AGXT2

Summary

AGXT2 (alanine–glyoxylate aminotransferase 2, HGNC:14412) is a protein-coding gene on chromosome 5p13.2, encoding Alanine–glyoxylate aminotransferase 2, mitochondrial (Q9BYV1). Multifunctional aminotransferase with a broad substrate specificity.

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.

Source: NCBI Gene 64902 — RefSeq curated summary.

At a glance

• GWAS associations: 34
• Clinical variants (ClinVar): 93 total — 1 pathogenic
• Phenotypes (HPO): 2
• MANE Select transcript: NM_031900

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14412
Approved symbol	AGXT2
Name	alanine–glyoxylate aminotransferase 2
Location	5p13.2
Locus type	gene with protein product
Status	Approved
Aliases	AGT2
Ensembl gene	ENSG00000113492
Ensembl biotype	protein_coding
OMIM	612471
Entrez	64902

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 12 protein_coding, 3 retained_intron

ENST00000231420, ENST00000505349, ENST00000505542, ENST00000510428, ENST00000512135, ENST00000618015, ENST00000853195, ENST00000853196, ENST00000853197, ENST00000853198, ENST00000853199, ENST00000853200, ENST00000853201, ENST00000853202, ENST00000946517

RefSeq mRNA: 2 — MANE Select: NM_031900 NM_001306173, NM_031900

CCDS: CCDS3908, CCDS78000

Canonical transcript exons

ENST00000231420 — 14 exons

Exon	Start	End
ENSE00000828264	35025763	35025855
ENSE00000828265	35026410	35026510
ENSE00000828266	35032732	35032825
ENSE00000828267	35033460	35033553
ENSE00000828271	35040575	35040663
ENSE00002076121	35047805	35047949
ENSE00003469036	35003763	35003861
ENSE00003533872	35010000	35010149
ENSE00003556683	35036942	35037065
ENSE00003576342	35012954	35013045
ENSE00003610765	35035222	35035316
ENSE00003623389	35013987	35014119
ENSE00003679840	35039324	35039508
ENSE00003848964	34998102	34998826

Expression profiles

Bgee: expression breadth broad, 52 present calls, max score 99.50.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.5156 / max 202.1707, expressed in 32 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
61256	0.3912	28
61255	0.0559	9
61252	0.0302	9
61254	0.0209	9
61253	0.0174	8

Top tissues by expression

232 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.50	gold quality
right lobe of liver	UBERON:0001114	95.97	gold quality
adult mammalian kidney	UBERON:0000082	94.69	gold quality
liver	UBERON:0002107	94.50	gold quality
adult organism	UBERON:0007023	91.11	gold quality
kidney	UBERON:0002113	89.79	gold quality
renal medulla	UBERON:0000362	81.67	gold quality
cortex of kidney	UBERON:0001225	79.23	gold quality
buccal mucosa cell	CL:0002336	74.77	silver quality
metanephros cortex	UBERON:0010533	70.35	gold quality
jejunal mucosa	UBERON:0000399	69.66	gold quality
epithelial cell of pancreas	CL:0000083	68.01	gold quality
metanephros	UBERON:0000081	67.71	gold quality
oocyte	CL:0000023	65.57	gold quality
pancreatic ductal cell	CL:0002079	62.31	silver quality
ileal mucosa	UBERON:0000331	61.39	silver quality
gall bladder	UBERON:0002110	59.50	gold quality
epithelium of nasopharynx	UBERON:0001951	58.75	gold quality
skin of hip	UBERON:0001554	56.92	silver quality
jejunum	UBERON:0002115	56.44	gold quality
endothelial cell	CL:0000115	56.16	gold quality
cerebellar vermis	UBERON:0004720	55.58	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.96	gold quality
small intestine Peyer’s patch	UBERON:0003454	54.73	gold quality
small intestine	UBERON:0002108	54.59	gold quality
tibialis anterior	UBERON:0001385	54.38	silver quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
colonic epithelium	UBERON:0000397	53.60	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
vena cava	UBERON:0004087	53.40	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	66.64
E-ANND-3	yes	8.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting AGXT2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-520E-5P	99.27	68.90	1513
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-499A-3P	99.18	69.20	1392
HSA-MIR-499B-3P	99.18	69.27	1391
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-4720-3P	98.50	68.88	988
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-6804-5P	98.39	65.77	1084
HSA-MIR-653-3P	98.31	67.71	1542
HSA-MIR-4638-3P	97.90	65.75	905
HSA-MIR-203B-3P	97.82	66.27	979
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-526B-5P	97.41	67.99	1074

