Incidental Mutation 'R4669:Gnmt'
ID 352312
Institutional Source Beutler Lab
Gene Symbol Gnmt
Ensembl Gene ENSMUSG00000002769
Gene Name glycine N-methyltransferase
Synonyms glycine N methyl transferase
MMRRC Submission 041925-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.320) question?
Stock # R4669 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 47036590-47040091 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) A to T at 47037225 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Stop codon at position 186 (C186*)
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 null
Transcript: ENSMUST00000002846
AA Change: C186*
SMART Domains Protein: ENSMUSP00000002846
Gene: ENSMUSG00000002769
AA Change: C186*

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency
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: 98 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acad8 A G 9: 26,901,923 (GRCm39) L147P probably damaging Het
Acan A G 7: 78,750,890 (GRCm39) E464G probably benign Het
Agap1 A G 1: 89,765,528 (GRCm39) probably null Het
Akap13 A G 7: 75,378,842 (GRCm39) T2128A probably damaging Het
Ap2a1 A T 7: 44,552,343 (GRCm39) probably benign Het
Arap3 T C 18: 38,129,307 (GRCm39) D217G probably benign Het
Arl2 C A 19: 6,184,716 (GRCm39) R179L probably damaging Het
Atg2a T A 19: 6,309,017 (GRCm39) probably null Het
B3gat1 T A 9: 26,663,052 (GRCm39) L6Q probably benign Het
Bcl10 A G 3: 145,636,327 (GRCm39) N75S probably damaging Het
Bmpr2 T C 1: 59,906,875 (GRCm39) L656S probably damaging Het
Brms1l A G 12: 55,888,356 (GRCm39) E48G possibly damaging Het
C2cd2l A T 9: 44,226,322 (GRCm39) N414K possibly damaging Het
Capn2 C T 1: 182,298,345 (GRCm39) C640Y probably benign Het
Ccdc153 G T 9: 44,157,021 (GRCm39) R99M probably damaging Het
Ccdc51 A G 9: 108,920,030 (GRCm39) N142S probably benign Het
Cdipt A G 7: 126,577,578 (GRCm39) H108R possibly damaging Het
Ceacam20 T C 7: 19,719,952 (GRCm39) Y495H probably damaging Het
Celf2 T C 2: 6,726,339 (GRCm39) I47V probably benign Het
Cts3 C T 13: 61,714,637 (GRCm39) E223K probably benign Het
Cyp2a22 T C 7: 26,637,280 (GRCm39) D168G possibly damaging Het
Cyp2c67 T A 19: 39,632,098 (GRCm39) H90L probably benign Het
Ddx4 T C 13: 112,758,778 (GRCm39) Y261C probably damaging Het
Dnah17 T C 11: 117,965,119 (GRCm39) T2308A probably benign Het
Dnah6 T C 6: 73,014,671 (GRCm39) T3587A probably damaging Het
Dpy19l1 C T 9: 24,343,664 (GRCm39) V494I possibly damaging Het
Dse T G 10: 34,029,008 (GRCm39) Y694S probably damaging Het
Emilin3 T C 2: 160,752,717 (GRCm39) I78V probably benign Het
Esam T A 9: 37,447,952 (GRCm39) Y195* probably null Het
Extl3 T A 14: 65,313,745 (GRCm39) N479I possibly damaging Het
Fat2 A G 11: 55,202,441 (GRCm39) V211A probably benign Het
Ganc G T 2: 120,261,548 (GRCm39) V343F probably benign Het
Ggt5 T C 10: 75,438,865 (GRCm39) L121P probably damaging Het
Gpr75 A T 11: 30,842,072 (GRCm39) I326F probably damaging Het
Gsdme C T 6: 50,185,102 (GRCm39) V451M probably damaging Het
H2-T23 G T 17: 36,342,690 (GRCm39) D149E probably damaging Het
Hmcn2 G T 2: 31,325,804 (GRCm39) R4277L probably benign Het
Irf9 C A 14: 55,843,223 (GRCm39) H94N probably benign Het
Jhy T C 9: 40,872,449 (GRCm39) N20S probably benign Het
Klf17 C A 4: 117,617,568 (GRCm39) C263F probably damaging Het
Lama5 T C 2: 179,822,430 (GRCm39) Y2881C probably damaging Het
Lig1 T G 7: 13,044,953 (GRCm39) I882S probably damaging Het
Ltn1 A T 16: 87,215,375 (GRCm39) M420K possibly damaging Het
Mael T C 1: 166,063,077 (GRCm39) E125G probably damaging Het
Mib2 C T 4: 155,741,872 (GRCm39) D275N possibly damaging Het
