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

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; AllianceGenome:HGNC:4415
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: mouse all
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Genomic context

Location:: 6p21.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (42960754..42963880)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (42789900..42793018)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (42928492..42931618)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ERVK13-1/miR-873-5p/GNMT Axis Promotes Metastatic Potential in Human Bladder Cancer though Sarcosine Production.
Title: ERVK13-1/miR-873-5p/GNMT Axis Promotes Metastatic Potential in Human Bladder Cancer though Sarcosine Production.
Folic Acid Ameliorates Renal Injury in Experimental Obstructive Nephropathy: Role of Glycine N-Methyltransferase.
Title: Folic Acid Ameliorates Renal Injury in Experimental Obstructive Nephropathy: Role of Glycine N-Methyltransferase.
Chemical Biopsy for GNMT as Noninvasive and Tumorigenesis-Relevant Diagnosis of Liver Cancer.
Title: Chemical Biopsy for GNMT as Noninvasive and Tumorigenesis-Relevant Diagnosis of Liver Cancer.
Downregulation of Methionine Cycle Genes MAT1A and GNMT Enriches Protein-Associated Translation Process and Worsens Hepatocellular Carcinoma Prognosis.
Title: Downregulation of Methionine Cycle Genes MAT1A and GNMT Enriches Protein-Associated Translation Process and Worsens Hepatocellular Carcinoma Prognosis.
Polymorphisms in GNMT and DNMT3b are associated with methotrexate treatment outcome in plaque psoriasis.
Title: Polymorphisms in GNMT and DNMT3b are associated with methotrexate treatment outcome in plaque psoriasis.
Total liver phosphatidylcholine content associates with non-alcoholic steatohepatitis and glycine N-methyltransferase expression.
Title: Total liver phosphatidylcholine content associates with non-alcoholic steatohepatitis and glycine N-methyltransferase expression.
miR-224 can target the glycine N-methyltransferase (GNMT) mRNA coding sequence and plays an important role in GNMT suppression during liver tumorigenesis
Title: MicroRNA-224 down-regulates Glycine N-methyltransferase gene expression in Hepatocellular Carcinoma.
Exosomal miR-224 can decrease the expression of GNMT by directly targeting the 3'-UTR of GNMT mRNA to promote the proliferation and invasion of hepatocellular carcinoma (HCC) cells. In addition, serum exosomal miR-224 may be used as a biomarker for the diagnosis of HCC and a prognostic factor for patients with HCC.
Title: Mechanism of exosomal microRNA-224 in development of hepatocellular carcinoma and its diagnostic and prognostic value.
Common glycine N-methyltransferase variant genotypes increase the risk of cleft lip with or without cleft palate.
Title: Common polymorphism in the glycine N-methyltransferase gene as a novel risk factor for cleft lip with or without cleft palate.
Elevated GNMT protein expression is associated with pathogenesis of hepatocellular carcinoma.
Title: Characterization of the GNMT-HectH9-PREX2 tripartite relationship in the pathogenesis of hepatocellular carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (33)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

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

EBI 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. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GNMT (e-PCR)
- UniSTS:253981

D6S1532E (e-PCR)
- UniSTS:153976

STS-D20352 (e-PCR)
- UniSTS:66451

STS-U56602 (e-PCR)
- UniSTS:38315

Readthrough CNPY3-GNMT

Readthrough gene: CNPY3-GNMT, Included gene: CNPY3

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables S-adenosyl-L-methionine binding	IBA Inferred from Biological aspect of Ancestor more info
enables folic acid binding	IEA Inferred from Electronic Annotation more info
enables glycine N-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycine N-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables glycine binding	IBA Inferred from Biological aspect of Ancestor more info
enables glycine binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in S-adenosylhomocysteine metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in S-adenosylmethionine metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in S-adenosylmethionine metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in glycogen metabolic process	IEA Inferred from Electronic Annotation more info
involved_in methionine metabolic process	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in one-carbon metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein homotetramerization	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein homotetramerization	IPI Inferred from Physical Interaction more info	PubMed
involved_in protein modification process	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of gluconeogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in sarcosine metabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: glycine N-methyltransferase

Names: epididymis secretory sperm binding protein Li 182mP

NP_001305794.1

EC 2.1.1.20

NP_061833.1

EC 2.1.1.20

NCBI Reference Sequences (RefSeq)

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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

NG_008396.1 RefSeqGene

Range

4993..8119

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001318865.2 → NP_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/TrEMBL

A0A0S2Z5F2

Conserved Domains (1) summary

pfam12847
Location:58 → 158

Methyltransf_18; Methyltransferase domain
NM_018960.6 → NP_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, Q5T8W2, Q9NNZ1, Q9NS24

UniProtKB/TrEMBL

V9HW60

Related

ENSP00000361894.3, ENST00000372808.4

Conserved Domains (2) summary

COG4976
Location:16 → 95

COG4976; Predicted methyltransferase, contains TPR repeat [General function prediction only]

pfam13649
Location:61 → 171

Methyltransf_25; Methyltransferase domain

RNA

NR_134899.2 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