Literature-anchored findings (GeneRIF, showing 21)

• mitochondrially localized human AGXT2 is able to effectively metabolize ADMA in vivo resulting in decreased ADMA levels and improved endothelial NO production. (PMID:20018850)
• Alanine-glyoxylate aminotransferase-2 metabolizes endogenous methylarginines, regulates NO, and controls blood pressure. (PMID:23023372)
• AGXT2 has an important role in SDMA metabolism in humans and may additionally have an unanticipated role in the autonomic nervous system regulation of cardiac function. (PMID:24159190)
• SNPs of AGXT2 affect plasma as well as urinary BAIB. (PMID:24586340)
• The results of this study that the AGXT2 gene is not associated with schizophrenia in Japanese subjects. (PMID:24727203)
• AGXT2 rs37369 polymorphism is associated with increased risk for CHD in smokers and in diabetes mellitus patients (PMID:24834905)
• The AGXT2 genotype may be an important factor underlying atherosclerosis. (PMID:25620171)
• The Alanine-glyoxylate aminotransferase 2 p.V498L polymorphism is associated with both paroxysmal and chronic forms of atrial fibrillation in coronary angiographic patients without structural heart disease in ultrasound, and earlier age at onset of ischemic stroke in patients undergoing exercise stress testing. (PMID:26984639)
• AGXT2 rs37369 polymorphism is associated with increased risk for chronic heart failure, which may due to distinct disparities of alleles in asymmetric dimethylarginine degradation (PMID:27423328)
• 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 (PMID:27752063)
• 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. (PMID:28357606)
• Single nucleotide polymorphism in AGXT2 gene is associated with renal dysfunction in patients with chronic heart failure. (PMID:28942034)
• 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 (PMID:30284143)
• 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. (PMID:31062169)
• The role of alanine glyoxylate transaminase-2 (agxt2) in beta-alanine and carnosine metabolism of healthy mice and humans. (PMID:32948897)
• Effects of AGXT2 variants on blood pressure and blood sugar among 750 older Japanese subjects recruited by the complete enumeration survey method. (PMID:33879046)
• Disease-specific eQTL screening reveals an anti-fibrotic effect of AGXT2 in non-alcoholic fatty liver disease. (PMID:33892010)
• Functional AGXT2 SNP rs37369 Variant Is a Risk Factor for Diabetes Mellitus: Baseline Data From the Aidai Cohort Study in Japan. (PMID:35961823)
• Genetic loci of beta-aminoisobutyric acid are associated with aging-related mild cognitive impairment. (PMID:37120436)
• Functional AGXT2 SNP rs180749 variant and depressive symptoms: Baseline data from the Aidai Cohort Study in Japan. (PMID:38261033)
• Discusses the cloning of the rat gene. (PMID:7592550)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	agxt2	ENSDARG00000100709
mus_musculus	Agxt2	ENSMUSG00000089678
rattus_norvegicus	Agxt2	ENSRNOG00000017821
drosophila_melanogaster	CG11241	FBGN0037186
caenorhabditis_elegans	T09B4.8	WBGENE00020382

Paralogs (4): OAT (ENSG00000065154), ETNPPL (ENSG00000164089), PHYKPL (ENSG00000175309), ABAT (ENSG00000183044)

Protein

Protein identifiers

Alanine–glyoxylate aminotransferase 2, mitochondrial — Q9BYV1 (reviewed: Q9BYV1)