Mical3 C T 6: 120,934,664 (GRCm39) R1805Q probably damaging Het
Mix23 A G 16: 35,903,089 (GRCm39) D27G probably damaging Het
Mllt10 A G 2: 18,208,444 (GRCm39) D158G probably damaging Het
Mocs1 A G 17: 49,761,613 (GRCm39) D569G possibly damaging Het
Msh6 T C 17: 88,292,234 (GRCm39) S330P possibly damaging Het
Mtmr2 T C 9: 13,707,260 (GRCm39) S199P probably damaging Het
Ndufaf5 T C 2: 140,029,675 (GRCm39) V164A probably benign Het
Nek9 T C 12: 85,360,978 (GRCm39) E518G probably benign Het
Nfatc2 T C 2: 168,413,410 (GRCm39) I72V probably benign Het
Nlrp9c C T 7: 26,074,793 (GRCm39) A746T possibly damaging Het
Nup42 A G 5: 24,387,415 (GRCm39) R402G probably benign Het
Ogdh G T 11: 6,290,600 (GRCm39) C406F probably benign Het
Or3a1d A G 11: 74,237,789 (GRCm39) V207A probably benign Het
Or4c120 G A 2: 89,001,245 (GRCm39) H104Y probably damaging Het
Or8b35 A T 9: 37,904,381 (GRCm39) I198F possibly damaging Het
Or8g17 T A 9: 38,930,675 (GRCm39) Y54F probably benign Het
Or8j3 A T 2: 86,028,277 (GRCm39) M273K possibly damaging Het
Otof A G 5: 30,578,318 (GRCm39) probably null Het
Pcdhb17 T C 18: 37,619,259 (GRCm39) S350P probably damaging Het
Phf3 T C 1: 30,869,027 (GRCm39) T674A probably damaging Het
Pikfyve T A 1: 65,289,432 (GRCm39) C1235S probably damaging Het
Ppfia3 T C 7: 45,001,517 (GRCm39) E465G probably damaging Het
Prkg1 T A 19: 31,641,639 (GRCm39) I15F probably damaging Het
Rab5c A G 11: 100,610,843 (GRCm39) F22L probably damaging Het
Raf1 A G 6: 115,609,880 (GRCm39) S220P probably damaging Het
Rgl1 T G 1: 152,397,122 (GRCm39) R716S probably damaging Het
Rhbg C A 3: 88,153,273 (GRCm39) W205L probably damaging Het
Rimbp3 A G 16: 17,027,053 (GRCm39) E159G possibly damaging Het
Ryr1 T C 7: 28,759,256 (GRCm39) D3338G probably null Het
Sash1 T C 10: 8,606,149 (GRCm39) N747S probably benign Het
Serpina3g A T 12: 104,205,479 (GRCm39) I73F probably damaging Het
Sfxn2 C A 19: 46,574,213 (GRCm39) N134K probably damaging Het
Slc12a6 A G 2: 112,184,640 (GRCm39) H853R probably damaging Het
Slc16a12 C T 19: 34,649,965 (GRCm39) D357N probably damaging Het
Slc39a8 T C 3: 135,561,772 (GRCm39) Y164H probably benign Het
Snx9 A G 17: 5,977,499 (GRCm39) K518E probably damaging Het
Spdye4c G A 2: 128,434,273 (GRCm39) V5I possibly damaging Het
Spef2 A G 15: 9,676,459 (GRCm39) V704A probably benign Het
Stard3nl T A 13: 19,560,689 (GRCm39) N29Y probably damaging Het
Strap C A 6: 137,712,384 (GRCm39) S11* probably null Het
Synpo2 A G 3: 122,906,712 (GRCm39) L868P probably damaging Het
Tenm2 A G 11: 35,901,314 (GRCm39) V2474A probably damaging Het
Tm9sf4 T A 2: 153,029,228 (GRCm39) V92D probably damaging Het
Tmf1 A T 6: 97,147,388 (GRCm39) M526K probably benign Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Ttc39d A G 17: 80,525,068 (GRCm39) I576V probably benign Het
Upk1a T G 7: 30,304,554 (GRCm39) T193P probably benign Het
Vmn2r67 A T 7: 84,799,732 (GRCm39) V502E probably benign Het
Wdr17 A G 8: 55,143,083 (GRCm39) V189A possibly damaging Het
Wrap73 A T 4: 154,236,153 (GRCm39) S161C probably benign Het
Zfp568 A G 7: 29,722,702 (GRCm39) H549R probably damaging Het
Zfp605 T A 5: 110,275,227 (GRCm39) M115K possibly damaging Het
Zp1 T A 19: 10,896,269 (GRCm39) H152L probably benign 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
R4498:Gnmt UTSW 17 47,036,662 (GRCm39) utr 3 prime probably benign
R4659:Gnmt UTSW 17 47,036,892 (GRCm39) missense probably damaging 1.00
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'- TAGTCCAGGGTTACCATGTGGG -3'
(R):5'- AGACCTGCATTTTGCCTGTC -3'

Sequencing Primer
(F):5'- CAGGGTTACCATGTGGGCTTTG -3'
(R):5'- CTGGCACTTGGGAGGGAGAC -3'
Posted On 2015-10-08