Incidental Mutation 'R1907:Mtr'
ID 214502
Institutional Source Beutler Lab
Gene Symbol Mtr
Ensembl Gene ENSMUSG00000021311
Gene Name 5-methyltetrahydrofolate-homocysteine methyltransferase
Synonyms methionine synthase, D830038K18Rik, MS
MMRRC Submission 039926-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1907 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 12197598-12272999 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 12240418 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 530 (T530I)
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: T530I

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000097442
Gene: ENSMUSG00000021311
AA Change: T530I

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 0.7367 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 97.0%
  • 10x: 95.6%
  • 20x: 93.4%
Validation Efficiency 98% (104/106)
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: 104 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca4 C A 3: 121,862,661 (GRCm39) S206R probably damaging Het
Abcc6 G T 7: 45,663,593 (GRCm39) A357E probably benign Het
Abhd13 T A 8: 10,038,170 (GRCm39) C256S probably benign Het
Actrt3 A G 3: 30,652,716 (GRCm39) V126A probably damaging Het
Adgrv1 A G 13: 81,740,670 (GRCm39) probably benign Het
Alyref2 A G 1: 171,331,838 (GRCm39) D205G probably damaging Het
Amigo3 G A 9: 107,930,835 (GRCm39) R86Q probably benign Het
Ankrd50 G C 3: 38,508,201 (GRCm39) P1389A probably damaging Het
Aoah A G 13: 21,094,264 (GRCm39) D183G probably damaging Het
Arap3 A T 18: 38,129,724 (GRCm39) S146T probably benign Het
Atp2c2 T C 8: 120,476,615 (GRCm39) probably benign Het
Atp8b2 C T 3: 89,853,583 (GRCm39) V682M probably benign Het
Cacna1i T C 15: 80,259,465 (GRCm39) I1245T probably damaging Het
Card14 A G 11: 119,222,085 (GRCm39) N460S probably benign Het
Ceacam5 A G 7: 17,486,309 (GRCm39) D602G possibly damaging Het
Cecr2 T A 6: 120,738,121 (GRCm39) H921Q probably benign Het
Cyb5d1 T C 11: 69,285,566 (GRCm39) D115G probably benign Het
Dbp C T 7: 45,357,744 (GRCm39) T67I possibly damaging Het
Dennd5b C T 6: 148,943,074 (GRCm39) V601I probably benign Het
Dnah11 G A 12: 118,091,291 (GRCm39) A947V possibly damaging Het
Dpysl3 T A 18: 43,571,193 (GRCm39) D27V probably damaging Het
Drd1 A T 13: 54,207,271 (GRCm39) D307E possibly damaging Het
Dscaml1 G A 9: 45,651,778 (GRCm39) G277D probably damaging Het
Eif4g3 C T 4: 137,885,726 (GRCm39) R842W probably damaging Het
Enam C T 5: 88,652,481 (GRCm39) T1330I possibly damaging Het
Fabp6 T C 11: 43,486,994 (GRCm39) probably null Het
Fcsk A T 8: 111,620,010 (GRCm39) L289* probably null Het
Fhip1a T C 3: 85,579,940 (GRCm39) D755G probably benign Het
Fsip2 C T 2: 82,813,772 (GRCm39) P3364S possibly damaging Het
Gad1 C T 2: 70,409,482 (GRCm39) S191F possibly damaging Het
Gcm1 A C 9: 77,972,055 (GRCm39) N332T probably benign Het
Gin1 G A 1: 97,703,172 (GRCm39) probably benign Het
Gpr25 T C 1: 136,188,538 (GRCm39) D25G probably benign Het
Gstm4 T C 3: 107,948,593 (GRCm39) T172A probably benign Het
Hnrnpll A G 17: 80,342,758 (GRCm39) probably null Het
Il12rb2 T A 6: 67,272,270 (GRCm39) K339* probably null Het
Inpp1 A G 1: 52,828,829 (GRCm39) *397Q probably null Het
Kcp G T 6: 29,497,834 (GRCm39) probably benign Het
Kdm1b G A 13: 47,217,596 (GRCm39) V352I probably benign Het
Klhdc2 G T 12: 69,343,734 (GRCm39) probably benign Het
Krt75 T A 15: 101,481,801 (GRCm39) T156S possibly damaging Het
Lag3 T A 6: 124,886,450 (GRCm39) I168F possibly damaging Het
Lama4 T G 10: 38,948,754 (GRCm39) V839G probably benign Het
Lmtk2 G T 5: 144,111,928 (GRCm39) V883L probably benign Het
Lrrc37a C A 11: 103,347,982 (GRCm39) K2904N unknown Het
Macf1 A T 4: 123,266,192 (GRCm39) I4775N probably damaging Het
Map2k3 T G 11: 60,823,055 (GRCm39) S3A possibly damaging Het
