Incidental Mutation 'R5024:Shmt1'
Institutional Source Beutler Lab
Gene Symbol Shmt1
Ensembl Gene ENSMUSG00000020534
Gene Nameserine hydroxymethyltransferase 1 (soluble)
Synonymsmshmt1, Shmt, mshmt2, mshmt
MMRRC Submission 042615-MU
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #R5024 (G1)
Quality Score210
Status Validated
Chromosomal Location60788104-60811718 bp(-) (GRCm38)
Type of Mutationintron
DNA Base Change (assembly) A to T at 60797479 bp
Amino Acid Change
Gene Model predicted gene model for transcript(s): [ENSMUST00000018744]
Predicted Effect probably benign
Transcript: ENSMUST00000018744
SMART Domains Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534

Pfam:SHMT 20 419 1.3e-211 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124227
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135081
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172804
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173260
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173698
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174093
Predicted Effect probably benign
Transcript: ENSMUST00000174174
SMART Domains Protein: ENSMUSP00000134703
Gene: ENSMUSG00000020534

Pfam:SHMT 20 79 7.1e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174214
SMART Domains Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534

Pfam:SHMT 20 408 4.6e-196 PFAM
Pfam:Aminotran_1_2 153 409 3.1e-6 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174719
SMART Domains Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534

Pfam:SHMT 20 268 6.4e-137 PFAM
Pfam:SHMT 265 380 3.9e-51 PFAM
Meta Mutation Damage Score 0.062 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.4%
Validation Efficiency 99% (95/96)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice with deficiencies in this gene display abnormalities in hepatic partioning of methylenetetrahydrofolate but are otherwise healthy and fertile. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrd1 A G 5: 129,171,895 N575S probably damaging Het
Akap6 C T 12: 53,142,562 T2253M probably benign Het
Arhgef37 A C 18: 61,506,440 N289K probably damaging Het
Armc4 T C 18: 7,088,555 M1005V probably benign Het
Atad2b A C 12: 4,937,534 T121P probably benign Het
Atp4a A C 7: 30,715,864 D303A possibly damaging Het
BC005561 A G 5: 104,522,258 K1549E possibly damaging Het
Calu A T 6: 29,374,519 probably benign Het
Ccdc141 A C 2: 77,054,703 N531K probably benign Het
Ccdc146 T C 5: 21,399,614 probably null Het
Cd207 G A 6: 83,674,319 T218I probably damaging Het
Cd2ap A C 17: 42,805,345 probably null Het
Clip3 G A 7: 30,292,219 probably benign Het
Clstn1 G A 4: 149,635,294 R432H possibly damaging Het
Csmd2 A G 4: 128,321,348 Y521C possibly damaging Het
Dnah8 A T 17: 30,736,096 E2033V probably damaging Het
Eng T G 2: 32,673,392 V319G probably benign Het
Erp44 C T 4: 48,241,296 W57* probably null Het
Etv1 T A 12: 38,854,234 probably null Het
Eva1c T C 16: 90,876,193 probably null Het
Fam196a A G 7: 134,918,478 S108P probably damaging Het
Fam221b T A 4: 43,659,674 N482I probably damaging Het
Fam83h T C 15: 76,005,142 H202R probably damaging Het
Fbxw13 T C 9: 109,179,335 T449A probably benign Het
Fbxw25 A T 9: 109,663,374 probably null Het
Frmd3 T A 4: 74,098,144 S99T probably benign Het
Gm5155 A G 7: 17,910,682 I575V probably benign Het
Gm5174 G T 10: 86,656,587 noncoding transcript Het
Gm6904 T C 14: 59,258,483 probably null Het
Gm815 C T 19: 26,887,775 Q49* probably null Het
H2-DMa A T 17: 34,138,487 I245F possibly damaging Het
Herc1 A T 9: 66,470,326 K3458M possibly damaging Het
Hirip3 A G 7: 126,864,489 probably null Het
Hjurp A T 1: 88,275,050 Y71N possibly damaging Het
