Incidental Mutation 'R7108:Shmt1'
ID 551343
Institutional Source Beutler Lab
Gene Symbol Shmt1
Ensembl Gene ENSMUSG00000020534
Gene Name serine hydroxymethyltransferase 1 (soluble)
Synonyms mshmt, mshmt2, mshmt1, Shmt
MMRRC Submission 045200-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7108 (G1)
Quality Score 225.009
Status Not validated
Chromosome 11
Chromosomal Location 60678933-60702091 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 60689470 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 178 (D178G)
Ref Sequence ENSEMBL: ENSMUSP00000018744 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018744]
AlphaFold P50431
PDB Structure RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE) [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000018744
AA Change: D178G

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: D178G

DomainStartEndE-ValueType
Pfam:SHMT 20 419 1.3e-211 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174174
SMART Domains Protein: ENSMUSP00000134703
Gene: ENSMUSG00000020534

DomainStartEndE-ValueType
Pfam:SHMT 20 79 7.1e-26 PFAM
Predicted Effect
SMART Domains Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
AA Change: D177G

DomainStartEndE-ValueType
Pfam:SHMT 20 408 4.6e-196 PFAM
Pfam:Aminotran_1_2 153 409 3.1e-6 PFAM
Predicted Effect
SMART Domains Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: D177G

