Incidental Mutation 'R3843:Amt'
ID 277251
Institutional Source Beutler Lab
Gene Symbol Amt
Ensembl Gene ENSMUSG00000032607
Gene Name aminomethyltransferase
Synonyms EG434437
MMRRC Submission 040783-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3843 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 108174104-108179501 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 108174420 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Cysteine at position 62 (R62C)
Ref Sequence ENSEMBL: ENSMUSP00000035230 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035227] [ENSMUST00000035230]
AlphaFold Q8CFA2
Predicted Effect probably benign
Transcript: ENSMUST00000035227
Predicted Effect possibly damaging
Transcript: ENSMUST00000035230
AA Change: R62C

PolyPhen 2 Score 0.744 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000035230
Gene: ENSMUSG00000032607
AA Change: R62C

DomainStartEndE-ValueType
Pfam:GCV_T 38 291 7.8e-86 PFAM
Pfam:GCV_T_C 300 392 1.6e-23 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160025
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160675
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162568
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192035
Predicted Effect noncoding transcript
Transcript: ENSMUST00000194496
Predicted Effect noncoding transcript
Transcript: ENSMUST00000195695
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.6%
  • 20x: 96.0%
Validation Efficiency 100% (35/35)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
PHENOTYPE: Mice homozygous for a gene trapped allele develop neural tubes defects at high frequency and exhibit prenatal lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 35 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aass A T 6: 23,092,495 (GRCm39) Y168* probably null Het
Arid2 C T 15: 96,249,721 (GRCm39) T145I possibly damaging Het
Ccdc8 T C 7: 16,729,039 (GRCm39) V176A probably damaging Het
Cdhr1 G T 14: 36,806,884 (GRCm39) F440L probably benign Het
Ckap2 A T 8: 22,665,774 (GRCm39) N424K probably damaging Het
Col6a1 C T 10: 76,547,175 (GRCm39) R730H unknown Het
Dennd1b C A 1: 138,981,092 (GRCm39) P102Q probably damaging Het
E2f1 A G 2: 154,402,748 (GRCm39) S340P probably benign Het
Eef1akmt2 C T 7: 132,433,305 (GRCm39) V134I probably damaging Het
Elp3 A T 14: 65,802,932 (GRCm39) probably null Het
Grap T G 11: 61,551,151 (GRCm39) probably null Het
Heatr1 T C 13: 12,450,002 (GRCm39) Y1999H probably benign Het
Hectd4 G T 5: 121,397,936 (GRCm39) W288L possibly damaging Het
Hnf4g G A 3: 3,716,362 (GRCm39) C262Y probably benign Het
Hrh4 A G 18: 13,155,343 (GRCm39) Y294C possibly damaging Het
Igkv5-39 C A 6: 69,877,526 (GRCm39) G77W probably damaging Het
Kdm2b A T 5: 123,072,856 (GRCm39) Y341N probably damaging Het
Kif26b T C 1: 178,755,742 (GRCm39) L1952P probably damaging Het
Lgr4 C T 2: 109,827,118 (GRCm39) probably benign Het
Nlrc3 G A 16: 3,782,828 (GRCm39) R194W probably benign Het
Nup214 T C 2: 31,941,112 (GRCm39) F547L probably damaging Het
Or5m3 A G 2: 85,838,548 (GRCm39) I143V probably benign Het
Pdp1 T C 4: 11,961,961 (GRCm39) K117E probably benign Het
Phtf2 G A 5: 20,979,020 (GRCm39) A31V probably damaging Het
Pip4p2 T A 4: 14,886,553 (GRCm39) Y42* probably null Het
Pkhd1 A T 1: 20,628,947 (GRCm39) C667S probably benign Het
Pnp2 T A 14: 51,200,878 (GRCm39) L121Q probably null Het
Ppfia1 C T 7: 144,058,707 (GRCm39) R698Q probably benign Het
Sidt1 A T 16: 44,104,587 (GRCm39) F275I probably benign Het
Slc50a1 A T 3: 89,177,207 (GRCm39) I70N probably damaging Het
Sytl2 C G 7: 90,009,367 (GRCm39) T123R possibly damaging Het
Tlk1 T A 2: 70,579,671 (GRCm39) T214S probably benign Het
Tmco3 A G 8: 13,346,114 (GRCm39) probably benign Het
Trim71 T C 9: 114,344,914 (GRCm39) T335A probably benign Het
Zbtb47 T A 9: 121,592,499 (GRCm39) V273E possibly damaging Het
Other mutations in Amt
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02657:Amt APN 9 108,178,579 (GRCm39) missense probably damaging 1.00
IGL03277:Amt APN 9 108,178,418 (GRCm39) missense probably benign
R1333:Amt UTSW 9 108,178,296 (GRCm39) missense probably benign 0.04
R1856:Amt UTSW 9 108,174,361 (GRCm39) missense probably damaging 1.00
R3844:Amt UTSW 9 108,174,420 (GRCm39) missense possibly damaging 0.74
R3903:Amt UTSW 9 108,174,420 (GRCm39) missense possibly damaging 0.74
R3904:Amt UTSW 9 108,174,420 (GRCm39) missense possibly damaging 0.74
R4729:Amt UTSW 9 108,177,851 (GRCm39) missense probably damaging 1.00
R4814:Amt UTSW 9 108,176,979 (GRCm39) missense probably benign
R5149:Amt UTSW 9 108,178,650 (GRCm39) missense possibly damaging 0.59
R6000:Amt UTSW 9 108,178,684 (GRCm39) missense probably benign 0.20
R6044:Amt UTSW 9 108,174,450 (GRCm39) missense probably damaging 1.00
R6911:Amt UTSW 9 108,178,428 (GRCm39) critical splice donor site probably null
R6957:Amt UTSW 9 108,177,032 (GRCm39) missense possibly damaging 0.51
R7618:Amt UTSW 9 108,177,077 (GRCm39) missense probably damaging 1.00
R7658:Amt UTSW 9 108,174,430 (GRCm39) missense probably damaging 0.98
R7783:Amt UTSW 9 108,174,414 (GRCm39) nonsense probably null
R9276:Amt UTSW 9 108,178,410 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CACTCAGTTCTGTACAGGTGGG -3'
(R):5'- ATCTCCTGAGTTAGCCCTCTAG -3'

Sequencing Primer
(F):5'- CTCAGTTCTGTACAGGTGGGATAAAG -3'
(R):5'- GAGTTAGCCCTCTAGAGTCCCTAAC -3'
Posted On 2015-04-06