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GNMT glycine N-methyltransferase [ Homo sapiens (human) ]

Gene ID: 27232, updated on 19-Mar-2019

Summary

Official Symbol
GNMTprovided by HGNC
Official Full Name
glycine N-methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:4415
See related
Ensembl:ENSG00000124713 MIM:606628
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HEL-S-182mP
Summary
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]
Expression
Biased expression in liver (RPKM 73.9), pancreas (RPKM 27.4) and 1 other tissue See more
Orthologs

Genomic context

See GNMT in Genome Data Viewer
Location:
6p21.1
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (42960754..42963880)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42928500..42931618)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CNPY3-GNMT readthrough Neighboring gene canopy FGF signaling regulator 3 Neighboring gene ribosomal protein L24 pseudogene 4 Neighboring gene peroxisomal biogenesis factor 6 Neighboring gene male-enhanced antigen 1 Neighboring gene protein phosphatase 2 regulatory subunit B'delta Neighboring gene kelch domain containing 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Glycine N-methyltransferase deficiency
MedGen: C1847720 OMIM: 606664 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke.
NHGRI GWA Catalog

Pathways from BioSystems

  • Glycine, serine and threonine metabolism, organism-specific biosystem (from KEGG)
    Glycine, serine and threonine metabolism, organism-specific biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Glycine, serine and threonine metabolism, conserved biosystem (from KEGG)
    Glycine, serine and threonine metabolism, conserved biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Glyoxylate metabolism and glycine degradation, organism-specific biosystem (from REACTOME)
    Glyoxylate metabolism and glycine degradation, organism-specific biosystemGlyoxylate is generated in the course of glycine and hydroxyproline catabolism and can be converted to oxalate. In humans, this process takes place in the liver. Defects in two enzymes of glyoxylate ...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of amino acids and derivatives, organism-specific biosystem (from REACTOME)
    Metabolism of amino acids and derivatives, organism-specific biosystemThis group of reactions is responsible for: 1) the breakdown of amino acids; 2) the synthesis of urea from ammonia and amino groups generated by amino acid breakdown; 3) the synthesis of the ten amin...
  • Metabolism of ingested SeMet, Sec, MeSec into H2Se, organism-specific biosystem (from REACTOME)
    Metabolism of ingested SeMet, Sec, MeSec into H2Se, organism-specific biosystemInorganic (selenite, SeO3(2-); and selenate, SeO4(2-)) and organic (selenocysteine, Sec; and selenomethionine, SeMet) forms of selenium can introduced in the diet where they are transformed into the ...
  • Selenoamino acid metabolism, organism-specific biosystem (from REACTOME)
    Selenoamino acid metabolism, organism-specific biosystemSelenium (Se) is a trace element essential for the normal function of the body. Selenoamino acids are defined as those amino acids where selenium has been substituted for sulphur. Selenium and sulp...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough CNPY3-GNMT

Readthrough gene: CNPY3-GNMT, Included gene: CNPY3

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
S-adenosyl-L-methionine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
folic acid binding IEA
Inferred from Electronic Annotation
more info
 
glycine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
glycine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
S-adenosylhomocysteine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
S-adenosylmethionine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
S-adenosylmethionine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
cellular nitrogen compound metabolic process TAS
Traceable Author Statement
more info
 
cellular protein modification process NAS
Non-traceable Author Statement
more info
PubMed 
glycogen metabolic process IEA
Inferred from Electronic Annotation
more info
 
methionine metabolic process IEA
Inferred from Electronic Annotation
more info
 
methylation IEA
Inferred from Electronic Annotation
more info
 
one-carbon metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homotetramerization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homotetramerization IPI
Inferred from Physical Interaction
more info
PubMed 
regulation of gluconeogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sarcosine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
glycine N-methyltransferase
Names
epididymis secretory sperm binding protein Li 182mP
NP_001305794.1
NP_061833.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008396.1 RefSeqGene

    Range
    4993..8119
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001318865.1NP_001305794.1  glycine N-methyltransferase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    BC032627, HY010451, KU178604
    UniProtKB/Swiss-Prot
    Q14749
    UniProtKB/TrEMBL
    A0A0S2Z5F2
    Conserved Domains (1) summary
    pfam12847
    Location:58158
    Methyltransf_18; Methyltransferase domain
  2. NM_018960.6NP_061833.1  glycine N-methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_061833.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC032627, HY010451
    Consensus CDS
    CCDS4876.1
    UniProtKB/Swiss-Prot
    Q14749
    UniProtKB/TrEMBL
    V9HW60
    Related
    ENSP00000361894.3, ENST00000372808.3
    Conserved Domains (2) summary
    pfam13649
    Location:61171
    Methyltransf_25; Methyltransferase domain
    cl28098
    Location:1695
    Tam; Trans-aconitate methyltransferase [Energy production and conversion]

RNA

  1. NR_134899.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC032627, HY010451, KU178605

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    42960754..42963880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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