DomainStartEndE-ValueType
Pfam:SHMT 20 268 6.4e-137 PFAM
Pfam:SHMT 265 380 3.9e-51 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the 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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2810021J22Rik T C 11: 58,771,750 (GRCm39) S411P probably damaging Het
4930503L19Rik A T 18: 70,601,547 (GRCm39) Y112N probably benign Het
Abcd2 A T 15: 91,075,477 (GRCm39) V112E probably benign Het
Acadm A T 3: 153,631,437 (GRCm39) Y353* probably null Het
Adra2c A G 5: 35,437,342 (GRCm39) D38G probably benign Het
Ankrd10 C T 8: 11,662,624 (GRCm39) G370R probably damaging Het
Arfgef2 T A 2: 166,715,528 (GRCm39) N1324K possibly damaging Het
Atp6v1b2 A G 8: 69,555,153 (GRCm39) T172A probably damaging Het
Bloc1s1 T A 10: 128,758,592 (GRCm39) K22M possibly damaging Het
Brpf3 A G 17: 29,036,099 (GRCm39) T599A probably benign Het
Cacna1e TTCCAGTCTC TTC 1: 154,344,741 (GRCm39) probably null Het
Ccdc186 T C 19: 56,787,192 (GRCm39) D592G probably damaging Het
Cfap161 A T 7: 83,442,518 (GRCm39) D98E possibly damaging Het
Cfi G A 3: 129,668,665 (GRCm39) V564M probably damaging Het
Cilp2 T A 8: 70,333,779 (GRCm39) Q1073L probably damaging Het
Cox6b1 A G 7: 30,322,929 (GRCm39) C40R possibly damaging Het
Cyp3a59 A T 5: 146,033,143 (GRCm39) M172L probably benign Het
Cyth1 T C 11: 118,073,739 (GRCm39) D198G probably damaging Het
Daam2 T C 17: 49,767,702 (GRCm39) D963G probably damaging Het
Ddi2 A T 4: 141,433,248 (GRCm39) D209E probably benign Het
Dnah12 G A 14: 26,500,869 (GRCm39) probably null Het
Dnai7 G A 6: 145,131,591 (GRCm39) Q351* probably null Het
Dpagt1 G T 9: 44,238,318 (GRCm39) probably benign Het
Drc3 T A 11: 60,261,380 (GRCm39) F177Y probably benign Het
Dsg2 T C 18: 20,734,920 (GRCm39) V966A probably damaging Het
E4f1 A G 17: 24,663,552 (GRCm39) V633A probably damaging Het
Eif2ak2 T A 17: 79,165,965 (GRCm39) R411* probably null Het
Frem2 T C 3: 53,560,934 (GRCm39) E1191G probably damaging Het
Fry T C 5: 150,319,251 (GRCm39) V972A probably damaging Het
Fry T A 5: 150,414,555 (GRCm39) C467S Het
Fscn1 T C 5: 142,946,270 (GRCm39) Y23H probably damaging Het
Gm16506 T A 14: 43,961,759 (GRCm39) I163F Het
Gm21103 T C 14: 17,484,768 (GRCm39) Y92C probably damaging Het
Golgb1 A G 16: 36,734,083 (GRCm39) H1151R probably benign Het
Gprc5c T C 11: 114,755,108 (GRCm39) Y262H probably damaging Het
Hc G T 2: 34,929,706 (GRCm39) N245K probably benign Het
Hps6 T A 19: 45,993,929 (GRCm39) L622Q probably damaging Het
Hsd17b1 T C 11: 100,970,035 (GRCm39) Y156H probably damaging Het
Ireb2 T A 9: 54,813,925 (GRCm39) F799L probably damaging Het
Irf1 A G 11: 53,665,238 (GRCm39) D205G probably damaging Het
Kif12 A T 4: 63,089,442 (GRCm39) F103L probably benign Het
Krt12 C T 11: 99,306,878 (GRCm39) V475M unknown Het
Lca5 T A 9: 83,305,222 (GRCm39) T195S probably benign Het
Lrrc17 T C 5: 21,780,337 (GRCm39) V437A possibly damaging Het
Malt1 G T 18: 65,597,122 (GRCm39) D468Y probably damaging Het
Man2b2 C T 5: 36,972,829 (GRCm39) A562T probably benign Het
Mrc1 C T 2: 14,308,957 (GRCm39) Q794* probably null Het
Muc16 T A 9: 18,566,529 (GRCm39) I1997L unknown Het
Muc6 AGGCGCAGAAACCCTGGC AGGC 7: 141,214,363 (GRCm39) probably null Het
Mycbp2 A T 14: 103,360,039 (GRCm39) F4518Y probably damaging Het
Myo5a T A 9: 75,037,274 (GRCm39) I159N probably damaging Het
Nat1 T C 8: 67,943,672 (GRCm39) V19A probably benign Het
Ndst4 A G 3: 125,355,120 (GRCm39) T343A probably damaging Het
Nlrp9b A T 7: 19,779,855 (GRCm39) L839F probably damaging Het
Nxnl1 A G 8: 72,019,198 (GRCm39) I9T probably benign Het
Odr4 T C 1: 150,258,041 (GRCm39) Y198C probably benign Het
Or1l4b C T 2: 37,036,272 (GRCm39) T16I probably benign Het
Or2ag12 G A 7: 106,277,255 (GRCm39) A146V probably benign Het
Or2t49 T A 11: 58,393,380 (GRCm39) M7L probably benign Het
Or52b4i A T 7: 102,191,199 (GRCm39) I19F probably damaging Het
Or7a35 C A 10: 78,853,483 (GRCm39) S109* probably null Het
Pou5f2 T C 13: 78,173,384 (GRCm39) S109P possibly damaging Het
Prkcz G A 4: 155,371,250 (GRCm39) Q321* probably null Het
Prr18 G T 17: 8,560,363 (GRCm39) R173L probably damaging Het
Ralgapb T C 2: 158,334,380 (GRCm39) Y1364H probably damaging Het
Ralgapb A T 2: 158,336,582 (GRCm39) I1407F probably damaging Het
Sacs T A 14: 61,448,458 (GRCm39) Y3501* probably null Het
Sall3 G A 18: 81,016,969 (GRCm39) P320S probably benign Het
Scn8a A T 15: 100,937,659 (GRCm39) H1676L probably benign Het
Slmap T C 14: 26,143,676 (GRCm39) K737R probably benign Het
Ssh2 G A 11: 77,345,620 (GRCm39) V1202I probably benign Het
Stard7 A G 2: 127,137,414 (GRCm39) D288G possibly damaging Het
Tek A T 4: 94,741,724 (GRCm39) D827V probably damaging Het
Tfap2e A G 4: 126,614,356 (GRCm39) L276P probably damaging Het
Tns3 T C 11: 8,387,251 (GRCm39) N1312S probably benign Het
Tubd1 T A 11: 86,448,631 (GRCm39) S315T probably damaging Het
Ube2f T A 1: 91,192,941 (GRCm39) C50* probably null Het
Vmn2r109 T C 17: 20,785,006 (GRCm39) I5V probably benign Het
Vmn2r39 T C 7: 9,026,667 (GRCm39) T445A probably damaging Het
Zfp764l1 A G 7: 126,990,695 (GRCm39) S431P probably benign Het
Other mutations in Shmt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02088:Shmt1 APN 11 60,680,479 (GRCm39) missense probably damaging 1.00
PIT4514001:Shmt1 UTSW 11 60,695,173 (GRCm39) missense probably damaging 1.00
R0470:Shmt1 UTSW 11 60,683,789 (GRCm39) missense possibly damaging 0.91
R0787:Shmt1 UTSW 11 60,683,802 (GRCm39) missense probably benign 0.00
R1768:Shmt1 UTSW 11 60,683,790 (GRCm39) missense probably damaging 1.00
R2179:Shmt1 UTSW 11 60,697,825 (GRCm39) missense possibly damaging 0.69
R3715:Shmt1 UTSW 11 60,688,402 (GRCm39) missense probably damaging 1.00
R4647:Shmt1 UTSW 11 60,692,291 (GRCm39) missense probably damaging 1.00
R5024:Shmt1 UTSW 11 60,688,305 (GRCm39) intron probably benign
R5183:Shmt1 UTSW 11 60,688,308 (GRCm39) intron probably benign
R5461:Shmt1 UTSW 11 60,685,725 (GRCm39) missense possibly damaging 0.94
R6014:Shmt1 UTSW 11 60,688,383 (GRCm39) missense probably damaging 1.00
R6618:Shmt1 UTSW 11 60,683,772 (GRCm39) splice site probably null
R6969:Shmt1 UTSW 11 60,695,153 (GRCm39) missense probably damaging 1.00
R7158:Shmt1 UTSW 11 60,681,068 (GRCm39) missense probably benign 0.03
R7215:Shmt1 UTSW 11 60,692,361 (GRCm39) missense probably damaging 0.99
R7514:Shmt1 UTSW 11 60,692,812 (GRCm39) missense probably damaging 1.00
R8717:Shmt1 UTSW 11 60,685,763 (GRCm39) missense probably benign 0.00
R9673:Shmt1 UTSW 11 60,692,769 (GRCm39) missense probably damaging 1.00
R9781:Shmt1 UTSW 11 60,692,329 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GTCTGGCTTGAAGAATAGCTCC -3'
(R):5'- CCCTTTATATCCTTGGACAGGC -3'

Sequencing Primer
(F):5'- CCTTAGGGCAGAATACGTCTC -3'
(R):5'- CAGGCTGAATACAGTGCCTTGTC -3'
Posted On 2019-05-15