Incidental Mutation 'R0047:Mtr'
ID 18526
Institutional Source Beutler Lab
Gene Symbol Mtr
Ensembl Gene ENSMUSG00000021311
Gene Name 5-methyltetrahydrofolate-homocysteine methyltransferase
Synonyms methionine synthase, D830038K18Rik, MS
MMRRC Submission 038341-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0047 (G1)
Quality Score
Status Validated
Chromosome 13
Chromosomal Location 12197598-12272999 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 12237112 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 569 (S569T)
Ref Sequence ENSEMBL: ENSMUSP00000097442 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000099856] [ENSMUST00000221290]
AlphaFold A6H5Y3
Predicted Effect probably damaging
Transcript: ENSMUST00000099856
AA Change: S569T

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000097442
Gene: ENSMUSG00000021311
AA Change: S569T

DomainStartEndE-ValueType
Pfam:S-methyl_trans 18 326 1.5e-93 PFAM
Pfam:Pterin_bind 363 601 4.6e-63 PFAM
B12-binding_2 657 743 6.42e-41 SMART
Pfam:B12-binding 761 861 3.3e-20 PFAM
Pfam:Met_synt_B12 953 1234 2.5e-114 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000221290
Meta Mutation Damage Score 0.6960 question?
Coding Region Coverage
  • 1x: 89.2%
  • 3x: 86.3%
  • 10x: 78.8%
  • 20x: 65.9%
Validation Efficiency 95% (110/116)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the 5-methyltetrahydrofolate-homocysteine methyltransferase. This enzyme, also known as cobalamin-dependent methionine synthase, catalyzes the final step in methionine biosynthesis. Mutations in MTR have been identified as the underlying cause of methylcobalamin deficiency complementation group G. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]
PHENOTYPE: Mice homozygous for a targeted null mutation exhibit embryonic lethality prior to E9.5. Heterozygous appear mostly similar to conrtols, except that they exhibit elevated plasma methionine and homocysteine levels. [provided by MGI curators]
Allele List at MGI

All alleles(6) : Targeted, knock-out(1) Gene trapped(5)

Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,772,025 (GRCm39) T405A probably damaging Het
Acer1 A T 17: 57,262,624 (GRCm39) D175E possibly damaging Het
Adamts9 G A 6: 92,882,287 (GRCm39) probably benign Het
Amigo3 T C 9: 107,931,857 (GRCm39) S427P probably benign Het
Arid4a T G 12: 71,122,193 (GRCm39) L858W probably damaging Het
Bbox1 A G 2: 110,098,647 (GRCm39) F310S probably damaging Het
Bltp1 T A 3: 36,962,341 (GRCm39) L481M possibly damaging Het
Bmper T A 9: 23,317,982 (GRCm39) C534S probably damaging Het
Cacna1d T G 14: 30,068,747 (GRCm39) probably benign Het
Capn12 G A 7: 28,589,812 (GRCm39) probably null Het
Chchd1 T C 14: 20,754,231 (GRCm39) S48P possibly damaging Het
Cnot7 A G 8: 40,948,962 (GRCm39) probably benign Het
Cux1 T C 5: 136,392,107 (GRCm39) probably benign Het
Cyp2b19 T A 7: 26,466,251 (GRCm39) D351E probably benign Het
Dctn1 G T 6: 83,159,614 (GRCm39) G31* probably null Het
Duox1 T A 2: 122,177,122 (GRCm39) probably benign Het
Egflam T G 15: 7,282,911 (GRCm39) E382A possibly damaging Het
Ext1 T C 15: 53,208,542 (GRCm39) N73S probably benign Het
Glg1 A T 8: 111,892,214 (GRCm39) M866K probably damaging Het
Gm3333 A G 13: 62,422,285 (GRCm39) noncoding transcript Het
Golm1 T A 13: 59,792,914 (GRCm39) H197L probably benign Het
