Mutagenetix > Incidental Mutation

Incidental Mutation 'R2497:Smyd2'

251028

Institutional Source

Beutler Lab

Gene Symbol

Smyd2

Ensembl Gene

ENSMUSG00000026603

Gene Name

SET and MYND domain containing 2

Synonyms

Zmynd14, 1110020E07Rik, KMT3C

MMRRC Submission

040411-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2497 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

189612689-189654560 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 189617534 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 300 (N300I)

Ref Sequence

ENSEMBL: ENSMUSP00000027897 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027897]

AlphaFold

Q8R5A0

PDB Structure

Crystal structure of histone lysine methyltransferase SmyD2 in complex with the cofactor product AdoHcy [X-RAY DIFFRACTION]
Crystal structure of histone lysine methyltransferase SmyD2 in complex with the methyltransferase inhibitor sinefungin [X-RAY DIFFRACTION]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000027897
AA Change: N300I

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000027897
Gene: ENSMUSG00000026603
AA Change: N300I

Domain	Start	End	E-Value	Type
SET	7	247	2.88e-2	SMART
SCOP:d1elra_	344	411	8e-5	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130804

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132289

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144452

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193794

Meta Mutation Damage Score

0.2658

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.3%

Validation Efficiency

100% (60/60)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] SET domain-containing proteins, such as SMYD2, catalyze lysine methylation (Brown et al., 2006 [PubMed 16805913]).[supplied by OMIM, Nov 2008]
PHENOTYPE: Mice homozygous for a targeted allele exhibit increased circulating total and LDL cholesterol levels and decreased circulating sodium and chloride levels. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acox2	A	G	14: 8,251,612 (GRCm38)	V295A	probably benign	Het
Agrn	T	C	4: 156,258,268 (GRCm39)	E959G	probably benign	Het
Aqp5	T	C	15: 99,489,180 (GRCm39)	F10L	possibly damaging	Het
Arhgap39	C	A	15: 76,609,585 (GRCm39)	V1025L	probably damaging	Het
Atg4d	C	T	9: 21,184,682 (GRCm39)	R459*	probably null	Het
Atp11b	A	G	3: 35,909,294 (GRCm39)	S1163G	probably damaging	Het
Atp13a5	G	T	16: 29,157,889 (GRCm39)	S173*	probably null	Het
Atp6v1g2	T	A	17: 35,455,762 (GRCm39)	I8N	probably damaging	Het
Ccdc77	C	T	6: 120,302,433 (GRCm39)	G430R	possibly damaging	Het
Cdc34b	A	G	11: 94,633,207 (GRCm39)	T136A	probably benign	Het
Cdkal1	A	G	13: 29,658,524 (GRCm39)	S23P	unknown	Het
Cdkl2	T	A	5: 92,156,857 (GRCm39)	H566L	probably benign	Het
Cers6	T	C	2: 68,901,790 (GRCm39)		probably benign	Het
Cfap251	T	C	5: 123,421,432 (GRCm39)	V98A	probably damaging	Het
Clspn	A	G	4: 126,466,140 (GRCm39)	T557A	possibly damaging	Het
Cmya5	T	C	13: 93,234,513 (GRCm39)	T192A	possibly damaging	Het
Csmd3	CCTTTGCGCTT	CCTT	15: 47,604,632 (GRCm39)		probably null	Het
Dnah17	T	G	11: 117,977,850 (GRCm39)		probably null	Het
Dnah8	C	T	17: 30,960,339 (GRCm39)	Q2239*	probably null	Het
Dscaml1	T	C	9: 45,656,376 (GRCm39)	V1572A	probably benign	Het
Elfn2	C	G	15: 78,558,464 (GRCm39)	E28Q	probably damaging	Het
Enam	T	A	5: 88,650,553 (GRCm39)	N687K	probably benign	Het
Flywch1	G	A	17: 23,974,685 (GRCm39)	R652W	probably benign	Het
Gm5612	T	C	9: 18,338,975 (GRCm39)		probably benign	Het
Hgsnat	C	T	8: 26,435,280 (GRCm39)	W618*	probably null	Het
Mmp3	A	G	9: 7,450,131 (GRCm39)	T288A	probably benign	Het
Mtmr4	T	A	11: 87,491,649 (GRCm39)	F168L	probably damaging	Het
Mtres1	T	C	10: 43,401,263 (GRCm39)		probably benign	Het
Myo1d	T	A	11: 80,565,647 (GRCm39)	N393Y	probably damaging	Het
Nacc2	A	T	2: 25,979,580 (GRCm39)	Y285*	probably null	Het
Nf1	G	T	11: 79,334,710 (GRCm39)	G844V	probably damaging	Het
Nox4	T	A	7: 86,945,084 (GRCm39)	Y113*	probably null	Het
Pcdha3	T	C	18: 37,080,556 (GRCm39)	C433R	probably benign	Het
Pde6c	A	G	19: 38,142,142 (GRCm39)	I358V	probably damaging	Het
Pdgfrb	A	T	18: 61,211,700 (GRCm39)	D819V	possibly damaging	Het
Phf3	C	A	1: 30,869,095 (GRCm39)	R651L	probably damaging	Het
Prrx1	A	G	1: 163,075,834 (GRCm39)	V244A	possibly damaging	Het
Ptges	C	T	2: 30,782,722 (GRCm39)	G110D	possibly damaging	Het
Rab27a	T	C	9: 72,992,263 (GRCm39)	L97P	probably damaging	Het
Rnf20	G	A	4: 49,652,676 (GRCm39)		probably null	Het
Sdad1	T	C	5: 92,447,958 (GRCm39)	N259S	probably benign	Het
Serpinb9d	T	C	13: 33,380,500 (GRCm39)	S129P	probably damaging	Het
Slc1a4	T	C	11: 20,282,620 (GRCm39)		probably benign	Het
Snd1	A	G	6: 28,888,078 (GRCm39)	I875V	probably benign	Het
Ssh1	T	C	5: 114,096,919 (GRCm39)	N174S	probably damaging	Het
Stimate	C	T	14: 30,594,537 (GRCm39)	L217F	probably damaging	Het
Tanc2	T	C	11: 105,564,319 (GRCm39)		probably null	Het
Tectb	C	G	19: 55,169,431 (GRCm39)		probably benign	Het
Tpcn1	C	T	5: 120,677,063 (GRCm39)		probably null	Het
Unc45b	A	T	11: 82,827,269 (GRCm39)	I699F	probably damaging	Het
Uspl1	C	T	5: 149,124,664 (GRCm39)	P27L	probably damaging	Het
Ylpm1	C	G	12: 85,043,535 (GRCm39)	P91R	probably damaging	Het
Zdhhc23	G	A	16: 43,794,278 (GRCm39)	T132M	probably damaging	Het
Zfp148	T	C	16: 33,316,755 (GRCm39)	Y434H	probably damaging	Het
Zhx2	T	C	15: 57,686,551 (GRCm39)	V640A	possibly damaging	Het

