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Aliases for AGXT Gene

Aliases for AGXT Gene

  • Alanine-Glyoxylate Aminotransferase 2 3 5
  • L-Alanine: Glyoxylate Aminotransferase 1 2 3
  • SPAT 3 4
  • AGT1 3 4
  • AGT 3 4
  • SPT 3 4
  • Hepatic Peroxisomal Alanine:Glyoxylate Aminotransferase 3
  • Alanine--Glyoxylate Aminotransferase 4
  • Serine--Pyruvate Aminotransferase 3
  • Serine:Pyruvate Aminotransferase 2
  • Primary Hyperoxaluria Type 1 2
  • Glycolicaciduria 2
  • EC 2.6.1.51 4
  • EC 2.6.1.44 4
  • Oxalosis I 2
  • AGXT1 3
  • TLH6 3
  • PH1 3

External Ids for AGXT Gene

Previous HGNC Symbols for AGXT Gene

  • SPAT

Previous GeneCards Identifiers for AGXT Gene

  • GC02P239620
  • GC02M240478
  • GC02P241827
  • GC02P242128
  • GC02P241528
  • GC02P241456
  • GC02P233568
  • GC02P241807

Summaries for AGXT Gene

Entrez Gene Summary for AGXT Gene

  • This gene is expressed only in the liver and the encoded protein is localized mostly in the peroxisomes, where it is involved in glyoxylate detoxification. Mutations in this gene, some of which alter subcellular targetting, have been associated with type I primary hyperoxaluria. [provided by RefSeq, Jul 2008]

GeneCards Summary for AGXT Gene

AGXT (Alanine-Glyoxylate Aminotransferase) is a Protein Coding gene. Diseases associated with AGXT include Hyperoxaluria, Primary, Type I and Primary Hyperoxaluria. Among its related pathways are Glyoxylate metabolism and glycine degradation and Viral mRNA Translation. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and pyridoxal phosphate binding.

Gene Wiki entry for AGXT Gene

Additional gene information for AGXT Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AGXT Gene

Genomics for AGXT Gene

GeneHancer (GH) Regulatory Elements for AGXT Gene

Promoters and enhancers for AGXT Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I240868 Promoter 1.1 EPDnew 550.8 +0.0 45 0.1 FOXA2 ARID4B DMAP1 RAD21 THRB ZBTB40 YY1 SLC30A9 THAP11 EGR2 AGXT C2orf54
GH02I240869 Promoter 1.1 EPDnew 550.8 +0.3 326 0.1 ELF3 ARID4B DMAP1 RAD21 THRB ZNF48 RARA YY1 SLC30A9 THAP11 AGXT C2orf54
GH02I240856 Enhancer 1.2 FANTOM5 ENCODE 10.6 -10.9 -10899 1.2 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 ETS1 YY1 SLC30A9 ATF7 C2orf54 AGXT GPR35 KIF1A
GH02I240895 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 7.4 +28.9 28866 3.9 PKNOX1 ARID4B KLF17 ZNF48 RAD21 RARA ZEB1 GLIS2 FOS RXRA C2orf54 AGXT CROCC2
GH02I240912 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 6.3 +47.1 47145 5.8 ARID4B KLF17 ZNF76 ZNF2 RAD21 GLIS2 ZNF143 FOS THAP11 ZNF654 C2orf54 AGXT ENSG00000223991 SNED1 GPC1 RNPEPL1 CROCC2 GC02M240925
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around AGXT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the AGXT gene promoter:

Genomic Locations for AGXT Gene

Genomic Locations for AGXT Gene
chr2:240,868,479-240,880,502
(GRCh38/hg38)
Size:
12,024 bases
Orientation:
Plus strand
chr2:241,807,896-241,819,919
(GRCh37/hg19)

Genomic View for AGXT Gene

Genes around AGXT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AGXT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AGXT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AGXT Gene

