Mutagenetix > Incidental Mutation

Incidental Mutation 'R4352:Shmt2'

327351

Institutional Source

Beutler Lab

Gene Symbol

Shmt2

Ensembl Gene

ENSMUSG00000025403

Gene Name

serine hydroxymethyltransferase 2 (mitochondrial)

Synonyms

2700043D08Rik

MMRRC Submission

041668-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4352 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

127352992-127358313 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 127354686 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 333 (A333V)

Ref Sequence

ENSEMBL: ENSMUSP00000026470 (fasta)

Gene Model

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

AlphaFold

Q9CZN7

Predicted Effect

probably damaging
Transcript: ENSMUST00000026470
AA Change: A333V

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: A333V

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 damaging
Transcript: ENSMUST00000219239
AA Change: A330V

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000220356

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218492

Meta Mutation Damage Score

0.7106

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.6%

Validation Efficiency

96% (79/82)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	C	T	6: 128,557,349 (GRCm39)	A115T	probably benign	Het
Abtb2	T	A	2: 103,513,738 (GRCm39)	D382E	possibly damaging	Het
Adamts1	T	A	16: 85,599,234 (GRCm39)	D122V	probably benign	Het
Ankrd54	A	T	15: 78,939,662 (GRCm39)	F176I	probably benign	Het
Ano3	T	A	2: 110,576,239 (GRCm39)	E94V	possibly damaging	Het
Arid1b	A	T	17: 5,147,859 (GRCm39)	Q587L	possibly damaging	Het
Atg2a	G	A	19: 6,307,487 (GRCm39)	V1474M	probably benign	Het
Bcl2a1d	A	G	9: 88,613,552 (GRCm39)	V74A	probably damaging	Het
Bmper	A	G	9: 23,395,248 (GRCm39)	I660V	probably benign	Het
Cdh20	A	G	1: 104,906,814 (GRCm39)	D547G	probably damaging	Het
Cds2	T	A	2: 132,105,365 (GRCm39)	M1K	probably null	Het
Ctr9	T	A	7: 110,648,525 (GRCm39)	Y722N	probably damaging	Het
Ddx47	C	T	6: 134,995,018 (GRCm39)	T161I	probably benign	Het
Dvl3	T	C	16: 20,344,394 (GRCm39)	Y257H	possibly damaging	Het
Dzip1	T	C	14: 119,120,938 (GRCm39)	D673G	probably benign	Het
Efcab3	T	A	11: 104,630,140 (GRCm39)	L957Q	probably null	Het
Emilin2	T	C	17: 71,587,726 (GRCm39)	M129V	probably benign	Het
Eml1	A	T	12: 108,501,096 (GRCm39)		probably benign	Het
Espnl	A	T	1: 91,262,443 (GRCm39)	D296V	probably damaging	Het
Fam161a	T	G	11: 22,970,798 (GRCm39)	S109R	possibly damaging	Het
Fat3	T	G	9: 16,158,074 (GRCm39)	T1179P	possibly damaging	Het
Gfra1	A	T	19: 58,255,456 (GRCm39)	N330K	probably benign	Het
Gfy	T	C	7: 44,827,040 (GRCm39)	E352G	probably benign	Het
Gm20775	A	T	Y: 10,641,648 (GRCm39)		noncoding transcript	Het
Gm5885	T	A	6: 133,508,152 (GRCm39)		noncoding transcript	Het
Gpatch11	T	C	17: 79,148,446 (GRCm39)	L128P	probably damaging	Het
H2-Q1	A	G	17: 35,539,919 (GRCm39)	N63D	possibly damaging	Het
Itgb2	A	T	10: 77,392,001 (GRCm39)	N358I	probably benign	Het