Alternative names: (R)-3-amino-2-methylpropionate–pyruvate transaminase, Beta-ALAAT II, Beta-alanine-pyruvate aminotransferase, D-3-aminoisobutyrate-pyruvate aminotransferase, D-AIBAT, D-beta-aminoisobutyrate-pyruvate aminotransferase

All UniProt accessions (1): Q9BYV1

UniProt curated annotations — full annotation on UniProt →

Function. Multifunctional aminotransferase with a broad substrate specificity. Catalyzes the conversion of glyoxylate to glycine using alanine as the amino donor. Catalyzes metabolism of not L- but the D-isomer of D-beta-aminoisobutyric acid to generate 2-methyl-3-oxopropanoate and alanine. Catalyzes the transfer of the amino group from beta-alanine to pyruvate to yield L-alanine and 3-oxopropanoate. Can metabolize NG-monomethyl-L-arginine (NMMA), asymmetric NG,NG-dimethyl-L-arginine (ADMA) and symmetric NG,N’G-dimethyl-L-arginine (SDMA). ADMA is a potent inhibitor of nitric-oxide (NO) synthase, and this activity provides mechanism through which the kidney regulates blood pressure.

Subunit / interactions. Homotetramer.

Subcellular location. Mitochondrion.

Tissue specificity. Expressed in the convoluted tubule in the kidney and in the liver hepatocytes (at protein level).

Polymorphism. Genetic variants in AGXT2 are association with beta-aminoisobutyric aciduria (BAIBA)[MIM:210100]. Excretion of beta-aminoisobutyric acid in urine is a common, benign, metabolic trait.

Similarity. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BYV1-1	1	yes
Q9BYV1-2	2

RefSeq proteins (2): NP_001293102, NP_114106* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005814	Aminotrans_3	Family
IPR015421	PyrdxlP-dep_Trfase_major	Homologous_superfamily
IPR015422	PyrdxlP-dep_Trfase_small	Homologous_superfamily
IPR015424	PyrdxlP-dep_Trfase	Homologous_superfamily
IPR049704	Aminotrans_3_PPA_site	Conserved_site

Pfam: PF00202

Enzyme classification (BRENDA):

• EC 2.6.1.44 — alanine-glyoxylate transaminase (BRENDA: 51 organisms, 96 substrates, 25 inhibitors, 130 Km, 68 kcat entries)

Substrate kinetics (BRENDA)

11 substrates with measured Km, best-characterized 11. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
L-ALANINE	0.24–149	58
GLYOXYLATE	0.038–64	52
PYRUVATE	0.21–51	4
L-GLUTAMATE	1.7–3.32	3
L-SERINE	0.39–256	3
2-AMINOBUTYRATE	60–100	2
GLYCINE	22	2
2-OXOBUTYRATE	2.7	1
3-HYDROXYKYNURENINE	18	1
KYNURENINE	3.7	1
L-CYSTEINE	1	1

Catalyzed reactions (Rhea), 12 shown:

• 3-oxopropanoate + L-alanine = beta-alanine + pyruvate (RHEA:14077)
• (R)-3-amino-2-methylpropanoate + pyruvate = 2-methyl-3-oxopropanoate + L-alanine (RHEA:18393)
• glyoxylate + L-alanine = glycine + pyruvate (RHEA:24248)
• N(omega),N(omega)-dimethyl-L-arginine + pyruvate = 5-(3,3-dimethylguanidino)-2-oxopentanoate + L-alanine (RHEA:77303)
• N(omega),N(‘omega)-dimethyl-L-arginine + pyruvate = 5-(3,3’-dimethylguanidino)-2-oxopentanoate + L-alanine (RHEA:77307)
• N(omega),N(omega)-dimethyl-L-arginine + glyoxylate = 5-(3,3-dimethylguanidino)-2-oxopentanoate + glycine (RHEA:77311)
• N(omega),N(‘omega)-dimethyl-L-arginine + glyoxylate = 5-(3,3’-dimethylguanidino)-2-oxopentanoate + glycine (RHEA:77315)
• N(omega)-methyl-L-arginine + pyruvate = 5-(3-methylguanidino)-2-oxopentanoate + L-alanine (RHEA:77319)
• N(omega)-methyl-L-arginine + glyoxylate = 5-(3-methylguanidino)-2-oxopentanoate + glycine (RHEA:77323)
• L-ornithine + pyruvate = 5-amino-2-oxopentanoate + L-alanine (RHEA:77327)
• L-ornithine + glyoxylate = 5-amino-2-oxopentanoate + glycine (RHEA:77331)
• (2S)-2-aminobutanoate + glyoxylate = 2-oxobutanoate + glycine (RHEA:77339)

