AMT aminomethyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: AMTprovided by HGNC
Official Full Name: aminomethyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:473
See related: Ensembl:ENSG00000145020 MIM:238310; AllianceGenome:HGNC:473
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: GCE; NKH; GCE2; GCST; GCVT
Summary: 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]
Expression: Ubiquitous expression in kidney (RPKM 16.6), liver (RPKM 14.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (49416778..49422473, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (49446157..49451857, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (49454211..49459906, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

The position and frequency of the breakpoint for CNVs correlated with intron size and presence of Alu elements. Missense mutations, most often recurring, were the most common type of disease-causing mutation in AMT
Title: The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT.
Data indicate no mutation was found in glycine cleavage system protein-H (GCSH) and suggest that mutations in both glycine decarboxylase (GLDC) and aminomethyltransferase (AMT) are the main cause of glycine encephalopathy in Malaysian population.
Title: Mutation analysis of glycine decarboxylase, aminomethyltransferase and glycine cleavage system protein-H genes in 13 unrelated families with glycine encephalopathy.
Two unique non-synonymous changes were identified in the AMT gene in patients with neural tube defects.
Title: Mutations in genes encoding the glycine cleavage system predispose to neural tube defects in mice and humans.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Observational study of genotype prevalence. (HuGE Navigator)
Title: Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia.
x-ray crystallographic structure of human T-protein of glycine cleavage system
Title: Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia.

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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 encephalopathy 2 MedGen: C5830559 OMIM: 620398 GeneReviews: Not available	Compare labs
Non-ketotic hyperglycinemia MedGen: C0751748 GeneReviews: Nonketotic Hyperglycinemia	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of aminomethyltransferase (AMT) by siRNA enhances HIV-1 replication in CD4+/CCR5+/CXCR4+ TZM-bl HeLa cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH17372 (e-PCR)
- UniSTS:4660

GDB:366601 (e-PCR)
- UniSTS:156814

GDB:366602 (e-PCR)
- UniSTS:156815

GDB:366605 (e-PCR)
- UniSTS:156816

D3S3344 (e-PCR)
- UniSTS:65202

A002R20 (e-PCR)
- UniSTS:23278

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables aminomethyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables aminomethyltransferase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transaminase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in glycine catabolic process	TAS Traceable Author Statement more info
involved_in glycine decarboxylation via glycine cleavage system	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of glycine cleavage complex	IEA Inferred from Electronic Annotation more info
located_in mitochondrial matrix	TAS Traceable Author Statement more info
located_in mitochondrion	HTP more info	PubMed
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	IC Inferred by Curator more info	PubMed
located_in mitochondrion	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: aminomethyltransferase, mitochondrial

Names: glycine cleavage system T protein; nonketotic hyperglycinemia

NP_000472.2

EC 2.1.2.10

NP_001158182.1

EC 2.1.2.10

NP_001158183.1

EC 2.1.2.10

NP_001158184.1

EC 2.1.2.10

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_015986.1 RefSeqGene

Range

5001..10901

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_537

mRNA and Protein(s)

NM_000481.4 → NP_000472.2 aminomethyltransferase, mitochondrial isoform 1 precursor

See identical proteins and their annotated locations for NP_000472.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).

Source sequence(s)

D13811, GD148179

Consensus CDS

CCDS2797.1

UniProtKB/Swiss-Prot

A8K3I5, B4DE61, B4DJQ0, E9PBG1, P48728, Q96IG6

UniProtKB/TrEMBL

A0A1B0GTM2

Related

ENSP00000273588.3, ENST00000273588.9

Conserved Domains (3) summary

PLN02319
Location:16 → 400

PLN02319; aminomethyltransferase

pfam01571
Location:39 → 291

GCV_T; Aminomethyltransferase folate-binding domain

pfam08669
Location:301 → 392

GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
NM_001164710.2 → NP_001158182.1 aminomethyltransferase, mitochondrial isoform 2 precursor

See identical proteins and their annotated locations for NP_001158182.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.

Source sequence(s)

AK296177, DC387800, GD148179

Consensus CDS

CCDS54584.1

UniProtKB/TrEMBL

B3KRJ7

Related

ENSP00000415619.2, ENST00000458307.6

Conserved Domains (3) summary

PLN02319
Location:16 → 356

PLN02319; aminomethyltransferase

pfam01571
Location:39 → 247

GCV_T; Aminomethyltransferase folate-binding domain

pfam08669
Location:257 → 348

GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
NM_001164711.2 → NP_001158183.1 aminomethyltransferase, mitochondrial isoform 3 precursor

See identical proteins and their annotated locations for NP_001158183.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.

Source sequence(s)

AC104452, AK293481, DC387800, GD148179

Consensus CDS

CCDS54583.1

UniProtKB/TrEMBL

B4DGG9

Related

ENSP00000489758.1, ENST00000636522.1

Conserved Domains (2) summary

pfam01571
Location:29 → 235

GCV_T; Aminomethyltransferase folate-binding domain

pfam08669
Location:245 → 336

GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
NM_001164712.2 → NP_001158184.1 aminomethyltransferase, mitochondrial isoform 4 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region that results in a frameshift compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

BC007546, DC387800

Consensus CDS

CCDS54585.1

UniProtKB/TrEMBL

A0A1B0GTA8

Related

ENSP00000378747.2, ENST00000395338.7

Conserved Domains (3) summary

PLN02319
Location:16 → 379

PLN02319; aminomethyltransferase

pfam01571
Location:39 → 291

GCV_T; Aminomethyltransferase folate-binding domain

pfam08669
Location:301 → 379

GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain

RNA

NR_028435.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site in the 5' coding region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK096062, GD148179

Related

ENST00000538581.6