Mutagenetix > Incidental Mutation

Incidental Mutation 'R8465:Shmt2'

656779

Institutional Source

Beutler Lab

Gene Symbol

Shmt2

Ensembl Gene

ENSMUSG00000025403

Gene Name

serine hydroxymethyltransferase 2 (mitochondrial)

Synonyms

2700043D08Rik

MMRRC Submission

067909-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8465 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

127352992-127358313 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 127355945 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 133 (V133A)

Ref Sequence

ENSEMBL: ENSMUSP00000151616 (fasta)

Gene Model

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

AlphaFold

Q9CZN7

Predicted Effect

probably damaging
Transcript: ENSMUST00000026470
AA Change: V136A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: V136A

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

probably damaging
Transcript: ENSMUST00000219239
AA Change: V133A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (80/80)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot6	A	T	12: 84,153,215 (GRCm39)		probably null	Het
Adamtsl3	A	T	7: 82,247,330 (GRCm39)	N1429Y	probably benign	Het
Adk	T	C	14: 21,153,892 (GRCm39)	S32P	possibly damaging	Het
Akap13	A	T	7: 75,376,786 (GRCm39)	M2005L	probably benign	Het
Atp10a	A	T	7: 58,478,058 (GRCm39)	D1367V	probably benign	Het
Bckdhb	A	G	9: 83,870,915 (GRCm39)	I142V	probably benign	Het
Brap	C	T	5: 121,817,358 (GRCm39)	Q322*	probably null	Het
Carmil3	A	T	14: 55,734,305 (GRCm39)	N401I	probably damaging	Het
Cdan1	A	T	2: 120,558,921 (GRCm39)	S426T	possibly damaging	Het
Cdc27	C	A	11: 104,408,317 (GRCm39)	S531I	probably benign	Het
Cela3a	A	T	4: 137,131,185 (GRCm39)	Y184*	probably null	Het
Cep63	T	C	9: 102,490,576 (GRCm39)	K178R	probably benign	Het
Cfb	G	A	17: 35,076,290 (GRCm39)	Q152*	probably null	Het
Cnpy2	G	A	10: 128,162,044 (GRCm39)	V106I	probably benign	Het
Cntn1	GCTGTCTTC	GC	15: 92,237,404 (GRCm39)		probably null	Het
Ctc1	G	A	11: 68,917,045 (GRCm39)	G67D	probably damaging	Het
Cwc27	G	T	13: 104,940,772 (GRCm39)	P196T	probably benign	Het
Cwc27	C	A	13: 104,940,776 (GRCm39)	L194F	possibly damaging	Het
Cyp2d12	T	G	15: 82,439,378 (GRCm39)	S11A	possibly damaging	Het
Ddx55	T	A	5: 124,697,184 (GRCm39)		probably null	Het
Dedd2	G	T	7: 24,918,331 (GRCm39)	R75S	probably damaging	Het
Fat2	G	A	11: 55,147,530 (GRCm39)	S3904F	possibly damaging	Het
Fibp	G	A	19: 5,513,215 (GRCm39)	V177I	probably damaging	Het
Fsip2	A	T	2: 82,810,284 (GRCm39)	E2201V	probably benign	Het
Gbp11	C	T	5: 105,472,928 (GRCm39)	D499N	probably benign	Het
Gfm1	A	G	3: 67,339,032 (GRCm39)	E45G	probably damaging	Het
H2-D1	A	G	17: 35,482,487 (GRCm39)	Y69C	probably damaging	Het
Hcar1	A	G	5: 124,017,109 (GRCm39)	F194S	probably damaging	Het
Heatr4	A	T	12: 84,024,707 (GRCm39)		probably null	Het
Kcnd2	G	A	6: 21,216,695 (GRCm39)	C133Y	probably damaging	Het
Kcnq1	A	T	7: 142,979,711 (GRCm39)	Q619L	probably benign	Het
Kctd12	T	A	14: 103,218,901 (GRCm39)	R326W	probably damaging	Het
Kel	A	G	6: 41,666,472 (GRCm39)		probably null	Het
Lipk	A	T	19: 34,024,197 (GRCm39)	I332F	probably benign	Het
Lrrc37	T	A	11: 103,506,947 (GRCm39)		probably benign	Het