Proteins for AGXT Gene

  • Protein details for AGXT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P21549-SPYA_HUMAN
    Recommended name:
    Serine--pyruvate aminotransferase
    Protein Accession:
    P21549
    Secondary Accessions:
    • Q53QU6

    Protein attributes for AGXT Gene

    Size:
    392 amino acids
    Molecular mass:
    43010 Da
    Cofactor:
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for AGXT Gene

neXtProt entry for AGXT Gene

Post-translational modifications for AGXT Gene

No Post-translational modifications

Other Protein References for AGXT Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for AGXT Gene

Domains & Families for AGXT Gene

Gene Families for AGXT Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

P21549

UniProtKB/Swiss-Prot:

SPYA_HUMAN :
  • Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family.
Family:
  • Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family.
genes like me logo Genes that share domains with AGXT: view

Function for AGXT Gene

Molecular function for AGXT Gene

GENATLAS Biochemistry:
alanine
UniProtKB/Swiss-Prot CatalyticActivity:
L-serine + pyruvate = 3-hydroxypyruvate + L-alanine.
UniProtKB/Swiss-Prot CatalyticActivity:
L-alanine + glyoxylate = pyruvate + glycine.

Enzyme Numbers (IUBMB) for AGXT Gene

Phenotypes From GWAS Catalog for AGXT Gene

Gene Ontology (GO) - Molecular Function for AGXT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004760 serine-pyruvate transaminase activity IBA --
GO:0005102 receptor binding IPI 20178365
GO:0005515 protein binding IPI 15911627
GO:0008453 alanine-glyoxylate transaminase activity TAS 2363689
GO:0008483 transaminase activity IEA,IDA 18492492
genes like me logo Genes that share ontologies with AGXT: view
genes like me logo Genes that share phenotypes with AGXT: view

Human Phenotype Ontology for AGXT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for AGXT Gene

MGI Knock Outs for AGXT:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for AGXT Gene

Localization for AGXT Gene

Subcellular locations from UniProtKB/Swiss-Prot for AGXT Gene

Peroxisome. Mitochondrion. Note=Predominantly localized in the peroxisomes. Mitochondrial mistargeting occurs in variant proteins Arg-41, Arg-47, Ile-152, Arg-170 and Thr-244 associated with the disease HP1. {ECO:0000269 PubMed:23229545}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for AGXT gene
Compartment Confidence
peroxisome 5
mitochondrion 4
cytosol 3
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for AGXT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix IEA --
GO:0005777 peroxisome IDA,IEA 1703535
GO:0005782 peroxisomal matrix IDA,TAS --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with AGXT: view

Pathways & Interactions for AGXT Gene

genes like me logo Genes that share pathways with AGXT: view

Gene Ontology (GO) - Biological Process for AGXT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007219 Notch signaling pathway IEA --
GO:0009436 glyoxylate catabolic process IDA 22198249
GO:0019265 glycine biosynthetic process, by transamination of glyoxylate IEA,IDA 22198249
GO:0019448 L-cysteine catabolic process IDA 18492492
GO:0034641 cellular nitrogen compound metabolic process TAS --
genes like me logo Genes that share ontologies with AGXT: view

No data available for SIGNOR curated interactions for AGXT Gene

Drugs & Compounds for AGXT Gene

(17) Drugs for AGXT Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycine Approved, Vet_approved Nutra Full agonist, Agonist, Target 254
L-Alanine Approved Nutra Full agonist, Agonist, Target Glycine receptor agonist 0
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
calcium Approved Nutra 0
Glutamic Acid Approved Nutra Full agonist, Agonist 251

(10) Additional Compounds for AGXT Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
genes like me logo Genes that share compounds with AGXT: view

Transcripts for AGXT Gene

Unigene Clusters for AGXT Gene

Alanine-glyoxylate aminotransferase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for AGXT Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
SP1:
SP2: - -
SP3:
SP4: -
SP5: - -

Relevant External Links for AGXT Gene

GeneLoc Exon Structure for
AGXT
ECgene alternative splicing isoforms for
AGXT

Expression for AGXT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AGXT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for AGXT Gene

This gene is overexpressed in Liver (x52.4).

