Incidental Mutation 'R5568:Shmt2'
ID 437044
Institutional Source Beutler Lab
Gene Symbol Shmt2
Ensembl Gene ENSMUSG00000025403
Gene Name serine hydroxymethyltransferase 2 (mitochondrial)
Synonyms 2700043D08Rik
MMRRC Submission 043125-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5568 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 127352992-127358313 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 127356250 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 87 (S87P)
Ref Sequence ENSEMBL: ENSMUSP00000151616 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026470] [ENSMUST00000035735] [ENSMUST00000219239]
AlphaFold Q9CZN7
Predicted Effect probably damaging
Transcript: ENSMUST00000026470
AA Change: S90P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: S90P

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 probably damaging
Transcript: ENSMUST00000219239
AA Change: S87P

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: 99.9%
  • 3x: 99.6%
  • 10x: 98.3%
  • 20x: 95.0%
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: 96 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl4 T C 4: 144,349,364 (GRCm39) V207A probably benign Het
Abcc10 C A 17: 46,614,834 (GRCm39) probably null Het
Abcc9 A C 6: 142,634,742 (GRCm39) V174G possibly damaging Het
Abl1 C T 2: 31,669,086 (GRCm39) A155V probably damaging Het
Aco2 T A 15: 81,787,787 (GRCm39) D212E probably damaging Het
Adam26b A T 8: 43,973,529 (GRCm39) M491K probably benign Het
Anapc5 G A 5: 122,929,988 (GRCm39) probably benign Het
Atf7 A G 15: 102,471,757 (GRCm39) I46T probably damaging Het
Cacna1b A G 2: 24,497,612 (GRCm39) S2100P probably damaging Het
Capn5 T A 7: 97,775,137 (GRCm39) D501V probably damaging Het
Cc2d2a A G 5: 43,866,433 (GRCm39) M748V probably damaging Het
Cd300c2 T C 11: 114,891,662 (GRCm39) T71A probably damaging Het
Chmp2a T C 7: 12,767,758 (GRCm39) M56V probably benign Het
Cilp A C 9: 65,187,515 (GRCm39) R1203S probably benign Het
Clp1 T A 2: 84,556,322 (GRCm39) K53* probably null Het
Crhbp T A 13: 95,578,737 (GRCm39) D128V probably damaging Het
Crispld1 T A 1: 17,820,495 (GRCm39) I292N probably benign Het
Cyp2c68 A T 19: 39,677,526 (GRCm39) I488N probably benign Het
Cyp3a57 A T 5: 145,307,456 (GRCm39) M149L probably benign Het
Ddx24 T A 12: 103,390,547 (GRCm39) Q59L possibly damaging Het
Ddx27 A G 2: 166,871,439 (GRCm39) H512R possibly damaging Het
Dlgap4 T A 2: 156,604,821 (GRCm39) *993K probably null Het
Dmxl2 A T 9: 54,330,643 (GRCm39) probably null Het
Dus4l A T 12: 31,696,712 (GRCm39) F88L probably damaging Het
Ep400 A T 5: 110,904,071 (GRCm39) V176E probably damaging Het
Fat3 T A 9: 16,288,219 (GRCm39) K435* probably null Het
Fsip2 T C 2: 82,816,908 (GRCm39) C4214R probably benign Het
Garin5a T G 7: 44,150,428 (GRCm39) S207A probably damaging Het
Gfral T C 9: 76,072,087 (GRCm39) *394W probably null Het
Glis1 T C 4: 107,476,832 (GRCm39) S518P probably damaging Het
H2-T10 A G 17: 36,430,079 (GRCm39) probably null Het
Hsbp1l1 T C 18: 80,278,679 (GRCm39) T35A possibly damaging Het
Ighv5-12 A G 12: 113,665,837 (GRCm39) F87S probably damaging Het
Ints13 A C 6: 146,477,855 (GRCm39) D31E probably damaging Het
Kbtbd12 C T 6: 88,595,609 (GRCm39) D74N probably damaging Het
Klrb1c A G 6: 128,765,877 (GRCm39) probably benign Het
Kmt5b A T 19: 3,836,538 (GRCm39) H25L probably benign Het
Krt28 A T 11: 99,262,210 (GRCm39) M260K probably damaging Het
Krt79 A G 15: 101,838,220 (GRCm39) S512P probably damaging Het
Lama1 A T 17: 68,075,293 (GRCm39) probably null Het
Maneal T C 4: 124,750,937 (GRCm39) E273G possibly damaging Het