Other mutations in Smyd2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00480:Smyd2	APN	1	189,632,043 (GRCm39)	missense	probably damaging	1.00
IGL01060:Smyd2	APN	1	189,629,667 (GRCm39)	missense	possibly damaging	0.66
IGL01938:Smyd2	APN	1	189,621,079 (GRCm39)	missense	probably benign	0.05
IGL02113:Smyd2	APN	1	189,614,414 (GRCm39)	missense	probably damaging	0.99
IGL03075:Smyd2	APN	1	189,621,029 (GRCm39)	missense	probably damaging	0.98
R0739:Smyd2	UTSW	1	189,621,059 (GRCm39)	missense	possibly damaging	0.50
R2108:Smyd2	UTSW	1	189,629,623 (GRCm39)	missense	probably damaging	1.00
R4466:Smyd2	UTSW	1	189,614,349 (GRCm39)	missense	probably benign	0.09
R4605:Smyd2	UTSW	1	189,629,623 (GRCm39)	missense	probably damaging	1.00
R4672:Smyd2	UTSW	1	189,642,101 (GRCm39)	missense	probably damaging	1.00
R4872:Smyd2	UTSW	1	189,628,847 (GRCm39)	missense	probably damaging	1.00
R4963:Smyd2	UTSW	1	189,614,385 (GRCm39)	missense	probably damaging	1.00
R5419:Smyd2	UTSW	1	189,642,090 (GRCm39)	nonsense	probably null
R5660:Smyd2	UTSW	1	189,617,579 (GRCm39)	missense	possibly damaging	0.95
R6271:Smyd2	UTSW	1	189,616,049 (GRCm39)	missense	probably damaging	1.00
R8291:Smyd2	UTSW	1	189,632,288 (GRCm39)	intron	probably benign
R8820:Smyd2	UTSW	1	189,632,018 (GRCm39)	missense	probably benign	0.03
R9011:Smyd2	UTSW	1	189,628,833 (GRCm39)	missense	probably damaging	0.99
R9612:Smyd2	UTSW	1	189,612,983 (GRCm39)	makesense	probably null

Predicted Primers

PCR Primer
(F):5'- TTCAGTCTAGTGAGGACAGTCG -3'
(R):5'- TGCATCTGTGGGGATACAGG -3'

Sequencing Primer
(F):5'- TAGTGAGGACAGTCGCTCCTG -3'
(R):5'- TACAGGGATGATTTGAGCAGCTCC -3'

Posted On

2014-12-04