Mutagenetix > Incidental Mutation

Incidental Mutation 'R5654:Shmt2'

442184

Institutional Source

Beutler Lab

Gene Symbol

Shmt2

Ensembl Gene

ENSMUSG00000025403

Gene Name

serine hydroxymethyltransferase 2 (mitochondrial)

Synonyms

2700043D08Rik

MMRRC Submission

043300-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5654 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

127352992-127358313 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 127353668 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 499 (D499G)

Ref Sequence

ENSEMBL: ENSMUSP00000151616 (fasta)

Gene Model

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

AlphaFold

Q9CZN7

Predicted Effect

probably benign
Transcript: ENSMUST00000026470
AA Change: D502G

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: D502G

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: D499G

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218492

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000220356

Meta Mutation Damage Score

0.0999

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.6%
20x: 96.1%

Validation Efficiency

96% (69/72)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb6	T	C	1: 75,151,479 (GRCm39)		probably null	Het
Abcc9	G	A	6: 142,571,371 (GRCm39)		probably benign	Het
Acss2	T	C	2: 155,416,575 (GRCm39)		probably benign	Het
Atp8b4	G	A	2: 126,217,725 (GRCm39)	T597I	probably damaging	Het
Btaf1	A	T	19: 36,961,015 (GRCm39)	N796I	probably benign	Het
Caskin2	T	C	11: 115,690,905 (GRCm39)		probably null	Het
Cdhr2	A	G	13: 54,884,349 (GRCm39)	N1295D	probably benign	Het
Cog3	G	A	14: 75,962,239 (GRCm39)	T534M	probably benign	Het
Cpne1	A	G	2: 155,919,561 (GRCm39)	S303P	probably damaging	Het
Cs	G	A	10: 128,187,086 (GRCm39)	G74S	possibly damaging	Het
Cyb5r4	G	T	9: 86,929,533 (GRCm39)	S229I	probably damaging	Het
Ddr1	C	T	17: 35,997,400 (GRCm39)	A531T	probably benign	Het
Ect2l	C	T	10: 18,018,810 (GRCm39)	V529M	probably damaging	Het
Edaradd	C	A	13: 12,493,161 (GRCm39)	R177L	possibly damaging	Het
Esf1	T	C	2: 140,006,148 (GRCm39)	D333G	possibly damaging	Het
Fam8a1	T	A	13: 46,827,814 (GRCm39)	L334H	probably damaging	Het
Fbxl18	A	G	5: 142,871,558 (GRCm39)	I559T	probably damaging	Het
Fcrl2	A	C	3: 87,164,851 (GRCm39)	V225G	probably benign	Het
Ido1	C	T	8: 25,077,819 (GRCm39)	V83M	probably damaging	Het
Iffo1	T	G	6: 125,130,030 (GRCm39)	C419G	probably damaging	Het
Igfals	A	T	17: 25,100,439 (GRCm39)	Y510F	probably benign	Het
Ipo9	A	T	1: 135,313,210 (GRCm39)	Y1006*	probably null	Het
Itgb4	C	T	11: 115,874,983 (GRCm39)	R447W	probably benign	Het
Jmjd1c	T	A	10: 67,065,785 (GRCm39)	S1737T	probably benign	Het
Klhl32	C	T	4: 24,800,805 (GRCm39)		probably null	Het
Klk1b11	T	A	7: 43,427,810 (GRCm39)	C173S	probably damaging	Het
Klk1b24	A	T	7: 43,840,889 (GRCm39)	M106L	probably benign	Het
