Incidental Mutation 'R3899:Mtr'
ID 308893
Institutional Source Beutler Lab
Gene Symbol Mtr
Ensembl Gene ENSMUSG00000021311
Gene Name 5-methyltetrahydrofolate-homocysteine methyltransferase
Synonyms methionine synthase, D830038K18Rik, MS
MMRRC Submission 040809-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3899 (G1)
Quality Score 189
Status Validated
Chromosome 13
Chromosomal Location 12197598-12272999 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 12231735 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 656 (N656K)
Ref Sequence ENSEMBL: ENSMUSP00000097442 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000099856] [ENSMUST00000221290]
AlphaFold A6H5Y3
Predicted Effect probably benign
Transcript: ENSMUST00000099856
AA Change: N656K

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000097442
Gene: ENSMUSG00000021311
AA Change: N656K

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 0.0720 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 98% (62/63)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acss2 A G 2: 155,399,157 (GRCm39) probably benign Het
Ahctf1 A G 1: 179,605,345 (GRCm39) S730P possibly damaging Het
Ankrd26 T A 6: 118,526,389 (GRCm39) R327S probably benign Het
Anpep A G 7: 79,488,973 (GRCm39) S372P probably benign Het
Apob A T 12: 8,065,849 (GRCm39) I4273F possibly damaging Het
Ascl1 G T 10: 87,328,435 (GRCm39) H172Q probably benign Het
Azi2 A G 9: 117,876,571 (GRCm39) Y29C probably damaging Het
Baz1a A G 12: 54,981,589 (GRCm39) M355T probably benign Het
Brs3 G A X: 56,092,616 (GRCm39) V367M possibly damaging Het
Ccdc33 T C 9: 57,940,200 (GRCm39) D524G probably damaging Het
Cd300lf T C 11: 115,015,177 (GRCm39) T138A probably damaging Het
Cemip2 A G 19: 21,829,598 (GRCm39) T1236A probably benign Het
Ces1g T C 8: 94,029,678 (GRCm39) Y518C probably damaging Het
Chek2 C T 5: 111,013,479 (GRCm39) probably benign Het
Cherp A G 8: 73,223,780 (GRCm39) I201T possibly damaging Het
Cntnap2 A T 6: 45,968,837 (GRCm39) H193L probably benign Het
Crim1 C A 17: 78,588,783 (GRCm39) T286N probably benign Het
Cwc27 T A 13: 104,929,023 (GRCm39) K307* probably null Het
Dbx2 T C 15: 95,530,313 (GRCm39) D218G possibly damaging Het
Dclk1 G A 3: 55,154,750 (GRCm39) R60Q probably damaging Het
Dnah17 A T 11: 117,985,634 (GRCm39) I1481N possibly damaging Het
Dnah8 G A 17: 31,073,872 (GRCm39) R4514H probably damaging Het
Dpp10 A T 1: 123,281,286 (GRCm39) W588R probably damaging Het
Epg5 G A 18: 78,000,725 (GRCm39) E554K probably damaging Het
Eya1 T C 1: 14,340,971 (GRCm39) T139A probably benign Het
Fchsd2 A G 7: 100,841,006 (GRCm39) K172E possibly damaging Het
Foxd3 A G 4: 99,545,736 (GRCm39) Y292C unknown Het
Gli1 C T 10: 127,172,535 (GRCm39) M202I possibly damaging Het
Gm973 T C 1: 59,664,299 (GRCm39) Y634H probably benign Het
Gpr132 G T 12: 112,815,728 (GRCm39) A366E probably benign Het
Kcnd3 C T 3: 105,566,082 (GRCm39) A421V probably damaging Het
Kcnq3 C T 15: 65,902,372 (GRCm39) M201I probably benign Het
Khdc3 T C 9: 73,011,628 (GRCm39) probably benign Het
Lrrc37a A G 11: 103,388,372 (GRCm39) V2351A unknown Het
Mmrn2 G T 14: 34,121,517 (GRCm39) probably null Het
Mtus1 T C 8: 41,536,166 (GRCm39) T517A probably benign Het
Osgep G C 14: 51,162,200 (GRCm39) N12K probably damaging Het
Pcare A T 17: 72,057,155 (GRCm39) C841S probably benign Het
Prdx3 T A 19: 60,853,621 (GRCm39) T235S probably benign Het
Rasa3 G A 8: 13,628,635 (GRCm39) H608Y probably benign Het
Rd3 T C 1: 191,717,217 (GRCm39) V114A probably damaging Het
Setd2 C T 9: 110,421,586 (GRCm39) R273W probably damaging Het
Slc24a1 A T 9: 64,835,426 (GRCm39) S900R probably damaging Het
Slc30a5 T C 13: 100,954,655 (GRCm39) M170V probably benign Het
Slc4a9 T C 18: 36,668,616 (GRCm39) V732A probably benign Het
Slc7a2 C T 8: 41,358,590 (GRCm39) T311M possibly damaging Het
Smarcc1 T C 9: 109,947,586 (GRCm39) probably benign Het
Stk32b A G 5: 37,614,498 (GRCm39) S337P probably damaging Het
Thop1 G A 10: 80,916,278 (GRCm39) G429S probably damaging Het
Timp2 C T 11: 118,194,542 (GRCm39) D139N probably damaging Het
Tmem45a T C 16: 56,627,101 (GRCm39) E256G probably damaging Het
Tox4 T A 14: 52,517,299 (GRCm39) Y10N probably damaging Het
Trpm3 A G 19: 22,878,524 (GRCm39) M642V possibly damaging Het
Ttll10 T C 4: 156,120,257 (GRCm39) T508A probably damaging Het
Tut7 T A 13: 59,937,069 (GRCm39) K791* probably null Het
Ubash3b C T 9: 40,942,860 (GRCm39) D211N probably benign Het
Usp36 T A 11: 118,170,650 (GRCm39) D28V possibly damaging Het
Vmn2r97 T C 17: 19,167,873 (GRCm39) I709T probably damaging Het
Zfp936 T A 7: 42,839,158 (GRCm39) N207K possibly damaging Het
Zfp946 T G 17: 22,673,531 (GRCm39) I95S probably benign Het
Zhx3 A T 2: 160,622,371 (GRCm39) S599T possibly 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
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
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'- TCTGCCACACCCATCTATGAAG -3'
(R):5'- GATCCATGCTGAACACCCTG -3'

Sequencing Primer
(F):5'- TCAAATGAGTTGAGGACACTGGC -3'
(R):5'- CCCTGGGGTCTGGAAACTTGAAG -3'
Posted On 2015-04-17