Incidental Mutation 'R4498:Gnmt'
ID 331722
Institutional Source Beutler Lab
Gene Symbol Gnmt
Ensembl Gene ENSMUSG00000002769
Gene Name glycine N-methyltransferase
Synonyms glycine N methyl transferase
MMRRC Submission 041751-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.320) question?
Stock # R4498 (G1)
Quality Score 217
Status Validated
Chromosome 17
Chromosomal Location 47036590-47040091 bp(-) (GRCm39)
Type of Mutation utr 3 prime
DNA Base Change (assembly) ATTAGGGGATGGTCTTAGGG to ATTAGGG at 47036662 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change at position 294 (294)
Ref Sequence ENSEMBL: ENSMUSP00000002846 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002840] [ENSMUST00000002846]
AlphaFold Q9QXF8
PDB Structure Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragonal Form) [X-RAY DIFFRACTION]
Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form) [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000002840
SMART Domains Protein: ENSMUSP00000002840
Gene: ENSMUSG00000002763

DomainStartEndE-ValueType
low complexity region 17 31 N/A INTRINSIC
low complexity region 72 86 N/A INTRINSIC
low complexity region 87 104 N/A INTRINSIC
low complexity region 112 128 N/A INTRINSIC
low complexity region 173 200 N/A INTRINSIC
AAA 463 598 6.1e-7 SMART
AAA 737 875 6e-24 SMART
Blast:AAA 928 973 1e-14 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000002846
AA Change: 294
SMART Domains Protein: ENSMUSP00000002846
Gene: ENSMUSG00000002769
AA Change: 294

