Incidental Mutation 'R1493:Shmt2'
ID 165567
Institutional Source Beutler Lab
Gene Symbol Shmt2
Ensembl Gene ENSMUSG00000025403
Gene Name serine hydroxymethyltransferase 2 (mitochondrial)
Synonyms 2700043D08Rik
MMRRC Submission 039544-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1493 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 127352992-127358313 bp(-) (GRCm39)
Type of Mutation splice site (1789 bp from exon)
DNA Base Change (assembly) A to G at 127354812 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000042185 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026470] [ENSMUST00000035735] [ENSMUST00000219239]
AlphaFold Q9CZN7
Predicted Effect probably damaging
Transcript: ENSMUST00000026470
AA Change: F291S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: F291S

DomainStartEndE-ValueType
Pfam:SHMT 49 448 5.4e-211 PFAM
Predicted Effect probably null
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 probably damaging
Transcript: ENSMUST00000219239
AA Change: F288S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218492
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218313
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220356
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.2%
  • 10x: 96.2%
  • 20x: 92.9%
Validation Efficiency
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2810021J22Rik T C 11: 58,767,544 (GRCm39) S14P probably damaging Het
Abca15 A T 7: 119,981,513 (GRCm39) D989V probably benign Het
Abcg8 T C 17: 85,004,107 (GRCm39) S472P probably damaging Het
Ablim2 T C 5: 35,966,605 (GRCm39) F178S probably damaging Het
Adprm A G 11: 66,932,702 (GRCm39) V69A possibly damaging Het
Ankrd27 C T 7: 35,307,790 (GRCm39) S343L probably benign Het
Arfgef3 A G 10: 18,506,627 (GRCm39) S833P probably damaging Het
Arhgap42 T G 9: 9,030,798 (GRCm39) E339D probably benign Het
Axdnd1 T A 1: 156,174,271 (GRCm39) M799L probably benign Het
Cars2 A T 8: 11,567,817 (GRCm39) probably null Het
Cd7 T C 11: 120,928,967 (GRCm39) T95A probably damaging Het
Cep290 A T 10: 100,398,043 (GRCm39) T2200S probably benign Het
Cep44 A G 8: 56,985,870 (GRCm39) S299P probably damaging Het
Cfap58 C T 19: 47,976,943 (GRCm39) H731Y probably damaging Het
Ehbp1 T A 11: 21,956,866 (GRCm39) E1204V probably damaging Het
Fgd5 A G 6: 91,964,612 (GRCm39) K124E probably benign Het
Folh1 T C 7: 86,410,938 (GRCm39) D268G probably damaging Het
Gm4559 A T 7: 141,828,050 (GRCm39) C17* probably null Het
Helz A G 11: 107,504,751 (GRCm39) I413V probably benign Het
Hexd A G 11: 121,112,093 (GRCm39) I438V probably benign Het
Hrh1 G A 6: 114,457,838 (GRCm39) G373D probably damaging Het
Hs3st5 G A 10: 36,708,870 (GRCm39) G135D probably damaging Het
Iqcf6 T C 9: 106,504,641 (GRCm39) Y102H probably benign Het
Kmt2a A T 9: 44,758,202 (GRCm39) S1124R probably damaging Het
Map3k5 A G 10: 19,904,859 (GRCm39) D387G probably damaging Het
Morc2a A G 11: 3,628,557 (GRCm39) N337D probably benign Het
Musk C T 4: 58,354,003 (GRCm39) A352V probably benign Het
Myef2l A G 3: 10,153,944 (GRCm39) K238E probably damaging Het
Nans G A 4: 46,500,761 (GRCm39) E218K probably damaging Het
Niban1 T A 1: 151,581,841 (GRCm39) V479D probably damaging Het
Ninl T G 2: 150,822,015 (GRCm39) D29A probably damaging Het
Nod1 A G 6: 54,921,041 (GRCm39) F426L probably damaging Het
Notch4 T A 17: 34,786,656 (GRCm39) C265* probably null Het
Nsd3 A G 8: 26,203,407 (GRCm39) D1307G probably benign Het
Or51h1 T C 7: 102,308,220 (GRCm39) L64P probably damaging Het
Or52e18 T A 7: 104,609,709 (GRCm39) T77S probably damaging Het
Orai3 G A 7: 127,373,077 (GRCm39) V193M possibly damaging Het
Prkag1 T C 15: 98,711,551 (GRCm39) Y271C probably benign Het
Rfc4 T C 16: 22,936,758 (GRCm39) I116V probably damaging Het
Ric1 T C 19: 29,557,249 (GRCm39) Y445H probably benign Het
Rnmt G A 18: 68,446,778 (GRCm39) D268N probably damaging Het
Rsph1 C T 17: 31,484,873 (GRCm39) G139D probably damaging Het
Sez6l2 C A 7: 126,560,984 (GRCm39) P483Q probably damaging Het
Sgo2b A G 8: 64,379,889 (GRCm39) L981P probably damaging Het
Sorbs3 T C 14: 70,430,076 (GRCm39) T353A possibly damaging Het
Stk25 T C 1: 93,553,322 (GRCm39) T260A probably benign Het
Tasor A G 14: 27,171,926 (GRCm39) S425G probably damaging Het
Thap12 A G 7: 98,364,645 (GRCm39) H271R probably benign Het
Tmprss13 A G 9: 45,247,405 (GRCm39) T256A probably benign Het
Tpo A T 12: 30,181,808 (GRCm39) I29N possibly damaging Het
Trpc2 A T 7: 101,739,783 (GRCm39) N569I probably damaging Het
Unc13c T C 9: 73,546,350 (GRCm39) T1607A probably benign Het
Vldlr A G 19: 27,218,691 (GRCm39) N514S probably benign Het
Vps18 A G 2: 119,127,613 (GRCm39) Y812C probably damaging Het
Zfp692 A T 11: 58,204,866 (GRCm39) I409F probably damaging Het
Zfp735 G A 11: 73,601,305 (GRCm39) C83Y possibly damaging Het
Zic1 A G 9: 91,246,809 (GRCm39) S88P probably 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
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'- GCCTCGGCTTTAGGTACAAGGAAG -3'
(R):5'- CGGATGTTGTTACCACCACCACTC -3'

Sequencing Primer
(F):5'- AAAACCTCTGGCCCAGTG -3'
(R):5'- TATGCCAGTCATCCGTCTTC -3'
Posted On 2014-03-28