UniProt features (22 total): modified residue 11, sequence variant 8, transit peptide 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYV1-F1	91.02	0.87

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (11): 417, 420, 420, 71, 71, 84, 262, 262, 304, 350, 417

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-389661	Glyoxylate metabolism and glycine degradation
R-HSA-73621	Pyrimidine catabolism
R-HSA-1430728	Metabolism
R-HSA-15869	Metabolism of nucleotides
R-HSA-71291	Metabolism of amino acids and derivatives
R-HSA-8956319	Nucleotide catabolism

MSigDB gene sets: 90 (showing top): REACTOME_PYRIMIDINE_CATABOLISM, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, GOBP_MODIFIED_AMINO_ACID_CATABOLIC_PROCESS, GOBP_SERINE_FAMILY_AMINO_ACID_BIOSYNTHETIC_PROCESS, GOBP_ALDEHYDE_CATABOLIC_PROCESS, GOBP_AMINO_ACID_BIOSYNTHETIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_REACTIVE_NITROGEN_SPECIES_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_CATABOLIC_PROCESS, GOBP_GLYOXYLATE_METABOLIC_PROCESS, GOBP_GLYCINE_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_CATABOLIC_PROCESS

GO Biological Process (5): glyoxylate catabolic process (GO:0009436), obsolete glycine biosynthetic process, by transamination of glyoxylate (GO:0019265), obsolete L-alanine catabolic process, by transamination (GO:0019481), positive regulation of nitric oxide biosynthetic process (GO:0045429), obsolete N(omega),N(omega)-dimethyl-L-arginine catabolic process (GO:2001299)

GO Molecular Function (6): L-alanine:glyoxylate transaminase activity (GO:0008453), beta-alanine:pyruvate transaminase activity (GO:0016223), pyridoxal phosphate binding (GO:0030170), (R)-3-amino-2-methylpropionate:pyruvate transaminase activity (GO:0047305), transaminase activity (GO:0008483), transferase activity (GO:0016740)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Metabolism	2
Metabolism of amino acids and derivatives	1
Nucleotide catabolism	1
Metabolism of nucleotides	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
aldehyde catabolic process	1
glyoxylate metabolic process	1
monocarboxylic acid catabolic process	1
nitric oxide biosynthetic process	1
positive regulation of biosynthetic process	1
regulation of nitric oxide biosynthetic process	1
L-alanine:oxo-acid transaminase activity	1
amino acid transaminase activity	1
anion binding	1
vitamin B6 binding	1
transaminase activity	1
transferase activity, transferring nitrogenous groups	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

1806 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
AGXT2	AGXT	P21549	953
AGXT2	DDAH1	O94760	846
AGXT2	DDAH2	O95865	787
AGXT2	PEX5	P50542	628
AGXT2	GLDC	P23378	535
AGXT2	PRMT1	Q99873	504
AGXT2	AGMAT	Q9BSE5	502
AGXT2	GLS2	Q9UI32	464
AGXT2	GATM	P50440	462
AGXT2	SLC25A29	Q8N8R3	456
AGXT2	DPYS	Q14117	454
AGXT2	ALDH18A1	P54886	445
AGXT2	UPB1	Q9UBR1	444
AGXT2	PCCA	P05165	429
AGXT2	SLC7A9	P82251	421

