AGXT2 alanine--glyoxylate aminotransferase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: AGXT2provided by HGNC
Official Full Name: alanine--glyoxylate aminotransferase 2provided by HGNC
Primary source: HGNC:HGNC:14412
See related: Ensembl:ENSG00000113492 MIM:612471; AllianceGenome:HGNC:14412
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: AGT2; BAIBA; DAIBAT
Summary: The protein encoded by this gene is a class III pyridoxal-phosphate-dependent mitochondrial aminotransferase. It catalyzes the conversion of glyoxylate to glycine using L-alanine as the amino donor. It is an important regulator of methylarginines and is involved in the control of blood pressure in kidney. Polymorphisms in this gene affect methylarginine and beta-aminoisobutyrate metabolism, and are associated with carotid atherosclerosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
Expression: Biased expression in kidney (RPKM 69.3) and liver (RPKM 24.9) See more
Orthologs: mouse all
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Genomic context

Location:: 5p13.2

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (34998102..35047949, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (35245145..35294998, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (34998207..35048054, complement)

Chromosome 5 - NC_000005.10 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?

Functional AGXT2 SNP rs180749 variant and depressive symptoms: Baseline data from the Aidai Cohort Study in Japan.
Title: Functional AGXT2 SNP rs180749 variant and depressive symptoms: Baseline data from the Aidai Cohort Study in Japan.
Genetic loci of beta-aminoisobutyric acid are associated with aging-related mild cognitive impairment.
Title: Genetic loci of beta-aminoisobutyric acid are associated with aging-related mild cognitive impairment.
Functional AGXT2 SNP rs37369 Variant Is a Risk Factor for Diabetes Mellitus: Baseline Data From the Aidai Cohort Study in Japan.
Title: Functional AGXT2 SNP rs37369 Variant Is a Risk Factor for Diabetes Mellitus: Baseline Data From the Aidai Cohort Study in Japan.
Disease-specific eQTL screening reveals an anti-fibrotic effect of AGXT2 in non-alcoholic fatty liver disease.
Title: Disease-specific eQTL screening reveals an anti-fibrotic effect of AGXT2 in non-alcoholic fatty liver disease.
The role of alanine glyoxylate transaminase-2 (agxt2) in beta-alanine and carnosine metabolism of healthy mice and humans.
Title: The role of alanine glyoxylate transaminase-2 (agxt2) in β-alanine and carnosine metabolism of healthy mice and humans.
Effects of AGXT2 variants on blood pressure and blood sugar among 750 older Japanese subjects recruited by the complete enumeration survey method.
Title: Effects of AGXT2 variants on blood pressure and blood sugar among 750 older Japanese subjects recruited by the complete enumeration survey method.
Alanine-Glyoxylate Aminotransferase 2 (AGTX2)-dependent pathway is a relatively recently discovered alternative pathway of dimethylarginine catabolism and its role on Rheumatoid Arthritis -related atherosclerotic disease is yet to be established. Gene variants of AGTX-2 may influence dimethylarginine levels in Rheumatoid Arthritis patients and provide the rationale for larger studies in this field.
Title: Genetic regulation of dimethylarginines and endothelial dysfunction in rheumatoid arthritis.
Carriers of AGXT2 rs37369-T allele (CT + TT genotypes) and AGXT2 rs16899974-A allele (CA + AA genotypes) had 2.4- and 2.08-fold higher risk of having coronary artery disease than CC genotype in both SNPs (p = 0.0050 and 0.0192, respectively). AGXT2 rs37369 TT and AGXT2 rs16899974 AA genotypes were associated with the highest serum ADMA and SDMA
Title: AGXT2 and DDAH-1 genetic variants are highly correlated with serum ADMA and SDMA levels and with incidence of coronary artery disease in Egyptians.
We purified human AGXT2 from tissues of AGXT2 transgenic mice and demonstrated its ability to metabolize homoarginine to 6-guanidino-2-oxocaproic acid (GOCA). After incubation of HepG2 cells overexpressing AGXT2 with isotope-labeled homoarginine-d4 we were able to detect labeled GOCA in the medium
Title: A Novel Pathway for Metabolism of the Cardiovascular Risk Factor Homoarginine by alanine:glyoxylate aminotransferase 2.
study in a well-characterized rheumatoid arthritis population did not show an association between serum concentrations of dimethylarginines and genetic variants of the AGXT2 gene.
Title: Genetic variations in the alanine-glyoxylate aminotransferase 2 (AGXT2) gene and dimethylarginines levels in rheumatoid arthritis.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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
Beta-aminoisobutyric acid, urinary excretion of MedGen: C1859518 OMIM: 210100 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association study of metabolic traits in human urine. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-Wide Association Study of L-Arginine and Dimethylarginines Reveals Novel Metabolic Pathway for Symmetric Dimethylarginine. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality. 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

