Incidental Mutation 'R6167:Shmt2'
ID 490200
Institutional Source Beutler Lab
Gene Symbol Shmt2
Ensembl Gene ENSMUSG00000025403
Gene Name serine hydroxymethyltransferase 2 (mitochondrial)
Synonyms 2700043D08Rik
MMRRC Submission 044313-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6167 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 127352992-127358313 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 127353731 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 478 (R478H)
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: R481H

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: R481H

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: R478H

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220356
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218492
Meta Mutation Damage Score 0.0599 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.8%
Validation Efficiency 98% (50/51)
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
Abca5 T A 11: 110,182,931 (GRCm39) E1042V probably benign Het
Ahnak2 T C 12: 112,747,750 (GRCm39) E1035G probably benign Het
Aip T G 19: 4,165,188 (GRCm39) D227A probably benign Het
Ankrd13d T C 19: 4,323,081 (GRCm39) H283R probably damaging Het
Aox4 C T 1: 58,303,094 (GRCm39) T1175I probably damaging Het
Atn1 T C 6: 124,723,700 (GRCm39) probably benign Het
Camkk2 A G 5: 122,902,187 (GRCm39) S41P probably damaging Het
Ceacam16 G A 7: 19,595,182 (GRCm39) probably benign Het
Dcaf15 T C 8: 84,824,626 (GRCm39) N524D possibly damaging Het
Dcaf7 A T 11: 105,928,077 (GRCm39) Y43F probably damaging Het
Epha3 T C 16: 63,433,287 (GRCm39) I453V probably benign Het
Etv1 A T 12: 38,915,640 (GRCm39) T413S possibly damaging Het
Evx2 A C 2: 74,489,606 (GRCm39) L53R probably damaging Het
Fam168b G A 1: 34,858,684 (GRCm39) A166V probably damaging Het
Fancm A T 12: 65,141,669 (GRCm39) Y430F probably benign Het
Fyb2 A G 4: 104,802,661 (GRCm39) T188A possibly damaging Het
Gabbr1 T C 17: 37,374,271 (GRCm39) I538T probably damaging Het
Glyctk T A 9: 106,033,691 (GRCm39) T208S possibly damaging Het
Golga7 T C 8: 23,735,904 (GRCm39) D114G probably damaging Het
Grip1 T C 10: 119,733,702 (GRCm39) probably null Het
Gtf2f1 G T 17: 57,311,161 (GRCm39) S351R probably damaging Het
Hook2 T C 8: 85,721,642 (GRCm39) L300P probably damaging Het
Hsf4 A G 8: 105,997,481 (GRCm39) S45G probably damaging Het
Iars1 T A 13: 49,876,190 (GRCm39) M825K probably damaging Het
Kcnj2 A G 11: 110,963,315 (GRCm39) I236V probably benign Het
Large2 G A 2: 92,197,433 (GRCm39) T354I probably benign Het
Mak C A 13: 41,206,828 (GRCm39) V101F probably benign Het
Mylk2 A G 2: 152,757,673 (GRCm39) probably null Het
Myo18b A T 5: 113,020,373 (GRCm39) probably null Het
Neb T A 2: 52,037,249 (GRCm39) H2955L probably benign Het
Neurl1a G C 19: 47,228,367 (GRCm39) G71A probably damaging Het
Ogfrl1 A T 1: 23,415,309 (GRCm39) L142Q probably damaging Het
Or11g27 C A 14: 50,771,612 (GRCm39) H248N probably damaging Het
Or1e27-ps1 A G 11: 73,556,160 (GRCm39) T242A probably damaging Het
P3h4 C A 11: 100,302,671 (GRCm39) A322S probably damaging Het
Piwil2 A C 14: 70,660,342 (GRCm39) probably null Het
Pkd2l2 A G 18: 34,561,297 (GRCm39) D435G probably damaging Het
Plekha6 A G 1: 133,207,145 (GRCm39) N567S probably null Het
Prss54 G A 8: 96,286,173 (GRCm39) P300L possibly damaging Het
Pxdn G A 12: 30,024,000 (GRCm39) R67Q probably damaging Het
Rapgef3 C A 15: 97,665,292 (GRCm39) probably benign Het
Sec24b C T 3: 129,782,550 (GRCm39) G1147S possibly damaging Het
Sh2b3 A T 5: 121,966,418 (GRCm39) probably null Het
Sh3glb1 A T 3: 144,397,664 (GRCm39) D358E probably damaging Het
Slc1a6 A G 10: 78,637,671 (GRCm39) E399G probably benign Het
Slc22a23 T A 13: 34,528,542 (GRCm39) Y80F probably damaging Het
Slc25a19 A G 11: 115,506,377 (GRCm39) V272A probably benign Het
Stk32a A T 18: 43,446,474 (GRCm39) D308V probably damaging Het
Tenm3 T C 8: 48,707,657 (GRCm39) I1698V possibly damaging Het
Thoc5 G A 11: 4,865,497 (GRCm39) V359M probably benign Het
Tmpo C T 10: 90,998,800 (GRCm39) R329H probably benign Het
Trim8 T C 19: 46,503,626 (GRCm39) S393P probably benign Het
Vill A T 9: 118,895,932 (GRCm39) Y103F probably damaging Het
Zfp948 T G 17: 21,807,911 (GRCm39) F368V probably benign Het
Zpld1 C T 16: 55,053,962 (GRCm39) E277K 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
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
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'- TAAATGGAAGGCCTCCCTCC -3'
(R):5'- CATTGGCTTGGAGGTGAAGC -3'

Sequencing Primer
(F):5'- TCCACTAAAACCCAGAGAGGAGTG -3'
(R):5'- CGCAAGACTGGTGAGTAGCTTC -3'
Posted On 2017-10-10