IntAct

4 interactions, top by confidence:

A	B	Type	Score
MOV10L1	AGXT2	psi-mi:“MI:0915”(physical association)	0.400
ALDOB	AGXT2	psi-mi:“MI:0915”(physical association)	0.370
CYP2E1	AGXT2	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (4): AGXT2 (Affinity Capture-MS), AGXT2 (Affinity Capture-MS), ALDOB (Two-hybrid), CYP2E1 (Two-hybrid)

ESM2 similar proteins: A0A098DDI1, B8BBZ7, O04866, O13427, O13940, O14433, O52250, O74267, O74548, O94562, P18492, P18544, P31593, P33189, P37303, P42799, P44951, P45621, P59315, P91408, Q01K11, Q01K12, Q05567, Q10174, Q17QF0, Q3UEG6, Q40147, Q42522, Q5RFA3, Q5WL78, Q64565, Q6BUP9, Q6YZE2, Q6ZCF0, Q75AW1, Q7XN11, Q7XN12, Q84P52, Q84P54, Q85WB7

Diamond homologs: A8AHE0, B5FHV3, B5QZ53, B5REH5, B9DIU0, B9EAM9, B9ITF9, C0ZBR4, C1EL61, C3LBX0, C3P3K3, C4L2E7, C5D6R2, E5Y945, H3ZR39, M1GRN3, O27392, O30156, O50131, O57878, O58478, O59401, O66442, P16932, P22256, P29758, P30268, P33189, P36839, P38021, P40829, P44951, P50457, P56744, P59315, P59316, P59322, P60297, P60298, P60299

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

93 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	73
Likely benign	4
Benign	4

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
687304	GRCh37/hg19 5p13.2-11(chr5:34453883-46389339)x3	Pathogenic

SpliceAI

2373 predictions. Top by Δscore:

Variant	Effect	Δscore
5:34998839:C:CT	acceptor_gain	1.0000
5:35010147:CAC:C	acceptor_gain	1.0000
5:35010148:ACCT:A	acceptor_loss	1.0000
5:35010149:CCTG:C	acceptor_loss	1.0000
5:35010150:CTGTT:C	acceptor_loss	1.0000
5:35010151:T:A	acceptor_loss	1.0000
5:35025761:A:AC	donor_gain	1.0000
5:35025762:C:CC	donor_gain	1.0000
5:35026408:A:AC	donor_gain	1.0000
5:35026409:C:CC	donor_gain	1.0000
5:35032750:T:TA	donor_gain	1.0000
5:35033458:A:AC	donor_gain	1.0000
5:35033459:C:CT	donor_gain	1.0000
5:35033549:CTCCT:C	acceptor_gain	1.0000
5:35033552:CT:C	acceptor_gain	1.0000
5:35033554:C:CC	acceptor_gain	1.0000
5:35035217:ATTAC:A	donor_loss	1.0000
5:35035218:TTAC:T	donor_loss	1.0000
5:35035219:TA:T	donor_loss	1.0000
5:35035220:ACCT:A	donor_loss	1.0000
5:35035221:C:G	donor_loss	1.0000
5:35039383:T:TA	donor_gain	1.0000
5:35039509:C:CC	acceptor_gain	1.0000
5:34998839:C:T	acceptor_gain	0.9900
5:34998840:A:T	acceptor_gain	0.9900
5:35003757:TCTTA:T	donor_loss	0.9900
5:35003758:CTTA:C	donor_loss	0.9900
5:35003760:T:TA	donor_loss	0.9900
5:35003761:A:AG	donor_loss	0.9900
5:35003762:CCT:C	donor_loss	0.9900