Lamp1	G	A	8: 13,221,388 (GRCm39)		probably null	Het
Mapk4	A	T	18: 74,103,365 (GRCm39)	V48E	probably damaging	Het
Marchf6	A	T	15: 31,486,082 (GRCm39)	D395E	probably damaging	Het
Mdp1	A	G	14: 55,896,465 (GRCm39)	F157S	probably damaging	Het
Mettl21e	A	T	1: 44,250,255 (GRCm39)	F50L	probably damaging	Het
Mrgpra2a	A	G	7: 47,077,153 (GRCm39)	I35T	probably benign	Het
Natd1	T	C	11: 60,796,892 (GRCm39)	Y91C	probably damaging	Het
Nbas	T	A	12: 13,633,476 (GRCm39)	Y2294N	probably damaging	Het
Nrcam	A	G	12: 44,610,841 (GRCm39)	T520A	probably benign	Het
Nrf1	A	G	6: 30,117,061 (GRCm39)	T324A	probably benign	Het
Or10a2	G	A	7: 106,673,394 (GRCm39)	A120T	probably damaging	Het
Or4k51	T	A	2: 111,585,326 (GRCm39)	I244N	probably damaging	Het
Or52a5	A	C	7: 103,427,182 (GRCm39)	D123E	probably damaging	Het
Or5m11b	A	G	2: 85,806,500 (GRCm39)	I304M	probably benign	Het
Pam	C	T	1: 97,792,123 (GRCm39)	V433I	probably benign	Het
Pck1	T	A	2: 173,000,353 (GRCm39)	Y595N	probably damaging	Het
Per2	C	T	1: 91,373,223 (GRCm39)		probably null	Het
Piezo2	G	C	18: 63,278,162 (GRCm39)	F247L	possibly damaging	Het
Pkdcc	A	G	17: 83,523,337 (GRCm39)	Y148C	probably damaging	Het
Plod2	A	G	9: 92,475,876 (GRCm39)	T320A	probably benign	Het
Ppip5k1	G	A	2: 121,147,157 (GRCm39)	R1155C	probably benign	Het
Ppp1r15b	C	T	1: 133,059,382 (GRCm39)		probably benign	Het
Prkn	C	T	17: 11,456,536 (GRCm39)	A119V	probably damaging	Het
Ptprz1	G	T	6: 22,986,133 (GRCm39)	C311F	probably damaging	Het
Rab11fip3	A	T	17: 26,235,038 (GRCm39)	V44E	probably damaging	Het
Rpl5	T	A	5: 108,051,514 (GRCm39)		probably benign	Het
Rttn	G	A	18: 89,066,556 (GRCm39)	V1201I	probably benign	Het
Sdk1	A	G	5: 141,921,853 (GRCm39)	N283S	probably damaging	Het
Shank3	T	A	15: 89,405,529 (GRCm39)	N418K	probably benign	Het
Slc25a46	A	G	18: 31,716,293 (GRCm39)	L403S	probably damaging	Het
Slc5a1	A	G	5: 33,303,955 (GRCm39)	T257A	probably benign	Het
Snrnp35	T	C	5: 124,628,535 (GRCm39)	V116A	probably benign	Het
Spag9	T	A	11: 93,981,538 (GRCm39)	F593I	probably damaging	Het
Tmem171	C	A	13: 98,828,574 (GRCm39)	R192L	probably benign	Het
Trappc3l	T	A	10: 33,978,703 (GRCm39)	L169Q	unknown	Het
Ube2s	T	C	7: 4,811,431 (GRCm39)	E148G	probably damaging	Het
Uspl1	T	C	5: 149,146,521 (GRCm39)	F424S	probably damaging	Het
Vmn1r2	T	C	4: 3,172,261 (GRCm39)	V60A	probably benign	Het
Wdfy4	T	C	14: 32,829,575 (GRCm39)		probably null	Het
Zfp735	C	T	11: 73,602,964 (GRCm39)	S636L	possibly damaging	Het
Zswim9	G	A	7: 12,995,094 (GRCm39)	S354F	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
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
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'- AGTTTATGCCTGGCTCTTGC -3'
(R):5'- GCAAGACTGGTGAGTAGCTTC -3'

Sequencing Primer
(F):5'- TCTTGCCCTAAATGGAAGGC -3'
(R):5'- AGCTTCAGAGGTCCTTGGTCAAC -3'

Posted On

2016-11-09