Mutagenetix > Incidental Mutation

Incidental Mutation 'R9099:Shmt2'

691558

Institutional Source

Beutler Lab

Gene Symbol

Shmt2

Ensembl Gene

ENSMUSG00000025403

Gene Name

serine hydroxymethyltransferase 2 (mitochondrial)

Synonyms

2700043D08Rik

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9099 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

127352992-127358313 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 127355962 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 130 (D130E)

Ref Sequence

ENSEMBL: ENSMUSP00000026470 (fasta)

Gene Model

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

AlphaFold

Q9CZN7

Predicted Effect

possibly damaging
Transcript: ENSMUST00000026470
AA Change: D130E

PolyPhen 2 Score 0.862 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: D130E

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

possibly damaging
Transcript: ENSMUST00000219239
AA Change: D127E

PolyPhen 2 Score 0.729 (Sensitivity: 0.86; Specificity: 0.92)

Meta Mutation Damage Score

0.1343

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

94% (61/65)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	A	T	11: 109,871,708 (GRCm39)	M90K	probably damaging	Het
Actn2	T	C	13: 12,303,516 (GRCm39)	D428G	probably damaging	Het
Arrb1	T	C	7: 99,243,836 (GRCm39)	V262A	probably damaging	Het
Bok	A	G	1: 93,622,661 (GRCm39)	I102V		Het
C87436	T	A	6: 86,439,567 (GRCm39)	F419L	probably damaging	Het
Capn15	A	G	17: 26,192,141 (GRCm39)	C34R	probably benign	Het
Ccdc8	T	A	7: 16,728,800 (GRCm39)	Y96*	probably null	Het
Cd274	T	A	19: 29,357,771 (GRCm39)	C154*	probably null	Het
Cfap251	A	G	5: 123,418,082 (GRCm39)		probably benign	Het
Ckap4	A	T	10: 84,369,402 (GRCm39)	L110Q	probably damaging	Het
Col26a1	A	T	5: 136,777,202 (GRCm39)	D335E	probably benign	Het
Crybg1	C	T	10: 43,874,844 (GRCm39)	V755I	probably benign	Het
Dhx38	A	T	8: 110,282,783 (GRCm39)	Y628N	probably damaging	Het
Dnah12	A	T	14: 26,492,325 (GRCm39)	K1155M	probably benign	Het
Ei24	A	G	9: 36,697,270 (GRCm39)	F153L	probably damaging	Het
Erg	T	A	16: 95,178,188 (GRCm39)	E246D	probably benign	Het
Exoc6b	T	C	6: 84,982,000 (GRCm39)	N99D	possibly damaging	Het
Fam222b	G	T	11: 78,046,020 (GRCm39)	R527L	probably damaging	Het
Fam83h	T	C	15: 75,875,135 (GRCm39)	Y734C	probably damaging	Het
Fbxo43	T	C	15: 36,162,619 (GRCm39)	E196G	possibly damaging	Het
Gata5	G	A	2: 179,976,131 (GRCm39)	P11L	possibly damaging	Het
Gbp3	A	T	3: 142,271,048 (GRCm39)	S151C	probably benign	Het
Gli3	T	C	13: 15,901,320 (GRCm39)	L1569P	probably damaging	Het
Helz	G	A	11: 107,523,041 (GRCm39)	V742M	probably damaging	Het
Ifi27l2b	A	T	12: 103,418,114 (GRCm39)	N175K	unknown	Het
Itga1	A	T	13: 115,185,856 (GRCm39)	Y49N	probably damaging	Het
Kcnk2	T	C	1: 188,991,072 (GRCm39)	T167A	probably damaging	Het
Kirrel2	T	A	7: 30,147,642 (GRCm39)	T669S	probably benign	Het
Krt9	TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC	TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC	11: 100,079,903 (GRCm39)		probably benign	Het
Lrit2	A	T	14: 36,790,812 (GRCm39)	T164S	possibly damaging	Het
Lrriq1	A	G	10: 103,051,864 (GRCm39)	V296A	probably damaging	Het
Malsu1	C	T	6: 49,050,731 (GRCm39)		probably benign	Het
Moxd1	G	A	10: 24,155,762 (GRCm39)	V289I	probably damaging	Het
Nfs1	C	T	2: 155,968,934 (GRCm39)	G380E	probably damaging	Het
Nol4l	C	A	2: 153,312,630 (GRCm39)	R226L	probably damaging	Het
Nsmaf	CAAACTTTTAAACTT	CAAACTT	4: 6,416,543 (GRCm39)		probably null	Het
Nup98	T	A	7: 101,844,173 (GRCm39)	N54I	probably damaging	Het
Or7g21	C	T	9: 19,032,890 (GRCm39)	P210L	probably benign	Het
Or8g22	A	T	9: 38,958,026 (GRCm39)	C230S	probably benign	Het
Or8g53	A	G	9: 39,683,514 (GRCm39)	I194T		Het
Otoa	T	A	7: 120,739,055 (GRCm39)	F755I	probably benign	Het
P4htm	A	T	9: 108,460,911 (GRCm39)	M187K	probably benign	Het
Phldb3	C	T	7: 24,323,727 (GRCm39)	R453C	probably benign	Het
Pkd1l1	C	T	11: 8,922,986 (GRCm39)	A94T		Het
Pkp1	A	G	1: 135,805,429 (GRCm39)	F669S	probably benign	Het
Prl8a2	C	G	13: 27,536,793 (GRCm39)	Y138*	probably null	Het
Prl8a2	T	A	13: 27,536,794 (GRCm39)	Y139N	probably benign	Het
Rtn4r	T	A	16: 17,969,068 (GRCm39)	N165K	probably benign	Het
Scaper	G	T	9: 55,669,616 (GRCm39)	D353E	probably damaging	Het
Scn4a	G	T	11: 106,211,000 (GRCm39)	D1672E	probably damaging	Het
She	A	G	3: 89,739,078 (GRCm39)	S90G	probably benign	Het
Slc2a12	T	A	10: 22,569,923 (GRCm39)	I538K	possibly damaging	Het
Snx29	T	A	16: 11,478,435 (GRCm39)	W322R	probably damaging	Het
Spp1	A	G	5: 104,588,387 (GRCm39)	D263G	probably benign	Het
Srek1ip1	T	C	13: 104,973,964 (GRCm39)	S124P	possibly damaging	Het
Tcp10b	C	T	17: 13,280,656 (GRCm39)		probably benign	Het
Thap12	T	C	7: 98,364,600 (GRCm39)	F256S	probably damaging	Het
Tpte	T	C	8: 22,845,497 (GRCm39)	Y516H		Het
Trem1	C	A	17: 48,544,271 (GRCm39)	Q99K	possibly damaging	Het
Umodl1	C	T	17: 31,178,147 (GRCm39)	P41L	probably benign	Het
Upp2	T	C	2: 58,457,542 (GRCm39)		probably null	Het
Zfand1	A	T	3: 10,406,148 (GRCm39)	M181K	probably damaging	Het
Zfp292	T	C	4: 34,809,228 (GRCm39)	E1277G	possibly damaging	Het
Zfp458	G	T	13: 67,405,696 (GRCm39)	P248T	probably damaging	Het
Zfp667	T	A	7: 6,308,322 (GRCm39)	M330K	probably benign	Het
Zfp827	A	G	8: 79,917,107 (GRCm39)	T561A		Het
Zfp947	C	T	17: 22,364,855 (GRCm39)	G273D	probably benign	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
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
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'- TTTACTGAACAGCGGCTGC -3'

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

Posted On

2021-12-30