Mutagenetix > Incidental Mutation

Incidental Mutation 'R2006:Shmt2'

225595

Institutional Source

Beutler Lab

Gene Symbol

Shmt2

Ensembl Gene

ENSMUSG00000025403

Gene Name

serine hydroxymethyltransferase 2 (mitochondrial)

Synonyms

2700043D08Rik

MMRRC Submission

040015-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2006 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

127352992-127358313 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 127355029 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 273 (V273A)

Ref Sequence

ENSEMBL: ENSMUSP00000026470 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026470] [ENSMUST00000035735] [ENSMUST00000219239]

AlphaFold

Q9CZN7

Predicted Effect

probably benign
Transcript: ENSMUST00000026470
AA Change: V273A

PolyPhen 2 Score 0.215 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: V273A

Domain	Start	End	E-Value	Type
Pfam:SHMT	49	448	5.4e-211	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000035735

SMART Domains

Protein: ENSMUSP00000042185
Gene: ENSMUSG00000040280

Domain	Start	End	E-Value	Type
Pfam:B12D	16	84	2.5e-32	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000217682

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218035

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218258

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218302

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218313

Predicted Effect

probably benign
Transcript: ENSMUST00000219239
AA Change: V270A

PolyPhen 2 Score 0.179 (Sensitivity: 0.92; Specificity: 0.87)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218492