Map4k3 T A 17: 80,971,427 (GRCm39) Y80F possibly damaging Het
Mbd6 A G 10: 127,119,297 (GRCm39) V946A possibly damaging Het
Mfsd14b A T 13: 65,219,936 (GRCm39) probably null Het
Mrpl46 C G 7: 78,430,242 (GRCm39) W176S probably damaging Het
Muc19 A G 15: 91,768,468 (GRCm39) noncoding transcript Het
Mup3 T G 4: 62,002,809 (GRCm39) E184A possibly damaging Het
Myo9a A G 9: 59,781,911 (GRCm39) H1699R probably benign Het
Ndrg2 T A 14: 52,144,420 (GRCm39) T269S probably damaging Het
Nfatc1 A T 18: 80,693,037 (GRCm39) V688D probably benign Het
Ninj2 T C 6: 120,175,670 (GRCm39) I101T probably benign Het
Nlrp10 T A 7: 108,523,468 (GRCm39) M671L probably benign Het
Npsr1 T A 9: 24,224,510 (GRCm39) L296I probably damaging Het
Or10d5 A G 9: 39,861,983 (GRCm39) L28P probably benign Het
Or52r1b G T 7: 102,691,517 (GRCm39) R272L possibly damaging Het
Pacsin1 T A 17: 27,927,022 (GRCm39) D242E probably damaging Het
Pcdh1 T C 18: 38,330,420 (GRCm39) Y861C probably damaging Het
Pcdha12 T C 18: 37,153,443 (GRCm39) L54P probably damaging Het
Pcdhb18 T A 18: 37,624,853 (GRCm39) S728T probably benign Het
Phyhd1 T A 2: 30,167,022 (GRCm39) H108Q probably damaging Het
Plcb1 A T 2: 135,212,513 (GRCm39) I1035F probably damaging Het
Plcl1 T C 1: 55,735,309 (GRCm39) S217P possibly damaging Het
Plppr2 G A 9: 21,852,425 (GRCm39) R103H probably damaging Het
Plxnb2 G A 15: 89,041,638 (GRCm39) T1722I probably damaging Het
Pole3 T C 4: 62,442,668 (GRCm39) N53S probably damaging Het
Ptk6 A T 2: 180,841,488 (GRCm39) N140K possibly damaging Het
Rab12 C T 17: 66,804,418 (GRCm39) R180H probably damaging Het
Rab36 G T 10: 74,888,311 (GRCm39) V252L probably benign Het
Ranbp3 T C 17: 57,008,543 (GRCm39) probably null Het
Rapgef2 A G 3: 79,011,308 (GRCm39) L259P probably damaging Het
Rigi T A 4: 40,222,140 (GRCm39) M380L probably benign Het
Scaf4 GGCTGCTGCTGCTGCTGCTGCTGCTG GGCTGCTGCTGCTGCTGCTGCTG 16: 90,026,745 (GRCm39) probably benign Het
Scd2 T C 19: 44,288,142 (GRCm39) F178S probably damaging Het
Slf1 T A 13: 77,194,823 (GRCm39) D834V probably damaging Het
Sorcs2 A C 5: 36,203,874 (GRCm39) Y540* probably null Het
Srpk2 T A 5: 23,730,697 (GRCm39) Q274L possibly damaging Het
Stradb T A 1: 59,031,901 (GRCm39) M271K possibly damaging Het
Tfec T A 6: 16,867,592 (GRCm39) Q16L possibly damaging Het
Tfg T C 16: 56,521,450 (GRCm39) T63A probably benign Het
Ticrr G A 7: 79,339,715 (GRCm39) probably null Het
Ticrr T A 7: 79,345,044 (GRCm39) C1636* probably null Het
Tln2 A G 9: 67,219,147 (GRCm39) I266T probably damaging Het
Tmcc1 G C 6: 115,999,071 (GRCm39) R323G possibly damaging Het
Tnnt3 A G 7: 142,065,777 (GRCm39) E138G probably damaging Het
Tpm2 C A 4: 43,522,692 (GRCm39) E75* probably null Het
Ttn T G 2: 76,580,922 (GRCm39) T23324P probably damaging Het
Ubr4 T G 4: 139,119,349 (GRCm39) L176R probably damaging Het
Uhrf2 G T 19: 30,016,488 (GRCm39) D46Y probably damaging Het
Ulbp1 A C 10: 7,423,281 (GRCm39) S21A unknown Het
Usp17lb C T 7: 104,490,415 (GRCm39) G170R probably damaging Het
Utp15 T C 13: 98,394,433 (GRCm39) N153S probably benign Het
Vcan T A 13: 89,836,790 (GRCm39) E2918V probably damaging Het
Vmn1r174 T A 7: 23,453,919 (GRCm39) I195K probably damaging Het
Vmn1r76 C T 7: 11,665,062 (GRCm39) V16I probably benign Het
Xdh T C 17: 74,250,880 (GRCm39) D24G possibly damaging Het
Xylb T A 9: 119,190,198 (GRCm39) H68Q probably benign 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
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'- CGTAGTATCTGCCGTGGAAG -3'
(R):5'- AATGTTGCTTCTGGTCCCGC -3'

Sequencing Primer
(F):5'- CGTGGAAGACGGACCGTAC -3'
(R):5'- CCCCATGTCTGGCGAGGAAC -3'
Posted On 2016-10-24