Incidental Mutation 'R0057:Shmt2'
ID 216075
Institutional Source Beutler Lab
Gene Symbol Shmt2
Ensembl Gene ENSMUSG00000025403
Gene Name serine hydroxymethyltransferase 2 (mitochondrial)
Synonyms 2700043D08Rik
MMRRC Submission 038351-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0057 (G1)
Quality Score 45
Status Validated
Chromosome 10
Chromosomal Location 127352992-127358313 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 127356917 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Methionine at position 31 (T31M)
Ref Sequence ENSEMBL: ENSMUSP00000151616 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026470] [ENSMUST00000035735] [ENSMUST00000095266] [ENSMUST00000219239]
AlphaFold Q9CZN7
Predicted Effect possibly damaging
Transcript: ENSMUST00000026470
AA Change: T34M

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: T34M

DomainStartEndE-ValueType
Pfam:SHMT 49 448 5.4e-211 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000035735
SMART Domains Protein: ENSMUSP00000042185
Gene: ENSMUSG00000040280

DomainStartEndE-ValueType
Pfam:B12D 16 84 2.5e-32 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000095266
SMART Domains Protein: ENSMUSP00000092900
Gene: ENSMUSG00000040258

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
Pfam:Neurexophilin 70 166 3e-32 PFAM
Pfam:Neurexophilin 217 304 1e-37 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 possibly damaging
Transcript: ENSMUST00000219239
AA Change: T31M

PolyPhen 2 Score 0.884 (Sensitivity: 0.82; Specificity: 0.94)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218313
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220356
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218492
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.9%
  • 10x: 97.7%
  • 20x: 95.9%
Validation Efficiency 100% (50/50)
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: 28 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam23 T A 1: 63,610,078 (GRCm39) H693Q probably damaging Het
Ap5z1 T C 5: 142,456,144 (GRCm39) probably benign Het
Bloc1s6 T A 2: 122,586,141 (GRCm39) probably benign Het
Caskin1 A G 17: 24,723,870 (GRCm39) N886S probably damaging Het
Ctse G T 1: 131,591,109 (GRCm39) D97Y probably damaging Het
Dcaf11 T C 14: 55,806,767 (GRCm39) V490A probably benign Het
Dctn1 A G 6: 83,156,874 (GRCm39) H7R probably benign Het
Dscam A C 16: 96,474,936 (GRCm39) W1209G probably damaging Het
Fcsk C T 8: 111,620,400 (GRCm39) probably benign Het
Gna11 A G 10: 81,366,774 (GRCm39) M312T probably benign Het
Hacd2 T A 16: 34,895,997 (GRCm39) V105D probably damaging Het
Htra4 C A 8: 25,528,824 (GRCm39) V23L probably benign Het
Marf1 C T 16: 13,960,398 (GRCm39) A549T probably damaging Het
Msh4 C T 3: 153,575,318 (GRCm39) A686T probably benign Het
Nbas T A 12: 13,440,958 (GRCm39) M1096K probably benign Het
Or5m10b C A 2: 85,699,597 (GRCm39) Y220* probably null Het
Ppp1r16a C T 15: 76,574,999 (GRCm39) probably benign Het
Prlr A G 15: 10,328,509 (GRCm39) Y328C probably damaging Het
Ros1 C T 10: 52,056,287 (GRCm39) V68I probably benign Het
Snapc1 C T 12: 74,021,806 (GRCm39) R81C probably damaging Het
Tas2r135 A G 6: 42,383,354 (GRCm39) T298A probably benign Het
Tmem175 C T 5: 108,787,428 (GRCm39) H92Y probably damaging Het
Top3a C T 11: 60,631,510 (GRCm39) A951T probably benign Het
Trpc4ap T C 2: 155,482,406 (GRCm39) E528G possibly damaging Het
Trpm6 T C 19: 18,764,119 (GRCm39) C242R probably benign Het
Vwa7 G A 17: 35,243,523 (GRCm39) S710N possibly damaging Het
Zfa-ps A T 10: 52,421,202 (GRCm39) noncoding transcript Het
Zfp770 T A 2: 114,027,713 (GRCm39) R119* probably null Het
Other mutations in Shmt2
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- CTCTTTTGAATCTGACAGGGAGGCG -3'
(R):5'- TCTCACCTGAATTGGAGGGACATGG -3'

Sequencing Primer
(F):5'- GGAGAAGTCACTACCGTGACC -3'
(R):5'- GTGTTAGAGTTGACCAAAACTGCC -3'
Posted On 2014-07-21