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000220356

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit lethlity after E13.5, decreased size, anemia and reduced MEF cellular respiration and proliferation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca5	A	T	11: 110,204,275 (GRCm39)	F333L	probably benign	Het
Abcc2	T	A	19: 43,793,500 (GRCm39)	F384Y	probably damaging	Het
Acr	C	T	15: 89,458,404 (GRCm39)	P362S	probably benign	Het
Acss3	T	C	10: 106,798,871 (GRCm39)	D484G	possibly damaging	Het
Actrt1	A	G	X: 45,418,593 (GRCm39)	T203A	probably benign	Het
Agtpbp1	A	T	13: 59,648,135 (GRCm39)	C562S	probably benign	Het
Ahnak	A	G	19: 8,984,439 (GRCm39)	K1908E	probably damaging	Het
Amph	G	A	13: 19,326,198 (GRCm39)	V643M	probably damaging	Het
Apaf1	A	T	10: 90,897,634 (GRCm39)	I283N	probably damaging	Het
Bbx	G	A	16: 50,044,758 (GRCm39)	T493M	possibly damaging	Het
Best2	C	T	8: 85,739,818 (GRCm39)		probably null	Het
C4bp	C	A	1: 130,575,769 (GRCm39)	E75*	probably null	Het
Calr3	A	T	8: 73,188,695 (GRCm39)	V144D	probably damaging	Het
Capn1	C	T	19: 6,041,613 (GRCm39)	G632D	probably damaging	Het
Catsper2	C	A	2: 121,236,838 (GRCm39)	E270*	probably null	Het
Ccdc110	A	T	8: 46,396,349 (GRCm39)	I747F	probably damaging	Het
Ccdc15	T	A	9: 37,226,768 (GRCm39)	D389V	possibly damaging	Het
Cd226	A	G	18: 89,265,435 (GRCm39)	I125V	probably benign	Het
Crb2	A	T	2: 37,673,446 (GRCm39)	D114V	probably damaging	Het
Crebbp	TTGCTGCTGCTGCTGCTG	TTGCTGCTGCTGCTG	16: 3,902,617 (GRCm39)		probably benign	Het
Crebrf	T	C	17: 26,961,857 (GRCm39)	V318A	possibly damaging	Het
Dab1	T	C	4: 104,462,522 (GRCm39)	I32T	probably damaging	Het
Daw1	T	C	1: 83,169,066 (GRCm39)	V181A	probably damaging	Het
Dlg2	G	A	7: 91,614,825 (GRCm39)	E255K	possibly damaging	Het
Dnah10	T	A	5: 124,906,651 (GRCm39)	D4170E	possibly damaging	Het
Dnah12	A	G	14: 26,536,416 (GRCm39)	T2111A	possibly damaging	Het
Dock10	T	C	1: 80,527,506 (GRCm39)	Y1081C	possibly damaging	Het
Dscam	T	C	16: 96,621,112 (GRCm39)	Y532C	probably damaging	Het
Fam83c	T	C	2: 155,672,223 (GRCm39)	D404G	probably benign	Het
Fam83g	A	G	11: 61,593,801 (GRCm39)	N445S	possibly damaging	Het
Ghr	C	T	15: 3,357,464 (GRCm39)	C268Y	probably damaging	Het
Gm8444	T	C	15: 81,727,775 (GRCm39)		probably benign	Het
Gp6	T	A	7: 4,387,988 (GRCm39)	K160N	probably benign	Het
Grm3	T	C	5: 9,639,793 (GRCm39)	Y84C	possibly damaging	Het
Gtf3c2	C	A	5: 31,325,440 (GRCm39)	G450C	probably damaging	Het
Icosl	A	T	10: 77,907,787 (GRCm39)	M116L	possibly damaging	Het
Il31ra	T	G	13: 112,666,890 (GRCm39)	Y396S	probably damaging	Het
Insig1	A	G	5: 28,276,464 (GRCm39)	N10S	probably benign	Het
Kcnh2	C	A	5: 24,531,568 (GRCm39)	G448C	probably damaging	Het
L1td1	C	T	4: 98,621,726 (GRCm39)	S96L	possibly damaging	Het
Mapre3	A	T	5: 31,019,168 (GRCm39)	N4I	probably damaging	Het
Mblac2	T	A	13: 81,859,860 (GRCm39)	D70E	probably benign	Het
Mki67	T	A	7: 135,300,238 (GRCm39)	K1599*	probably null	Het
Mpg	A	G	11: 32,181,840 (GRCm39)	I283V	probably benign	Het
Mrtfb	G	T	16: 13,199,440 (GRCm39)	E98*	probably null	Het
Mybpc1	C	A	10: 88,381,921 (GRCm39)	A576S	probably damaging	Het
Myo1h	T	G	5: 114,499,140 (GRCm39)	V129G	probably damaging	Het
Nars1	A	T	18: 64,638,099 (GRCm39)	V285E	probably damaging	Het
Nbas	T	A	12: 13,464,742 (GRCm39)		probably null	Het
Neb	T	C	2: 52,089,456 (GRCm39)	D5172G	probably null	Het
Npbwr1	T	A	1: 5,986,570 (GRCm39)	S315C	probably damaging	Het
Nyap1	T	C	5: 137,733,953 (GRCm39)	H360R	possibly damaging	Het
Nyx	A	G	X: 13,352,974 (GRCm39)	E276G	probably damaging	Het
Or10ag59	T	A	2: 87,405,536 (GRCm39)	M36K	probably benign	Het
Or1e1	G	T	11: 73,245,518 (GRCm39)	C313F	probably benign	Het
Or2l13b	A	G	16: 19,349,455 (GRCm39)	Y72H	probably benign	Het
Or2w6	T	C	13: 21,842,642 (GRCm39)	T284A	possibly damaging	Het
Or4c1	A	G	2: 89,133,160 (GRCm39)	Y259H	possibly damaging	Het
Or4c118	A	T	2: 88,975,241 (GRCm39)	V42E	probably benign	Het
Or5v1b	C	T	17: 37,841,597 (GRCm39)	S243F	probably damaging	Het
Or7e174	A	T	9: 20,012,165 (GRCm39)	M37L	probably benign	Het
Or7g16	G	A	9: 18,726,801 (GRCm39)	S263L	probably benign	Het
Or8g23	T	A	9: 38,971,729 (GRCm39)	T78S	probably damaging	Het
Paf1	C	A	7: 28,095,193 (GRCm39)		probably null	Het
Pcsk5	T	C	19: 17,455,280 (GRCm39)	D1050G	probably benign	Het
Pgap1	A	G	1: 54,590,220 (GRCm39)	S73P	possibly damaging	Het
Phtf1	G	A	3: 103,911,799 (GRCm39)		probably null	Het
Pik3c2b	G	T	1: 132,994,282 (GRCm39)	R82L	probably damaging	Het
Pik3ca	T	C	3: 32,504,206 (GRCm39)	L632P	probably damaging	Het
Plau	G	T	14: 20,888,760 (GRCm39)		probably null	Het
Pld4	A	T	12: 112,734,923 (GRCm39)	Q460L	possibly damaging	Het
Prdm2	T	A	4: 142,858,447 (GRCm39)	Q1614H	possibly damaging	Het
Ptprq	C	T	10: 107,502,407 (GRCm39)	G837D	probably damaging	Het
Rad9b	A	G	5: 122,477,842 (GRCm39)	V178A	possibly damaging	Het
Rfc1	G	T	5: 65,468,397 (GRCm39)	Y105*	probably null	Het
Sardh	G	A	2: 27,118,351 (GRCm39)	R460C	probably damaging	Het
Scn5a	C	A	9: 119,365,546 (GRCm39)	R367L	probably damaging	Het
Sdcbp	A	T	4: 6,386,536 (GRCm39)	I137L	probably benign	Het
Slc5a9	G	T	4: 111,737,423 (GRCm39)	P612H	probably benign	Het
Slitrk4	TTGT	TT	X: 63,314,294 (GRCm39)		probably null	Het
Slitrk4	TG	T	X: 63,314,295 (GRCm39)		probably null	Het
Spata1	A	T	3: 146,199,438 (GRCm39)	S9T	probably benign	Het
Syn3	T	C	10: 85,909,097 (GRCm39)	T328A	probably benign	Het
Tdrd6	A	G	17: 43,939,546 (GRCm39)	F501L	probably damaging	Het
Tekt5	T	C	16: 10,213,070 (GRCm39)	I72V	probably benign	Het
Ticrr	T	C	7: 79,343,821 (GRCm39)	S1229P	possibly damaging	Het
Tlr6	T	C	5: 65,110,748 (GRCm39)	S720G	probably damaging	Het
Tmem156	T	A	5: 65,237,294 (GRCm39)	D87V	probably damaging	Het
Togaram1	T	A	12: 65,065,914 (GRCm39)	D1639E	probably damaging	Het
Ucn2	A	G	9: 108,815,430 (GRCm39)	K64R	probably benign	Het
Vmn2r57	T	A	7: 41,098,001 (GRCm39)	Y22F	probably benign	Het
Vwa1	T	C	4: 155,855,307 (GRCm39)	T269A	probably benign	Het
Washc5	A	G	15: 59,213,004 (GRCm39)	L892P	possibly damaging	Het
Wdr20	T	C	12: 110,760,002 (GRCm39)	V296A	probably damaging	Het
Xxylt1	A	T	16: 30,869,586 (GRCm39)	H171Q	probably damaging	Het
Yju2	C	T	17: 56,271,543 (GRCm39)	Q155*	probably null	Het
Zfp275	A	G	X: 72,396,841 (GRCm39)	T118A	possibly damaging	Het