Gtse1 A G 15: 85,746,579 (GRCm39) K132E probably damaging Het
Gxylt2 A T 6: 100,710,339 (GRCm39) probably benign Het
Hrc T A 7: 44,986,113 (GRCm39) S421R probably benign Het
Ighg2c T A 12: 113,251,788 (GRCm39) probably benign Het
Ihh A G 1: 74,985,750 (GRCm39) I245T probably benign Het
Ilf3 T A 9: 21,300,010 (GRCm39) M65K possibly damaging Het
Kif9 A G 9: 110,314,106 (GRCm39) I33V probably benign Het
Lama1 A T 17: 68,102,181 (GRCm39) probably benign Het
Lamb1 T C 12: 31,328,600 (GRCm39) I188T possibly damaging Het
Lpp T A 16: 24,480,550 (GRCm39) probably benign Het
Mark2 A C 19: 7,260,942 (GRCm39) probably benign Het
Mmp3 T C 9: 7,451,910 (GRCm39) probably benign Het
Mthfd1l T A 10: 3,928,727 (GRCm39) probably benign Het
Myh13 T A 11: 67,258,063 (GRCm39) S1752T probably benign Het
Myo5a T A 9: 75,063,489 (GRCm39) L565H probably damaging Het
Numa1 A G 7: 101,658,660 (GRCm39) K296E probably damaging Het
Obi1 T A 14: 104,740,780 (GRCm39) probably null Het
Or51ab3 A T 7: 103,201,529 (GRCm39) Y179F probably damaging Het
Or5ac19 C T 16: 59,089,574 (GRCm39) G152D probably damaging Het
Or5b120 A G 19: 13,479,953 (GRCm39) E82G probably benign Het
Pla2g2c T C 4: 138,470,901 (GRCm39) probably benign Het
Pnpla7 A T 2: 24,901,618 (GRCm39) E548V probably damaging Het
Ppm1m C A 9: 106,073,895 (GRCm39) E273* probably null Het
Ppp2r1b C T 9: 50,772,873 (GRCm39) R117* probably null Het
Psg-ps1 A G 7: 17,411,806 (GRCm39) noncoding transcript Het
Rabgap1l G A 1: 160,059,359 (GRCm39) probably benign Het
Rapgef6 T A 11: 54,437,204 (GRCm39) M49K possibly damaging Het
Rtel1 T G 2: 180,965,198 (GRCm39) I146M probably damaging Het
Sdr9c7 A T 10: 127,739,541 (GRCm39) M219L probably benign Het
Serpinb1a A T 13: 33,034,259 (GRCm39) L44Q probably damaging Het
Slc13a4 A G 6: 35,264,297 (GRCm39) I190T possibly damaging Het
Slc46a2 A G 4: 59,914,392 (GRCm39) L177P probably damaging Het
Slc47a2 C T 11: 61,227,068 (GRCm39) V167M possibly damaging Het
Snrnp200 C T 2: 127,076,874 (GRCm39) probably benign Het
Snx13 C A 12: 35,151,123 (GRCm39) probably benign Het
Snx25 C T 8: 46,494,402 (GRCm39) A828T probably damaging Het
Spic A G 10: 88,511,803 (GRCm39) L151P probably damaging Het
Sptb G T 12: 76,669,724 (GRCm39) Q535K probably damaging Het
Ssu2 G A 6: 112,351,781 (GRCm39) H315Y probably damaging Het
Stk32a T C 18: 43,446,443 (GRCm39) probably benign Het
Tcaf2 A G 6: 42,606,547 (GRCm39) I469T probably benign Het
Tln2 A G 9: 67,147,954 (GRCm39) probably benign Het
Top2a T A 11: 98,888,682 (GRCm39) I1260L probably benign Het
Treml1 C A 17: 48,672,008 (GRCm39) S91* probably null Het
Trmt11 T C 10: 30,411,239 (GRCm39) N418S probably benign Het
Ttf1 A G 2: 28,974,667 (GRCm39) Y801C probably damaging Het
Usp34 C T 11: 23,414,403 (GRCm39) A2782V probably benign Het
Vps4a T C 8: 107,763,333 (GRCm39) L29P probably damaging Het
Wdfy3 A G 5: 102,091,899 (GRCm39) I480T probably damaging Het
Ywhag A T 5: 135,940,153 (GRCm39) V147E probably damaging Het
Other mutations in Mtr
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01299:Mtr APN 13 12,240,536 (GRCm39) splice site probably benign
IGL02456:Mtr APN 13 12,213,980 (GRCm39) missense probably damaging 0.98
IGL02573:Mtr APN 13 12,214,013 (GRCm39) missense possibly damaging 0.95
IGL02642:Mtr APN 13 12,210,118 (GRCm39) splice site probably benign
