Incidental Mutation 'R2358:Shmt2'
ID 247026
Institutional Source Beutler Lab
Gene Symbol Shmt2
Ensembl Gene ENSMUSG00000025403
Gene Name serine hydroxymethyltransferase 2 (mitochondrial)
Synonyms 2700043D08Rik
MMRRC Submission 040340-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2358 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 127352992-127358313 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 127353897 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 459 (T459A)
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: T462A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: T462A

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 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: T459A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218492
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220356
Meta Mutation Damage Score 0.0595 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.1%
Validation Efficiency 98% (55/56)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb9 CGG CG 5: 124,215,368 (GRCm39) probably null Het
Aif1l T A 2: 31,859,763 (GRCm39) F94L probably damaging Het
Ankzf1 C T 1: 75,171,895 (GRCm39) H209Y probably damaging Het
Ate1 A T 7: 130,117,895 (GRCm39) M30K probably damaging Het
Cd27 A G 6: 125,210,281 (GRCm39) Y189H probably damaging Het
Cela1 A G 15: 100,579,109 (GRCm39) I183T probably benign Het
Copg2 A T 6: 30,803,168 (GRCm39) L259* probably null Het
Dennd2b A T 7: 109,155,653 (GRCm39) S366T probably benign Het
Efcab7 T A 4: 99,719,823 (GRCm39) probably benign Het
Fcrl5 A G 3: 87,353,726 (GRCm39) E357G probably damaging Het
Fzr1 C T 10: 81,203,474 (GRCm39) probably null Het
Il12rb2 C T 6: 67,275,179 (GRCm39) A649T probably damaging Het
Itfg1 C A 8: 86,464,758 (GRCm39) V438F probably damaging Het
Jaml A C 9: 45,012,361 (GRCm39) I283L possibly damaging Het
Kif28 A T 1: 179,537,024 (GRCm39) H486Q probably damaging Het
Lrch4 A G 5: 137,636,810 (GRCm39) probably benign Het
Lrfn2 A G 17: 49,378,188 (GRCm39) E423G possibly damaging Het
Lrp4 T A 2: 91,332,299 (GRCm39) N1665K probably benign Het
Mrpl32 A T 13: 14,785,165 (GRCm39) V157E probably damaging Het
Mta3 A G 17: 84,070,417 (GRCm39) I193V probably damaging Het
Myom2 G A 8: 15,162,018 (GRCm39) V984I possibly damaging Het
Nedd4l G A 18: 65,342,790 (GRCm39) V909I possibly damaging Het
Nlrp4a A G 7: 26,163,623 (GRCm39) D930G probably benign Het
Or10al5 T A 17: 38,063,271 (GRCm39) C175* probably null Het
Or5d47 A T 2: 87,804,066 (GRCm39) N314K probably benign Het
Or7a35 T C 10: 78,854,022 (GRCm39) F289L probably damaging Het
Ovch2 A T 7: 107,394,122 (GRCm39) H110Q probably damaging Het
Pcnx3 G A 19: 5,733,367 (GRCm39) Q155* probably null Het
Pcnx3 C G 19: 5,733,368 (GRCm39) L1F probably null Het
Pi4k2a G A 19: 42,079,131 (GRCm39) R64Q probably damaging Het
Ptpn12 G A 5: 21,203,690 (GRCm39) P363S probably damaging Het
Rbm27 T C 18: 42,425,177 (GRCm39) probably benign Het
Ripor3 A G 2: 167,825,785 (GRCm39) probably benign Het
Rpl13-ps3 A G 14: 59,131,265 (GRCm39) noncoding transcript Het
Sap18b G A 8: 96,552,191 (GRCm39) R67H probably benign Het
Sdhb T C 4: 140,700,311 (GRCm39) V137A probably damaging Het
Siglecg A G 7: 43,058,846 (GRCm39) S200G possibly damaging Het
Slc6a15 T G 10: 103,252,646 (GRCm39) I603S probably benign Het
Smtn A T 11: 3,482,865 (GRCm39) probably null Het
Spata31d1a G A 13: 59,851,702 (GRCm39) S142L probably benign Het
Spopfm2 G A 3: 94,082,854 (GRCm39) A319V possibly damaging Het
Spopfm2 C A 3: 94,082,855 (GRCm39) A319S possibly damaging Het
Spopl C T 2: 23,427,392 (GRCm39) R221Q probably damaging Het
Strip1 A G 3: 107,523,135 (GRCm39) V633A probably benign Het
Sun2 A G 15: 79,612,114 (GRCm39) S522P possibly damaging Het
Tectb C G 19: 55,169,431 (GRCm39) probably benign Het
Terb2 T A 2: 122,028,913 (GRCm39) C157S probably benign Het
Themis T A 10: 28,739,376 (GRCm39) N615K possibly damaging Het
Tlnrd1 A T 7: 83,531,488 (GRCm39) D314E probably benign Het
Vmn1r205 T A 13: 22,776,566 (GRCm39) T179S probably benign Het
Vsig10l G A 7: 43,118,185 (GRCm39) R689H probably benign Het
Wt1 G A 2: 104,993,773 (GRCm39) probably benign Het
Zfp423 G T 8: 88,507,179 (GRCm39) A1034D possibly damaging Het
Zfy2 T C Y: 2,107,272 (GRCm39) E454G possibly damaging Het
Zyg11a G T 4: 108,053,343 (GRCm39) Q440K possibly damaging 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
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
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'- AAACGCTGGCTTGTCTCTG -3'
(R):5'- AGAACACCTGTCCTGGAGAC -3'

Sequencing Primer
(F):5'- CTCTGGGTCTTTGAGCAGGAAG -3'
(R):5'- AGACCGGAGCGCCATTACTC -3'
Posted On 2014-10-30