Other mutations in Shmt2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02862:Shmt2	APN	10	127,354,743 (GRCm39)	missense	probably benign	0.00
R0057:Shmt2	UTSW	10	127,356,917 (GRCm39)	missense	possibly damaging	0.88
R0057:Shmt2	UTSW	10	127,356,917 (GRCm39)	missense	possibly damaging	0.88
R0504:Shmt2	UTSW	10	127,355,941 (GRCm39)	missense	probably damaging	1.00
R1493:Shmt2	UTSW	10	127,354,812 (GRCm39)	splice site	probably null
R2342:Shmt2	UTSW	10	127,354,680 (GRCm39)	missense	possibly damaging	0.94
R2358:Shmt2	UTSW	10	127,353,897 (GRCm39)	missense	probably benign	0.00
R4352:Shmt2	UTSW	10	127,354,686 (GRCm39)	missense	probably damaging	0.97
R4998:Shmt2	UTSW	10	127,354,139 (GRCm39)	missense	probably damaging	1.00
R5242:Shmt2	UTSW	10	127,354,789 (GRCm39)	missense	probably benign	0.00
R5568:Shmt2	UTSW	10	127,356,250 (GRCm39)	missense	probably damaging	1.00
R5654:Shmt2	UTSW	10	127,353,668 (GRCm39)	missense	probably benign	0.05
R6167:Shmt2	UTSW	10	127,353,731 (GRCm39)	missense	probably benign
R8465:Shmt2	UTSW	10	127,355,945 (GRCm39)	missense	probably damaging	1.00
R8503:Shmt2	UTSW	10	127,354,789 (GRCm39)	missense	probably benign	0.00
R8776:Shmt2	UTSW	10	127,356,785 (GRCm39)	critical splice donor site	probably null
R8776-TAIL:Shmt2	UTSW	10	127,356,785 (GRCm39)	critical splice donor site	probably null
R9099:Shmt2	UTSW	10	127,355,962 (GRCm39)	missense	possibly damaging	0.86
R9124:Shmt2	UTSW	10	127,355,561 (GRCm39)	missense	possibly damaging	0.88
Z1176:Shmt2	UTSW	10	127,355,347 (GRCm39)	missense	possibly damaging	0.46
Z1177:Shmt2	UTSW	10	127,356,804 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GGAAGATGCATAGTCAGGCTC -3'
(R):5'- GGGACTGCCAATCAAGCTTTC -3'

Sequencing Primer
(F):5'- TGCATAGTCAGGCTCTAAAAGG -3'
(R):5'- CAATCAAGCTTTCCTCTATGGGGG -3'

Posted On

2014-08-25