMUSG00000036893
AA Change: V199A

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

possibly damaging
Transcript: ENSMUST00000114418
AA Change: V199A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000110061
Gene: ENSMUSG00000036893
AA Change: V199A

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

possibly damaging
Transcript: ENSMUST00000114432
AA Change: V199A

PolyPhen 2 Score 0.859 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000110075
Gene: ENSMUSG00000036893
AA Change: V199A

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

possibly damaging
Transcript: ENSMUST00000147147
AA Change: V199A

PolyPhen 2 Score 0.859 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000119057
Gene: ENSMUSG00000036893
AA Change: V199A

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: V201A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Predicted Effect

probably damaging
Transcript: ENSMUST00000152161
AA Change: V198A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000119854
Gene: ENSMUSG00000036893
AA Change: V198A

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000198923
AA Change: V75A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000143189
Gene: ENSMUSG00000036893
AA Change: V75A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000200655

Meta Mutation Damage Score

0.0758

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.3%

Validation Efficiency

99% (68/69)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9030624J02Rik	T	C	7: 118,813,576	I629T	probably damaging	Het
A630073D07Rik	T	C	6: 132,626,577	Q72R	unknown	Het
Abca15	T	C	7: 120,345,369	V409A	probably damaging	Het
Abcg3	A	C	5: 104,936,599	C577G	possibly damaging	Het
Adamtsl5	A	T	10: 80,345,148		probably benign	Het
Adgrg3	G	A	8: 95,039,864	V388I	probably benign	Het
Ank2	T	C	3: 126,959,768	Q288R	probably damaging	Het
Ccdc173	T	C	2: 69,787,258	T60A	possibly damaging	Het
Cdc45	C	T	16: 18,795,897	R205H	probably damaging	Het
Cdh3	A	G	8: 106,539,020	T232A	probably damaging	Het
Cntnap5c	A	T	17: 58,359,254	E1093V	probably benign	Het
Cwh43	A	G	5: 73,416,767	H258R	probably benign	Het
Cyp2j6	T	A	4: 96,535,556	I192F	probably damaging	Het
Dnaaf5	T	A	5: 139,152,862	V266E	probably damaging	Het
Egfr	G	A	11: 16,911,703	G1161S	probably benign	Het
Exoc7	C	A	11: 116,305,027	E28*	probably null	Het
Fam118a	C	T	15: 85,050,755	T195M	probably damaging	Het
Fancg	A	G	4: 43,003,019	F613L	probably benign	Het
Fbxo10	A	T	4: 45,042,036	I731N	possibly damaging	Het
Fchsd1	C	T	18: 37,959,873		probably benign	Het
Gfm2	G	A	13: 97,163,151	A406T	probably damaging	Het
Gnal	G	A	18: 67,213,107	R219K	possibly damaging	Het
Helz2	T	A	2: 181,234,846	E1285V	probably benign	Het
Ighv1-74	A	G	12: 115,802,881	S39P	probably damaging	Het
Ipo11	T	C	13: 106,833,973		probably benign	Het
Klc1	A	G	12: 111,795,621	K575R	possibly damaging	Het
Larp1	T	C	11: 58,050,808	V689A	possibly damaging	Het
Lman1l	A	T	9: 57,611,077	L343Q	probably damaging	Het
Mki67	A	T	7: 135,700,830	V825E	probably damaging	Het
Mmp9	T	A	2: 164,950,795		probably benign	Het
Myog	A	G	1: 134,290,326	K91E	probably damaging	Het
Nfil3	A	T	13: 52,967,620	V416E	probably damaging	Het
Nup160	G	T	2: 90,732,832	E1314*	probably null	Het
Olfr1277	T	G	2: 111,270,310	D19A	probably benign	Het
Olfr1284	T	C	2: 111,379,834	V278A	possibly damaging	Het
Olfr790	T	A	10: 129,501,514	V210E	probably damaging	Het
Olfr792	A	C	10: 129,541,265	M243L	probably benign	Het
Osbpl8	T	A	10: 111,270,557	V275E	probably benign	Het
Osbpl9	A	G	4: 109,066,155	S520P	probably damaging	Het
Ppp4r4	T	A	12: 103,606,888		probably null	Het
Proz	T	C	8: 13,061,049	L7P	probably damaging	Het
Ptpn13	G	A	5: 103,541,053	S904N	probably damaging	Het
Rap1gds1	A	G	3: 138,958,628	L322P	probably damaging	Het
Rnf5	A	G	17: 34,601,588	F175S	probably benign	Het
Sema4a	G	A	3: 88,437,036	S636F	probably damaging	Het
Sfrp2	A	G	3: 83,769,401	D193G	probably damaging	Het
Shoc2	T	C	19: 53,987,733	V18A	probably benign	Het
Skint8	C	A	4: 111,950,193	L359M	probably damaging	Het
Slc10a6	A	T	5: 103,609,092	C269S	probably damaging	Het
Slc34a2	A	G	5: 53,069,488	E651G	probably damaging	Het
Snx13	C	T	12: 35,144,325	Q956*	probably null	Het
Spg21	A	G	9: 65,468,802	I31V	probably benign	Het
Srpk2	T	C	5: 23,525,718	K268E	probably damaging	Het
Supt16	T	C	14: 52,162,698	E996G	probably damaging	Het
Syf2	A	G	4: 134,936,069	D184G	probably benign	Het
Tmem45a2	T	C	16: 57,039,007	D287G	possibly damaging	Het
Utrn	A	T	10: 12,727,769	D627E	probably damaging	Het
Vmn1r170	T	A	7: 23,606,455	I94N	probably damaging	Het
Vmn2r103	A	T	17: 19,793,034	N139I	probably benign	Het
Vmn2r15	T	A	5: 109,293,090	I301F	probably damaging	Het
Zfp949	A	C	9: 88,567,183	T14P	possibly damaging	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
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'- CAATGTATCACCTGGCTTTGCTG -3'
(R):5'- TTAAATAAACCAGCCCTGCAGG -3'

Sequencing Primer
(F):5'- ACCTGGCTTTGCTGTTCATATG -3'
(R):5'- CGTTGAGGACTCCCAACATTC -3'

Posted On

2016-07-22