Incidental Mutation 'R0787:Shmt1'
ID 76911
Institutional Source Beutler Lab
Gene Symbol Shmt1
Ensembl Gene ENSMUSG00000020534
Gene Name serine hydroxymethyltransferase 1 (soluble)
Synonyms mshmt1, Shmt, mshmt2, mshmt
MMRRC Submission 038967-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0787 (G1)
Quality Score 208
Status Validated
Chromosome 11
Chromosomal Location 60788104-60811718 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 60792976 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 337 (T337A)
Ref Sequence ENSEMBL: ENSMUSP00000018744 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018744] [ENSMUST00000056907]
AlphaFold P50431
Predicted Effect probably benign
Transcript: ENSMUST00000018744
AA Change: T337A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: T337A

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: ENSMUST00000173260
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 unknown
Transcript: ENSMUST00000174214
AA Change: T336A
SMART Domains Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
AA Change: T336A

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: T297A
SMART Domains Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: T297A

Pfam:SHMT 20 268 6.4e-137 PFAM
Pfam:SHMT 265 380 3.9e-51 PFAM
Meta Mutation Damage Score 0.0785 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 96.9%
  • 20x: 93.4%
Validation Efficiency 100% (56/56)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610037L13Rik T A 4: 107,890,129 L6Q probably damaging Het
1700001F09Rik A T 14: 43,345,493 probably null Het
Abca8a T A 11: 110,042,988 Y1197F possibly damaging Het
Abcc2 T C 19: 43,798,516 probably null Het
Adamts16 A T 13: 70,738,829 C979S probably damaging Het
Agap2 T A 10: 127,085,150 D523E unknown Het
Ankfy1 T A 11: 72,760,296 I1024N probably damaging Het
Ankrd13c A G 3: 157,994,678 S379G probably null Het
Arhgap40 T C 2: 158,547,790 S625P probably benign Het
Armc12 G C 17: 28,538,766 A291P probably damaging Het
Armc9 A G 1: 86,202,505 N524D probably damaging Het
Col12a1 G T 9: 79,638,485 T2305K probably damaging Het
Cyp2c54 T C 19: 40,047,635 N277S probably benign Het
E130311K13Rik A T 3: 63,920,298 V129E probably benign Het
Ehbp1l1 T C 19: 5,722,668 D79G possibly damaging Het
Epb41l1 A G 2: 156,494,090 E58G probably damaging Het
Fam217b T A 2: 178,420,909 V222E probably benign Het
Fat1 T A 8: 45,040,555 Y3913N probably damaging Het
Fgd4 A G 16: 16,423,901 probably benign Het
Hltf A T 3: 20,106,446 D759V probably damaging Het
Hsp90ab1 ACTTCTT ACTT 17: 45,569,499 probably benign Het
Isg15 C T 4: 156,199,939 R44H probably benign Het
Itga4 C T 2: 79,279,153 T232I probably benign Het
Kntc1 C A 5: 123,796,104 H1399Q probably benign Het
Lig1 A C 7: 13,299,069 K499Q probably benign Het
Lrrn3 C A 12: 41,454,231 C29F probably damaging Het
Mtmr10 T C 7: 64,300,615 I136T possibly damaging Het
Naip1 A G 13: 100,426,096 Y854H probably benign Het
Olfr770 T C 10: 129,133,526 N81D possibly damaging Het
Pcdh9 G A 14: 93,886,757 A659V possibly damaging Het
Phf20l1 T A 15: 66,615,630 probably benign Het
Phgdh A G 3: 98,334,549 V83A probably damaging Het
Pik3r1 A T 13: 101,690,523 M326K probably benign Het
Pirb A T 7: 3,717,638 L287Q probably benign Het
Pkd1l2 T C 8: 117,076,177 D235G possibly damaging Het
Pkhd1l1 C A 15: 44,529,264 P1665Q probably damaging Het
Ppp1r7 A G 1: 93,364,956 T326A probably damaging Het
Prr22 A T 17: 56,771,072 Y75F possibly damaging Het
Ptov1 A C 7: 44,865,470 probably null Het
Rasal2 A G 1: 157,158,696 S766P probably damaging Het
St5 G T 7: 109,525,620 R1068S possibly damaging Het
Tbc1d4 A T 14: 101,449,209 I1168N probably damaging Het
Tecpr2 T C 12: 110,946,343 V1126A probably benign Het
Tep1 A T 14: 50,829,230 S2304T possibly damaging Het
Tiam1 C A 16: 89,789,561 R1446M probably damaging Het
Tmem87a T C 2: 120,370,484 I425V probably benign Het
Ubr3 T C 2: 69,951,421 probably benign Het
Ubxn7 T A 16: 32,381,763 probably benign Het
Vmn2r13 A G 5: 109,156,847 S573P probably damaging Het
Wdfy3 A T 5: 101,957,388 V191E probably damaging Het
Zdhhc3 A T 9: 123,083,623 C153* probably null Het
Zfp407 A T 18: 84,209,022 V2154D probably damaging Het
Zfp407 A G 18: 84,209,346 V2046A probably benign Het
Zfr T A 15: 12,140,548 I227N unknown 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
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
R8717:Shmt1 UTSW 11 60794937 missense probably benign 0.00
R9673:Shmt1 UTSW 11 60801943 missense probably damaging 1.00
R9781:Shmt1 UTSW 11 60801503 missense probably damaging 1.00
Predicted Primers PCR Primer

Sequencing Primer
(R):5'- gggtggcagggtagttaag -3'
Posted On 2013-10-16