Incidental Mutation 'IGL02088:Shmt1'
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Shmt1
Ensembl Gene ENSMUSG00000020534
Gene Nameserine hydroxymethyltransferase 1 (soluble)
Synonymsmshmt1, Shmt, mshmt2, mshmt
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #IGL02088
Quality Score
Chromosomal Location60788104-60811718 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 60789653 bp
Amino Acid Change Threonine to Alanine at position 403 (T403A)
Ref Sequence ENSEMBL: ENSMUSP00000018744 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018744] [ENSMUST00000056907]
PDB Structure
Predicted Effect probably damaging
Transcript: ENSMUST00000018744
AA Change: T403A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: T403A

Pfam:SHMT 20 419 1.3e-211 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000056907
SMART Domains Protein: ENSMUSP00000055926
Gene: ENSMUSG00000049323

low complexity region 13 30 N/A INTRINSIC
Pfam:Folliculin 78 262 5e-12 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124227
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135081
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172804
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 unknown
Transcript: ENSMUST00000174719
AA Change: T363A
SMART Domains Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: T363A

Pfam:SHMT 20 268 6.4e-137 PFAM
Pfam:SHMT 265 380 3.9e-51 PFAM
Coding Region Coverage
Validation Efficiency
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: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ackr4 T C 9: 104,098,881 E289G probably damaging Het
Aldh1l1 A T 6: 90,580,590 probably benign Het
Ampd3 T A 7: 110,793,686 D220E probably benign Het
Ank3 T C 10: 69,999,373 V136A probably damaging Het
Atg14 T C 14: 47,542,859 K486R probably benign Het
Axin1 A G 17: 26,188,695 I637V probably benign Het
Axin2 T A 11: 108,923,616 F110Y probably damaging Het
Cdh12 A T 15: 21,480,339 K214* probably null Het
Cfap44 A C 16: 44,451,628 E1248A possibly damaging Het
Cryba4 A G 5: 112,251,009 probably benign Het
Cyp2c68 A G 19: 39,703,521 probably benign Het
Dnah5 G T 15: 28,459,118 probably null Het
Dok3 A T 13: 55,524,370 V165E probably damaging Het
Etl4 A T 2: 20,806,548 R1147S probably damaging Het
Fam212a A G 9: 107,984,457 F220S probably damaging Het
Fbxl6 G T 15: 76,535,906 C502* probably null Het
Gp2 A T 7: 119,454,469 Y90N probably damaging Het
H1fnt G T 15: 98,257,178 T30K probably damaging Het
Itfg2 A G 6: 128,411,606 V306A probably benign Het
Lrig2 T C 3: 104,467,108 Y219C probably damaging Het
Mccc1 A T 3: 35,974,202 I485N probably damaging Het
Mettl25 A G 10: 105,823,250 F391L probably damaging Het
Muc19 C T 15: 91,891,168 noncoding transcript Het
Muc2 T C 7: 141,751,504 C182R probably damaging Het
Nlrp4g T C 9: 124,350,453 noncoding transcript Het
Nms A G 1: 38,939,277 probably benign Het
Nr3c1 T C 18: 39,424,391 N503S probably damaging Het
Olfr1495 T C 19: 13,768,666 F108S probably damaging Het
Olfr186 A G 16: 59,027,052 L285P probably damaging Het
Olfr828 C T 9: 18,815,923 V124I probably benign Het
Pcdhb5 G A 18: 37,321,959 S464N probably benign Het
Pcgf6 T C 19: 47,050,804 T6A unknown Het
Rdx A G 9: 52,060,883 probably benign Het
Slc35d1 A G 4: 103,211,325 F148L probably benign Het
Tk1 A G 11: 117,824,665 probably benign Het
Tnks T A 8: 34,839,994 I1134F possibly damaging Het
Ttn A G 2: 76,726,691 V29990A probably damaging Het
Zcchc11 A G 4: 108,512,218 probably benign Het
Other mutations in Shmt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
R5024:Shmt1 UTSW 11 60797479 intron probably benign
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
R7514:Shmt1 UTSW 11 60801986 missense probably damaging 1.00
Posted On2015-04-16