Mast1 G A 8: 85,642,895 (GRCm39) R967C probably damaging Het
Mettl2 T G 11: 105,017,666 (GRCm39) S59A probably benign Het
Myo7b A T 18: 32,110,052 (GRCm39) C1137S possibly damaging Het
Nacad T A 11: 6,552,540 (GRCm39) H217L probably benign Het
Ncstn A T 1: 171,899,710 (GRCm39) V324E probably damaging Het
Ndufaf7 C A 17: 79,249,546 (GRCm39) H148N possibly damaging Het
Or10a49 T A 7: 108,467,705 (GRCm39) I219F possibly damaging Het
Or52a24 T A 7: 103,381,190 (GRCm39) I19N probably damaging Het
Or52n2b G A 7: 104,566,272 (GRCm39) T77I probably damaging Het
Or7g12 T C 9: 18,899,737 (GRCm39) I151T possibly damaging Het
Or8b12 T G 9: 37,657,729 (GRCm39) L100V probably benign Het
Or8k17 T C 2: 86,066,454 (GRCm39) K242E possibly damaging Het
Pcdh20 T C 14: 88,706,140 (GRCm39) I387V probably benign Het
Pclo A G 5: 14,728,525 (GRCm39) probably benign Het
Pcp2 G A 8: 3,674,904 (GRCm39) probably benign Het
Pde1a T A 2: 79,698,651 (GRCm39) D393V probably damaging Het
Pias4 T C 10: 80,990,197 (GRCm39) D421G possibly damaging Het
Pign T C 1: 105,565,940 (GRCm39) T362A possibly damaging Het
Pik3c2g A C 6: 139,789,768 (GRCm39) K304Q probably damaging Het
Pkd2 T A 5: 104,634,672 (GRCm39) W568R probably damaging Het
Pld2 T A 11: 70,435,010 (GRCm39) I306N probably damaging Het
Plppr3 T C 10: 79,709,903 (GRCm39) K9R probably damaging Het
Pramel11 T A 4: 143,622,061 (GRCm39) R431S possibly damaging Het
Psme4 T C 11: 30,760,922 (GRCm39) V397A probably damaging Het
Ptbp2 A T 3: 119,555,398 (GRCm39) S23R probably damaging Het
Ptpn13 A G 5: 103,728,575 (GRCm39) D2074G probably null Het
Rab34 T A 11: 78,082,081 (GRCm39) L166H probably damaging Het
Rabgap1l T A 1: 160,472,880 (GRCm39) R519S probably benign Het
Rasa1 A T 13: 85,374,691 (GRCm39) L218* probably null Het
Reln A G 5: 22,249,960 (GRCm39) probably null Het
Rer1 T C 4: 155,162,956 (GRCm39) D94G possibly damaging Het
Rhpn1 T C 15: 75,583,673 (GRCm39) V386A probably benign Het
Samd3 T A 10: 26,147,754 (GRCm39) C476* probably null Het
Sdk2 C T 11: 113,729,472 (GRCm39) silent Het
Sipa1l3 A G 7: 29,038,592 (GRCm39) S352P possibly damaging Het
Slc27a2 A G 2: 126,428,262 (GRCm39) Y549C probably benign Het
Slc7a9 A G 7: 35,149,279 (GRCm39) T7A probably benign Het
Slco4c1 C T 1: 96,770,224 (GRCm39) G280D probably damaging Het
Snx19 T A 9: 30,344,872 (GRCm39) V657E probably damaging Het
Spata31d1c A G 13: 65,183,690 (GRCm39) M411V probably benign Het
Spice1 T A 16: 44,178,193 (GRCm39) L72* probably null Het
Stard9 G T 2: 120,544,293 (GRCm39) V4471L probably damaging Het
Syt14 A G 1: 192,584,143 (GRCm39) L707P probably damaging Het
Tab1 T C 15: 80,037,869 (GRCm39) I234T probably damaging Het
Tas2r107 T C 6: 131,636,951 (GRCm39) M33V probably benign Het
Tbx4 T A 11: 85,805,349 (GRCm39) S479R possibly damaging Het
Tssk5 C T 15: 76,257,093 (GRCm39) R263Q probably benign Het
Ttn T C 2: 76,701,200 (GRCm39) probably benign Het
Ugt2b5 T A 5: 87,287,489 (GRCm39) Q226L probably benign Het
Ush2a C T 1: 188,447,261 (GRCm39) S2483L probably benign Het
Wdr95 A G 5: 149,475,891 (GRCm39) Y63C probably damaging Het
Xirp2 A G 2: 67,346,700 (GRCm39) I2980M probably damaging Het
Yeats4 G A 10: 117,051,636 (GRCm39) T207I probably benign Het
Ythdc1 A G 5: 86,978,489 (GRCm39) R561G probably damaging Het
Zbtb14 G A 17: 69,694,385 (GRCm39) E28K possibly damaging Het
Zfp931 A T 2: 177,711,684 (GRCm39) L21Q probably damaging Het
Zyg11b A C 4: 108,112,423 (GRCm39) M415R 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
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
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
Predicted Primers PCR Primer
(F):5'- GACAGGCATGTTACTATTCTCAGC -3'
(R):5'- CACATCTGTCTTTAGAAAACCACTGTG -3'

Sequencing Primer
(F):5'- GGCATGTTACTATTCTCAGCAAATC -3'
(R):5'- AATTCAGCCATTGAGATTTGAGTGG -3'
Posted On 2014-07-14