SHGC-105268 (e-PCR)
- UniSTS:169229

RH78189 (e-PCR)
- UniSTS:27177

D5S2573 (e-PCR)
- UniSTS:54105

SGC33361 (e-PCR)
- UniSTS:14984

RH99171 (e-PCR)
- UniSTS:90541

RH17937 (e-PCR)
- UniSTS:50880

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables (R)-3-amino-2-methylpropionate-pyruvate transaminase activity	IDA Inferred from Direct Assay more info	PubMed
enables alanine-glyoxylate transaminase activity	IBA Inferred from Biological aspect of Ancestor more info
enables alanine-glyoxylate transaminase activity	IDA Inferred from Direct Assay more info	PubMed
enables beta-alanine-pyruvate transaminase activity	IEA Inferred from Electronic Annotation more info
enables pyridoxal phosphate binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in L-alanine catabolic process, by transamination	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-alanine catabolic process, by transamination	IDA Inferred from Direct Assay more info	PubMed
involved_in N(omega),N(omega)-dimethyl-L-arginine catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycine biosynthetic process, by transamination of glyoxylate	IDA Inferred from Direct Assay more info	PubMed
involved_in glyoxylate catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in glyoxylate catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of nitric oxide biosynthetic process	IDA Inferred from Direct Assay more info	PubMed

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

General protein information

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Preferred Names: alanine--glyoxylate aminotransferase 2, mitochondrial

Names: (R)-3-amino-2-methylpropionate--pyruvate transaminase; D-3-aminoisobutyrate-pyruvate aminotransferase; D-beta-aminoisobutyrate-pyruvate aminotransferase; beta-ALAAT II; beta-alanine-pyruvate aminotransferase

NP_001293102.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

NP_114106.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_005248394.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_005248395.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_016865237.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_047273490.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_054209149.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_054209150.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_054209151.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

XP_054209152.1

EC 2.6.1.18

EC 2.6.1.40

EC 2.6.1.44

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.

mRNA and Protein(s)

NM_001306173.2 → NP_001293102.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform b precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two alternate exons, resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AJ292204, BC144268, DA633665

Consensus CDS

CCDS78000.1

UniProtKB/TrEMBL

B2RBJ5

Related

ENSP00000422799.1, ENST00000510428.1

Conserved Domains (1) summary

cd00610
Location:70 → 430

OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...
NM_031900.4 → NP_114106.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform a precursor

See identical proteins and their annotated locations for NP_114106.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AJ292204, DA633665

Consensus CDS

CCDS3908.1

UniProtKB/Swiss-Prot

B7ZM47, E9PDL7, Q53FB4, Q53FY7, Q53G03, Q5W7Q1, Q9BYV1

UniProtKB/TrEMBL

B2RBJ5

Related

ENSP00000231420.6, ENST00000231420.11

Conserved Domains (2) summary

cd00610
Location:70 → 505

OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...

COG0160
Location:65 → 508

GabT; 4-aminobutyrate aminotransferase or related aminotransferase [Amino acid transport and metabolism]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

34998102..35047949 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417534.1 → XP_047273490.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X4

UniProtKB/TrEMBL

B2RBJ5
XM_005248337.4 → XP_005248394.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X1

UniProtKB/TrEMBL

B2RBJ5

Conserved Domains (2) summary

cd00610
Location:69 → 504

OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...

COG0160
Location:64 → 507

GabT; 4-aminobutyrate aminotransferase or related aminotransferase [Amino acid transport and metabolism]
XM_005248338.4 → XP_005248395.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X2

UniProtKB/TrEMBL

B2RBJ5

Conserved Domains (2) summary

cd00610
Location:70 → 440

OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...

COG0160
Location:65 → 443

GabT; 4-aminobutyrate aminotransferase or related aminotransferase [Amino acid transport and metabolism]
XM_017009748.3 → XP_016865237.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X3

UniProtKB/TrEMBL

B2RBJ5

Related

ENSP00000479154.1, ENST00000618015.4

Conserved Domains (1) summary

cd00610
Location:70 → 430

OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

35245145..35294998 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054353177.1 → XP_054209152.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X4

UniProtKB/TrEMBL

B2RBJ5
XM_054353174.1 → XP_054209149.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X1

UniProtKB/TrEMBL

B2RBJ5
XM_054353175.1 → XP_054209150.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X2

UniProtKB/TrEMBL

B2RBJ5
XM_054353176.1 → XP_054209151.1 alanine--glyoxylate aminotransferase 2, mitochondrial isoform X3

UniProtKB/TrEMBL

B2RBJ5