Masp2	A	G	4: 148,696,516 (GRCm39)	D371G	possibly damaging	Het
Met	A	G	6: 17,571,809 (GRCm39)	E1376G	probably benign	Het
Mup5	A	T	4: 61,752,015 (GRCm39)	I78K	probably benign	Het
Mynn	A	T	3: 30,670,790 (GRCm39)	D526V	probably damaging	Het
Naip6	G	T	13: 100,433,423 (GRCm39)	T1138N	possibly damaging	Het
Neurod1	G	T	2: 79,284,696 (GRCm39)	P229Q	probably damaging	Het
Npepps	T	G	11: 97,139,085 (GRCm39)	R162S	probably damaging	Het
Ntrk3	T	A	7: 78,112,631 (GRCm39)	Q175L	probably damaging	Het
Obsl1	T	C	1: 75,480,032 (GRCm39)	T310A	probably damaging	Het
Or4g7	A	T	2: 111,309,425 (GRCm39)	T99S	probably benign	Het
Or8c9	A	T	9: 38,241,410 (GRCm39)	I176F	possibly damaging	Het
Or8j3c	A	T	2: 86,253,975 (GRCm39)	M15K	probably benign	Het
Or8k32	A	G	2: 86,368,731 (GRCm39)	I176T	probably damaging	Het
Pigf	G	A	17: 87,304,964 (GRCm39)	T193I	possibly damaging	Het
Pkp4	T	C	2: 59,172,525 (GRCm39)	V904A	possibly damaging	Het
Plekha6	C	T	1: 133,197,778 (GRCm39)	T141M	probably damaging	Het
Rapgef6	G	A	11: 54,582,308 (GRCm39)	D1407N	probably benign	Het
Rhobtb3	T	C	13: 76,087,741 (GRCm39)	D82G	probably damaging	Het
Rims1	T	C	1: 22,498,731 (GRCm39)	N767S	possibly damaging	Het
Ripor2	T	A	13: 24,849,451 (GRCm39)		probably benign	Het
Sec14l4	T	A	11: 3,993,948 (GRCm39)	I296N	probably damaging	Het
Serpinb12	G	T	1: 106,884,342 (GRCm39)	V363F	probably damaging	Het
Serpinb9c	A	G	13: 33,334,016 (GRCm39)	I342T	probably damaging	Het
Slc30a6	A	G	17: 74,722,661 (GRCm39)	M243V	probably benign	Het
Slfn2	T	A	11: 82,960,487 (GRCm39)	N155K	probably damaging	Het
Spata31h1	A	T	10: 82,152,298 (GRCm39)	L23M	possibly damaging	Het
Syne2	A	T	12: 75,900,898 (GRCm39)	D19V	possibly damaging	Het
Tcl1b3	A	T	12: 105,160,736 (GRCm39)	I116L	probably benign	Het
Tcp11	A	G	17: 28,286,766 (GRCm39)	I411T	probably damaging	Het
Tctn1	C	T	5: 122,379,859 (GRCm39)	A560T	probably benign	Het
Tenm3	C	A	8: 48,682,216 (GRCm39)	Q2471H	probably damaging	Het
Tnr	A	G	1: 159,713,645 (GRCm39)	D691G	probably benign	Het
Ube3b	C	T	5: 114,528,451 (GRCm39)	P150S	probably damaging	Het
Ugt2b5	T	C	5: 87,287,518 (GRCm39)	I216M	possibly damaging	Het
Unc5d	T	A	8: 29,156,877 (GRCm39)	R789S	probably damaging	Het
Ush2a	G	A	1: 188,147,875 (GRCm39)	G934D	probably damaging	Het
Usp6nl	A	T	2: 6,399,352 (GRCm39)	R70S	probably damaging	Het
Vmn1r181	T	C	7: 23,684,309 (GRCm39)	I258T	possibly damaging	Het
Vmn2r15	C	A	5: 109,445,302 (GRCm39)	D41Y	probably damaging	Het
Vmn2r17	T	A	5: 109,600,691 (GRCm39)	I663N	probably damaging	Het
Vnn3	C	A	10: 23,741,780 (GRCm39)	Q362K	possibly damaging	Het
Wdr72	A	G	9: 74,059,730 (GRCm39)	D380G	possibly damaging	Het
Wfdc10	G	A	2: 164,499,180 (GRCm39)	E97K	possibly damaging	Het
Xdh	A	T	17: 74,206,007 (GRCm39)	C1002*	probably null	Het
Zscan4e	A	C	7: 11,041,578 (GRCm39)	V126G	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
R5654:Shmt2	UTSW	10	127,353,668 (GRCm39)	missense	probably benign	0.05
R6167:Shmt2	UTSW	10	127,353,731 (GRCm39)	missense	probably benign
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'- GTGCTCAGTGTAACATGGGAC -3'
(R):5'- TTTACTGAACAGCGGCTGCC -3'

Sequencing Primer
(F):5'- GACAGTGTGGCCCATCTTCAC -3'
(R):5'- GGCTGCCCAGTCCTTTG -3'

Posted On

2021-01-18