Protein differential expression in normal tissues from HIPED for AGXT Gene

This gene is overexpressed in Liver, secretome (52.9) and Liver (10.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for AGXT Gene



Protein tissue co-expression partners for AGXT Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of AGXT Gene:

AGXT

SOURCE GeneReport for Unigene cluster for AGXT Gene:

Hs.144567

mRNA Expression by UniProt/SwissProt for AGXT Gene:

P21549-SPYA_HUMAN
Tissue specificity: Liver.

Evidence on tissue expression from TISSUES for AGXT Gene

  • Liver(4.8)
  • Kidney(3.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for AGXT Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • nervous
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • heart
  • heart valve
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
  • ureter
  • urinary bladder
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with AGXT: view

Primer Products

Orthologs for AGXT Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for AGXT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia AGXT 34 33
  • 98.94 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LOC100855679 33
  • 87.24 (n)
-- 34
  • 81 (a)
OneToMany
-- 34
  • 76 (a)
OneToMany
cow
(Bos Taurus)
Mammalia AGXT 34 33
  • 84.61 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Agxt 33
  • 79.17 (n)
mouse
(Mus musculus)
Mammalia Agxt 16 34 33
  • 77.81 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia AGXT 34
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia AGXT 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves AGXT 34 33
  • 69.05 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia AGXT 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia agxt 33
  • 64.68 (n)
Str.5789 33
African clawed frog
(Xenopus laevis)
Amphibia agt 33
zebrafish
(Danio rerio)
Actinopterygii agxta 33 34
  • 60.47 (n)
agxtb 34
  • 53 (a)
OneToMany
agxt 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13909 33
fruit fly
(Drosophila melanogaster)
Insecta Spat 35 33 34
  • 55.47 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003490 33
  • 54.64 (n)
worm
(Caenorhabditis elegans)
Secernentea T14D7.1 35 33 34
  • 48.4 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F08954g 33
  • 39.22 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes AGX1 33 34 36
  • 39.08 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AGT 33
  • 42.68 (n)
rice
(Oryza sativa)
Liliopsida Os08g0502700 33
  • 47.99 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01821 33
  • 45.81 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 23 (a)
OneToOne
Species where no ortholog for AGXT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for AGXT Gene

ENSEMBL:
Gene Tree for AGXT (if available)
TreeFam:
Gene Tree for AGXT (if available)

Paralogs for AGXT Gene

(1) SIMAP similar genes for AGXT Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with AGXT: view

No data available for Paralogs for AGXT Gene

Variants for AGXT Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for AGXT Gene

SPYA_HUMAN-P21549
Polymorphism at position 11 acts synergistically with different mutations in AGXT producing specific enzymic phenotypes in HP1 patients. The combined presence of Leu-11 and Met-340 polymorphisms defines the minor AGXT allele, whereas their absence defines the major allele. The minor allele has frequencies of 20% in normal European and North American populations, and 50% in HP1 patients.

Sequence variations from dbSNP and Humsavar for AGXT Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs10196315 uncertain-significance, Primary hyperoxaluria, type I 240,871,540(+) C/T intron_variant
rs10199038 uncertain-significance, Primary hyperoxaluria, type I 240,877,905(+) C/T intron_variant
rs1057516896 likely-pathogenic, Primary hyperoxaluria, type I 240,874,055(+) AAGG/ coding_sequence_variant, frameshift
rs111742810 pathogenic, Primary hyperoxaluria, type I 240,874,064(+) T/A splice_donor_variant
rs111996685 pathogenic, Primary hyperoxaluria, type I 240,874,063(+) G/A/C splice_donor_variant