DomainStartEndE-ValueType
Pfam:Methyltransf_23 27 217 9e-11 PFAM
Pfam:Methyltransf_31 56 224 1.3e-15 PFAM
Pfam:Methyltransf_18 57 176 1.5e-15 PFAM
Pfam:Methyltransf_25 61 169 1.4e-10 PFAM
Pfam:Methyltransf_12 62 171 4e-12 PFAM
Pfam:Methyltransf_11 62 173 2.4e-11 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144964
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147112
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148872
Predicted Effect noncoding transcript
Transcript: ENSMUST00000181301
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.2%
Validation Efficiency 91% (53/58)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an enzyme that catalyzes the conversion of S-adenosyl-L-methionine (along with glycine) to S-adenosyl-L-homocysteine and sarcosine. This protein is found in the cytoplasm and acts as a homotetramer. Defects in this gene are a cause of GNMT deficiency (hypermethioninemia). Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between the upstream CNPY3 (canopy FGF signaling regulator 3) gene and this gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]
PHENOTYPE: Mice homozygous for a null mutation display elevated levels of methionine and S-adenosylmethionine in the liver. Mice homozygous for another null allele exhibit hepatitis, increased hepatic glycogen storage, and hepatocellular carcinoma. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aco2 G A 15: 81,779,486 (GRCm39) A97T probably damaging Het
Acot9 T A X: 154,047,064 (GRCm39) L18* probably null Het
Arhgap12 A T 18: 6,111,774 (GRCm39) C69S probably damaging Het
Ccdc17 G T 4: 116,454,438 (GRCm39) probably benign Het
Ctnnd2 A C 15: 30,620,020 (GRCm39) D124A probably damaging Het
Cux1 T C 5: 136,341,847 (GRCm39) N424S probably damaging Het
Dhrs7c T C 11: 67,706,706 (GRCm39) F214S possibly damaging Het
Fat2 T C 11: 55,160,923 (GRCm39) D3269G possibly damaging Het
Fhod3 T A 18: 25,243,296 (GRCm39) probably null Het
Glul G T 1: 153,782,849 (GRCm39) G187* probably null Het
H2-Q7 A T 17: 35,658,506 (GRCm39) Y48F probably damaging Het
Hes3 T C 4: 152,371,542 (GRCm39) T136A probably benign Het
Krt40 T C 11: 99,433,900 (GRCm39) T29A possibly damaging Het
Lrrc37a C A 11: 103,392,624 (GRCm39) D934Y probably benign Het
Mctp2 T A 7: 71,833,599 (GRCm39) D581V probably damaging Het
Med27 T C 2: 29,361,354 (GRCm39) S38P probably damaging Het
Mff A G 1: 82,719,501 (GRCm39) probably benign Het
Mmadhc T C 2: 50,170,236 (GRCm39) K292R probably benign Het
Mmp24 A G 2: 155,655,908 (GRCm39) I449V possibly damaging Het
Mthfd1 G T 12: 76,361,764 (GRCm39) L123F probably damaging Het
Mug2 T A 6: 122,059,711 (GRCm39) L1363Q probably damaging Het
Myh4 T C 11: 67,142,578 (GRCm39) I913T probably damaging Het
Myo16 T A 8: 10,485,869 (GRCm39) N649K probably benign Het
Myo7b A G 18: 32,147,282 (GRCm39) I87T probably benign Het
Ndst4 A G 3: 125,232,007 (GRCm39) D192G probably damaging Het
Nup155 A G 15: 8,183,157 (GRCm39) D1239G possibly damaging Het
Or5b21 T C 19: 12,840,033 (GRCm39) V298A probably damaging Het
Or7e173 G C 9: 19,939,029 (GRCm39) N68K possibly damaging Het
Phf10 T A 17: 15,165,377 (GRCm39) N493I probably benign Het
Pramel32 A T 4: 88,547,129 (GRCm39) probably null Het
Prr12 T C 7: 44,695,338 (GRCm39) E1376G unknown Het
Rasa3 T C 8: 13,664,587 (GRCm39) H75R probably benign Het
Rin3 G A 12: 102,335,939 (GRCm39) V537M probably damaging Het
Samd4 C T 14: 47,333,566 (GRCm39) T272I probably damaging Het
Septin5 C T 16: 18,442,142 (GRCm39) G257D probably damaging Het
Serpina6 T C 12: 103,620,326 (GRCm39) K141R probably benign Het
Siglecf T A 7: 43,001,700 (GRCm39) I170N possibly damaging Het
Spopl C T 2: 23,407,957 (GRCm39) V241M probably damaging Het
Stk40 G A 4: 126,023,544 (GRCm39) probably null Het
Syne1 A G 10: 4,981,768 (GRCm39) S8700P probably benign Het
Tbc1d4 C T 14: 101,845,772 (GRCm39) G42E probably damaging Het
Tfap2c C T 2: 172,399,102 (GRCm39) Q425* probably null Het
Tmem255b T C 8: 13,505,998 (GRCm39) S202P probably damaging Het
Traf6 T C 2: 101,514,891 (GRCm39) S16P probably benign Het
Ttc12 A G 9: 49,383,705 (GRCm39) I66T probably damaging Het
Ttc21a G A 9: 119,787,885 (GRCm39) D818N possibly damaging Het
Zfp81 A T 17: 33,553,677 (GRCm39) I379N possibly damaging Het
Zgrf1 C A 3: 127,379,749 (GRCm39) S211* probably null Het
Other mutations in Gnmt
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01351:Gnmt APN 17 47,037,606 (GRCm39) missense probably benign 0.28
health_nut UTSW 17 47,037,271 (GRCm39) missense probably damaging 1.00
impulsive UTSW 17 47,036,892 (GRCm39) missense probably damaging 1.00
Incautious UTSW 17 47,038,313 (GRCm39) missense probably damaging 1.00
rash UTSW 17 47,036,662 (GRCm39) utr 3 prime probably benign
R0480:Gnmt UTSW 17 47,036,854 (GRCm39) missense probably benign 0.06
R0938:Gnmt UTSW 17 47,037,271 (GRCm39) missense probably damaging 1.00
R0939:Gnmt UTSW 17 47,037,271 (GRCm39) missense probably damaging 1.00
R0940:Gnmt UTSW 17 47,037,271 (GRCm39) missense probably damaging 1.00
R0941:Gnmt UTSW 17 47,037,271 (GRCm39) missense probably damaging 1.00
R3619:Gnmt UTSW 17 47,039,963 (GRCm39) missense possibly damaging 0.63
R4173:Gnmt UTSW 17 47,037,047 (GRCm39) missense probably damaging 1.00
R4456:Gnmt UTSW 17 47,039,910 (GRCm39) missense probably benign 0.07
R4659:Gnmt UTSW 17 47,036,892 (GRCm39) missense probably damaging 1.00
R4669:Gnmt UTSW 17 47,037,225 (GRCm39) nonsense probably null
R4827:Gnmt UTSW 17 47,038,245 (GRCm39) missense possibly damaging 0.77
R5112:Gnmt UTSW 17 47,037,256 (GRCm39) missense probably damaging 1.00
R5133:Gnmt UTSW 17 47,036,860 (GRCm39) missense probably benign
R5797:Gnmt UTSW 17 47,037,305 (GRCm39) missense probably damaging 1.00
R7423:Gnmt UTSW 17 47,037,066 (GRCm39) missense probably damaging 1.00
R7825:Gnmt UTSW 17 47,040,019 (GRCm39) missense probably damaging 0.99
R8785:Gnmt UTSW 17 47,038,313 (GRCm39) missense probably damaging 1.00
R8861:Gnmt UTSW 17 47,037,618 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCTCCTACTGGTCTTGTGAGAG -3'
(R):5'- TACCCACACTGTTTGGCGTC -3'

Sequencing Primer
(F):5'- CCTACTGGTCTTGTGAGAGGTTGC -3'
(R):5'- TCACGGAGTTGGTGCGAGC -3'
Posted On 2015-07-21