Hmcn1 T A 1: 150,680,688 E2449V possibly damaging Het
Igll1 G T 16: 16,863,793 H33N probably benign Het
Il6 T C 5: 30,019,514 L184P probably damaging Het
Impg2 T A 16: 56,260,100 S756T probably damaging Het
Kank4 T G 4: 98,785,661 D5A probably damaging Het
Kcna7 G A 7: 45,406,591 R77H probably damaging Het
Kcns2 A T 15: 34,839,537 T349S probably benign Het
Keap1 A G 9: 21,237,226 Y162H probably damaging Het
Kif9 T C 9: 110,483,093 F10L possibly damaging Het
Klk14 G A 7: 43,692,077 C51Y probably damaging Het
Lpar6 A G 14: 73,239,369 T257A probably damaging Het
Lpin1 A T 12: 16,554,006 L608Q probably benign Het
Lyst T C 13: 13,634,404 S220P probably benign Het
M1ap A G 6: 83,028,358 probably benign Het
Mbd6 C T 10: 127,286,441 V173I probably benign Het
Myo5b A T 18: 74,716,034 T1115S possibly damaging Het
Mysm1 C A 4: 94,951,016 V683F possibly damaging Het
Nlrp4g T A 9: 124,350,155 noncoding transcript Het
Olfr1040 G T 2: 86,146,533 A67E probably damaging Het
Olfr1062 C T 2: 86,423,461 G72S possibly damaging Het
Olfr292 A T 7: 86,694,881 M142L probably benign Het
Olfr318 T A 11: 58,720,950 I33F probably benign Het
Otud6b T A 4: 14,826,293 Q34L probably damaging Het
Parp11 C T 6: 127,471,636 T72I probably damaging Het
Pbx1 T A 1: 168,183,589 D343V possibly damaging Het
Ppp1r12b G T 1: 134,955,733 A17E probably benign Het
Pramef20 C A 4: 144,373,308 E296* probably null Het
Ranbp9 A T 13: 43,434,855 I67N probably damaging Het
Rasgrp4 A G 7: 29,148,407 E414G probably damaging Het
Rbbp5 A G 1: 132,490,488 H15R possibly damaging Het
Scd2 A G 19: 44,301,271 Y235C probably benign Het
Sdr16c5 C T 4: 4,010,365 G170S probably damaging Het
Sh3bp4 G T 1: 89,145,595 G722C probably damaging Het
Slc12a1 A G 2: 125,166,137 I206V probably benign Het
Slc26a3 A G 12: 31,453,908 D304G probably benign Het
Slc26a7 T A 4: 14,532,572 D434V possibly damaging Het
Slc6a16 G T 7: 45,259,966 M185I probably benign Het
Stat4 A G 1: 52,082,570 I363V possibly damaging Het
Tgfb1i1 G T 7: 128,248,217 M1I probably null Het
Tmem225 T C 9: 40,149,343 V66A probably benign Het
Tmtc4 T C 14: 122,941,302 probably null Het
Trpc4 T A 3: 54,194,796 N38K probably benign Het
Ttll12 A T 15: 83,587,113 Y218N probably damaging Het
Ttn A T 2: 76,948,425 probably null Het
Tulp1 A C 17: 28,351,995 Y178* probably null Het
Vmn2r58 A G 7: 41,864,322 V299A probably damaging Het
Washc4 C A 10: 83,583,336 Q911K possibly damaging Het
Wdr3 T C 3: 100,154,936 D221G probably benign Het
Zan A T 5: 137,461,893 C1245* probably null Het
Zfyve9 A C 4: 108,691,669 S773A probably benign Het
Other mutations in Shmt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02088:Shmt1 APN 11 60789653 missense probably damaging 1.00
PIT4514001:Shmt1 UTSW 11 60804347 missense probably damaging 1.00
R0470:Shmt1 UTSW 11 60792963 missense possibly damaging 0.91
R0787:Shmt1 UTSW 11 60792976 missense probably benign 0.00
R1768:Shmt1 UTSW 11 60792964 missense probably damaging 1.00
R2179:Shmt1 UTSW 11 60806999 missense possibly damaging 0.69
R3715:Shmt1 UTSW 11 60797576 missense probably damaging 1.00
R4647:Shmt1 UTSW 11 60801465 missense probably damaging 1.00
R5183:Shmt1 UTSW 11 60797482 intron probably benign
R5461:Shmt1 UTSW 11 60794899 missense possibly damaging 0.94
R6014:Shmt1 UTSW 11 60797557 missense probably damaging 1.00
R6618:Shmt1 UTSW 11 60792946 splice site probably null
R6969:Shmt1 UTSW 11 60804327 missense probably damaging 1.00
R7108:Shmt1 UTSW 11 60798644 missense probably damaging 0.98
R7158:Shmt1 UTSW 11 60790242 missense probably benign 0.03
R7215:Shmt1 UTSW 11 60801535 missense probably damaging 0.99
Predicted Primers PCR Primer

Sequencing Primer
Posted On2016-06-06