Structural Variations from Database of Genomic Variants (DGV) for AGXT Gene

Variant ID Type Subtype PubMed ID
nsv955294 CNV deletion 24416366
nsv584886 CNV loss 21841781
nsv584881 CNV gain 21841781
nsv584861 CNV gain 21841781
nsv470531 CNV loss 18288195
nsv460167 CNV gain 19166990
nsv1149735 CNV deletion 26484159
esv3594810 CNV loss 21293372
esv1710219 CNV insertion 17803354
esv1196389 CNV insertion 17803354
dgv771e199 CNV deletion 23128226
dgv7375n54 CNV loss 21841781
dgv7374n54 CNV loss 21841781

Variation tolerance for AGXT Gene

Residual Variation Intolerance Score: 83.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.69; 66.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AGXT Gene

Human Gene Mutation Database (HGMD)
AGXT
SNPedia medical, phenotypic, and genealogical associations of SNPs for
AGXT

Disorders for AGXT Gene

MalaCards: The human disease database

(14) MalaCards diseases for AGXT Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hyperoxaluria, primary, type i
  • hp1
primary hyperoxaluria
  • glycolic aciduria
nephrocalcinosis
  • hypercalcemic nephropathy
nephrolithiasis
  • nephrolithiasis, calcium oxalate
xanthinuria, type i
  • xan1
- elite association - COSMIC cancer census association via MalaCards
Search AGXT in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SPYA_HUMAN
  • Hyperoxaluria primary 1 (HP1) [MIM:259900]: An inborn error of glyoxylate metabolism characterized by increased excretion of oxalate and glycolate, and progressive tissue accumulation of insoluble calcium oxalate. Affected individuals are at risk for nephrolithiasis, nephrocalcinosis and early onset end-stage renal disease. {ECO:0000269 PubMed:10394939, ECO:0000269 PubMed:10453743, ECO:0000269 PubMed:10541294, ECO:0000269 PubMed:10862087, ECO:0000269 PubMed:10960483, ECO:0000269 PubMed:12559847, ECO:0000269 PubMed:12777626, ECO:0000269 PubMed:1301173, ECO:0000269 PubMed:1349575, ECO:0000269 PubMed:15253729, ECO:0000269 PubMed:15849466, ECO:0000269 PubMed:15961946, ECO:0000269 PubMed:15963748, ECO:0000269 PubMed:16971151, ECO:0000269 PubMed:1703535, ECO:0000269 PubMed:17495019, ECO:0000269 PubMed:2039493, ECO:0000269 PubMed:23229545, ECO:0000269 PubMed:24055001, ECO:0000269 PubMed:24934730, ECO:0000269 PubMed:26149463, ECO:0000269 PubMed:8101040, ECO:0000269 PubMed:9192270, ECO:0000269 PubMed:9604803}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for AGXT Gene

oxalosis (hyperoxaluria type I)

Additional Disease Information for AGXT

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with AGXT: view

Publications for AGXT Gene

  1. Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1. (PMID: 17495019) Williams E … Rumsby G (Clinical chemistry 2007) 3 4 22 44 58
  2. AGXT gene mutations and their influence on clinical heterogeneity of type 1 primary hyperoxaluria. (PMID: 11562405) Amoroso A … Marangella M (Journal of the American Society of Nephrology : JASN 2001) 3 22 25 44 58
  3. Characterization and chromosomal mapping of a genomic clone encoding human alanine:glyoxylate aminotransferase. (PMID: 2045108) Purdue PE … Danpure CJ (Genomics 1991) 2 3 4 22 58
  4. Primary hyperoxaluria type I due to a point mutation of T to C in the coding region of the serine:pyruvate aminotransferase gene. (PMID: 2039493) Nishiyama K … Ichiyama A (Biochemical and biophysical research communications 1991) 2 3 4 22 58
  5. Comprehensive mutation screening in 55 probands with type 1 primary hyperoxaluria shows feasibility of a gene-based diagnosis. (PMID: 17460142) Monico CG … Milliner DS (Journal of the American Society of Nephrology : JASN 2007) 3 22 44 58

Products for AGXT Gene

Sources for AGXT Gene

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