IGL03005:Mtr APN 13 12,250,335 (GRCm39) splice site probably benign
IGL03017:Mtr APN 13 12,262,777 (GRCm39) critical splice donor site probably null
IGL03036:Mtr APN 13 12,262,263 (GRCm39) missense probably damaging 1.00
H8930:Mtr UTSW 13 12,250,346 (GRCm39) missense probably damaging 1.00
PIT4431001:Mtr UTSW 13 12,227,329 (GRCm39) missense probably damaging 1.00
PIT4520001:Mtr UTSW 13 12,212,871 (GRCm39) nonsense probably null
R0011:Mtr UTSW 13 12,252,938 (GRCm39) splice site probably benign
R0047:Mtr UTSW 13 12,237,112 (GRCm39) missense probably damaging 1.00
R0304:Mtr UTSW 13 12,237,040 (GRCm39) critical splice donor site probably null
R0617:Mtr UTSW 13 12,236,318 (GRCm39) missense probably benign
R0842:Mtr UTSW 13 12,215,133 (GRCm39) missense probably damaging 1.00
R1101:Mtr UTSW 13 12,204,411 (GRCm39) missense possibly damaging 0.84
R1450:Mtr UTSW 13 12,208,619 (GRCm39) missense probably damaging 0.99
R1534:Mtr UTSW 13 12,250,430 (GRCm39) splice site probably benign
R1907:Mtr UTSW 13 12,240,418 (GRCm39) missense probably damaging 1.00
R2111:Mtr UTSW 13 12,259,487 (GRCm39) missense possibly damaging 0.86
R2354:Mtr UTSW 13 12,203,043 (GRCm39) splice site probably benign
R3849:Mtr UTSW 13 12,262,251 (GRCm39) missense probably benign 0.16
R3899:Mtr UTSW 13 12,231,735 (GRCm39) missense probably benign 0.00
R4012:Mtr UTSW 13 12,204,284 (GRCm39) missense probably damaging 1.00
R4012:Mtr UTSW 13 12,204,283 (GRCm39) missense probably damaging 1.00
R4075:Mtr UTSW 13 12,230,298 (GRCm39) critical splice donor site probably null
R4091:Mtr UTSW 13 12,245,943 (GRCm39) missense probably damaging 1.00
R4655:Mtr UTSW 13 12,242,679 (GRCm39) missense probably damaging 1.00
R4801:Mtr UTSW 13 12,210,137 (GRCm39) missense probably benign 0.01
R4802:Mtr UTSW 13 12,210,137 (GRCm39) missense probably benign 0.01
R4895:Mtr UTSW 13 12,231,752 (GRCm39) missense probably benign 0.01
R5481:Mtr UTSW 13 12,203,041 (GRCm39) critical splice acceptor site probably null
R5966:Mtr UTSW 13 12,230,453 (GRCm39) critical splice acceptor site probably null
R6209:Mtr UTSW 13 12,205,278 (GRCm39) missense probably benign 0.00
R6348:Mtr UTSW 13 12,262,840 (GRCm39) missense possibly damaging 0.49
R6463:Mtr UTSW 13 12,231,752 (GRCm39) missense probably benign 0.01
R6467:Mtr UTSW 13 12,202,992 (GRCm39) missense probably damaging 1.00
R7046:Mtr UTSW 13 12,205,095 (GRCm39) missense possibly damaging 0.58
R7505:Mtr UTSW 13 12,236,362 (GRCm39) missense probably benign 0.02
R7575:Mtr UTSW 13 12,213,963 (GRCm39) missense probably benign 0.01
R7705:Mtr UTSW 13 12,264,782 (GRCm39) missense probably benign
R7748:Mtr UTSW 13 12,242,725 (GRCm39) missense probably benign 0.00
R8161:Mtr UTSW 13 12,236,372 (GRCm39) missense probably damaging 0.99
R8290:Mtr UTSW 13 12,205,139 (GRCm39) missense probably damaging 1.00
R8988:Mtr UTSW 13 12,250,365 (GRCm39) missense probably benign
R9050:Mtr UTSW 13 12,231,748 (GRCm39) missense probably null 0.67
R9420:Mtr UTSW 13 12,268,764 (GRCm39) missense probably benign 0.04
R9655:Mtr UTSW 13 12,203,030 (GRCm39) missense probably damaging 1.00
X0064:Mtr UTSW 13 12,265,543 (GRCm39) missense probably damaging 1.00
Z1177:Mtr UTSW 13 12,264,752 (GRCm39) nonsense probably null
Z1177:Mtr UTSW 13 12,201,935 (GRCm39) missense probably benign 0.32
Posted On 2013-03-25