Jmjd1c	A	G	10: 67,080,588 (GRCm39)	T2247A	probably damaging	Het
Kcnma1	T	A	14: 23,361,720 (GRCm39)	K1036I	probably damaging	Het
Llgl1	C	T	11: 60,600,394 (GRCm39)	P581L	probably benign	Het
Lrch1	G	T	14: 75,056,018 (GRCm39)	S278R	probably damaging	Het
Lrp2	C	A	2: 69,262,526 (GRCm39)		probably null	Het
Lyn	G	A	4: 3,789,796 (GRCm39)	R443H	probably damaging	Het
Mecom	C	A	3: 30,020,887 (GRCm39)	V452L	possibly damaging	Het
Mpzl1	G	A	1: 165,433,376 (GRCm39)	Q36*	probably null	Het
Msantd5	A	G	11: 51,125,646 (GRCm39)	N190D	possibly damaging	Het
Npr2	T	C	4: 43,646,592 (GRCm39)	S647P	probably damaging	Het
Nrp2	A	G	1: 62,777,576 (GRCm39)	D127G	probably damaging	Het
Otogl	A	T	10: 107,705,396 (GRCm39)	C644S	probably damaging	Het
Pabpc4	C	T	4: 123,184,060 (GRCm39)	T191I	probably damaging	Het
Paqr3	T	C	5: 97,247,455 (GRCm39)	T218A	probably benign	Het
Pcdh7	C	T	5: 57,879,361 (GRCm39)	S972L	possibly damaging	Het
Pcnx2	T	C	8: 126,489,590 (GRCm39)	H1668R	probably damaging	Het
Prb1b	T	G	6: 132,290,624 (GRCm39)	Y25S	unknown	Het
Ralb	A	G	1: 119,411,282 (GRCm39)	M19T	probably benign	Het
Rcan1	A	G	16: 92,190,384 (GRCm39)	I185T	probably benign	Het
Rnf38	A	T	4: 44,149,100 (GRCm39)	N82K	possibly damaging	Het
Rock1	T	A	18: 10,079,237 (GRCm39)	Q1077L	probably damaging	Het
Sesn3	C	T	9: 14,231,669 (GRCm39)	A200V	probably damaging	Het
Shh	T	C	5: 28,663,187 (GRCm39)	E327G	probably benign	Het
Slc15a2	T	A	16: 36,592,390 (GRCm39)	I256F	probably benign	Het
Sptbn5	T	C	2: 119,913,680 (GRCm39)		noncoding transcript	Het
Sst	A	G	16: 23,708,565 (GRCm39)	S89P	probably damaging	Het
Taf10	A	G	7: 105,392,614 (GRCm39)		probably benign	Het
Tas2r139	T	A	6: 42,118,689 (GRCm39)	W274R	probably damaging	Het
Tbc1d20	T	A	2: 152,150,114 (GRCm39)		probably benign	Het
Tbc1d5	A	G	17: 51,089,429 (GRCm39)	S584P	probably damaging	Het
Tcstv1a	T	C	13: 120,355,407 (GRCm39)	D75G	probably damaging	Het
Tex10	T	G	4: 48,452,039 (GRCm39)	T696P	possibly damaging	Het
Tgfbr1	T	C	4: 47,402,863 (GRCm39)	F206S	probably damaging	Het
Tmem241	A	T	18: 12,246,496 (GRCm39)	H51Q	probably benign	Het
Trim5	A	T	7: 103,926,015 (GRCm39)	V182D	probably damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Txnl1	A	G	18: 63,804,750 (GRCm39)	V248A	possibly damaging	Het
Ubr5	A	G	15: 38,041,817 (GRCm39)	V204A	probably benign	Het
Ugp2	C	T	11: 21,279,026 (GRCm39)	V387I	probably damaging	Het
Unc45b	G	A	11: 82,804,035 (GRCm39)	D71N	probably damaging	Het
Usp34	A	T	11: 23,270,727 (GRCm39)	Y37F	possibly damaging	Het
Zfp943	A	T	17: 22,212,104 (GRCm39)	I397F	probably 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
R2006:Shmt2	UTSW	10	127,355,029 (GRCm39)	missense	probably benign	0.22
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
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'- TGTACTGAACAAGGAGGACTCC -3'
(R):5'- GTGGATCCTCTGAGCACCTATG -3'

Sequencing Primer
(F):5'- CATGACCCCGGCTTTGCTG -3'
(R):5'- GCACCTATGCCAGTCATCCG -3'

Posted On

2015-07-07