AlphaMissense

3396 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:35035273:G:T	A177D	0.985
5:35014034:T:A	K350I	0.983
5:35014046:A:T	V346D	0.983
5:35014021:A:C	N354K	0.980
5:35014021:A:T	N354K	0.980
5:35035261:G:T	A181D	0.980
5:35035286:C:G	A173P	0.980
5:35026432:C:T	G283E	0.979
5:35014083:A:G	W334R	0.977
5:35014083:A:T	W334R	0.977
5:35035296:A:C	S169R	0.977
5:35035296:A:T	S169R	0.977
5:35035298:T:G	S169R	0.977
5:35014001:A:T	V361D	0.976
5:35010043:C:G	R432P	0.975
5:35014008:C:G	A359P	0.974
5:35035262:C:G	A181P	0.974
5:35037014:G:C	S138R	0.974
5:35037014:G:T	S138R	0.974
5:35037016:T:G	S138R	0.974
5:35014005:C:G	A360P	0.973
5:35039399:A:G	L96P	0.973
5:35014099:C:A	R328S	0.970
5:35014099:C:G	R328S	0.970
5:35014007:G:T	A359E	0.969
5:35014109:C:T	G325E	0.969
5:35039341:A:C	S115R	0.969
5:35039341:A:T	S115R	0.969
5:35039343:T:G	S115R	0.969
5:35014004:G:T	A360E	0.968

dbSNP variants (sampled 300 via entrez): RS1000010591 (5:35013125 T>C), RS1000041772 (5:35013408 C>T), RS1000147378 (5:35014503 C>T), RS1000250418 (5:35037385 A>G), RS1000279392 (5:35007212 C>A), RS1000281721 (5:35037661 C>A), RS1000371001 (5:35041662 A>C), RS1000400112 (5:35044311 G>A,C,T), RS1000433571 (5:35001268 C>A,T), RS1000482238 (5:35013316 T>A,C), RS1000564489 (5:35019701 A>G), RS1000596531 (5:35026827 C>G,T), RS1000687161 (5:35007602 C>A,G), RS1000701037 (5:35013608 T>C), RS1000756498 (5:35009078 T>C)

Disease associations

OMIM: gene MIM:612471 | disease phenotypes: MIM:210100

GenCC curated gene-disease

Mondo (1): beta-aminoisobutyric acid, urinary excretion of (MONDO:0008860)

Orphanet (0):

HPO phenotypes

2 total (2 of 2 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0032480	Beta-aminoisobutyric aciduria

GWAS associations

34 associations (top):

Study	Trait	p-value
GCST001073_4	Urinary metabolites	2.000000e-182
GCST001220_2	Metabolite levels	1.000000e-06
GCST002239_13	Symmetrical dimethylarginine levels	1.000000e-40
GCST002242_19	Serum dimethylarginine levels (asymmetric/symetric ratio)	2.000000e-32
GCST002364_10	Urinary metabolites (H-NMR features)	3.000000e-16
GCST002364_11	Urinary metabolites (H-NMR features)	4.000000e-15
GCST002364_12	Urinary metabolites (H-NMR features)	9.000000e-37
GCST002364_13	Urinary metabolites (H-NMR features)	2.000000e-31
GCST002364_14	Urinary metabolites (H-NMR features)	6.000000e-15
GCST002364_5	Urinary metabolites (H-NMR features)	8.000000e-15
GCST002364_6	Urinary metabolites (H-NMR features)	3.000000e-29
GCST002364_7	Urinary metabolites (H-NMR features)	1.000000e-63
GCST002364_8	Urinary metabolites (H-NMR features)	3.000000e-26
GCST002364_9	Urinary metabolites (H-NMR features)	3.000000e-23
GCST002622_1	Symmetrical dimethylarginine levels	4.000000e-36
GCST003119_15	Urinary metabolites	7.000000e-262
GCST003119_5	Urinary metabolites	2.000000e-252
GCST009733_113	Urinary metabolite levels in chronic kidney disease	1.000000e-14
GCST009733_145	Urinary metabolite levels in chronic kidney disease	6.000000e-119
GCST009733_216	Urinary metabolite levels in chronic kidney disease	6.000000e-27
GCST009733_218	Urinary metabolite levels in chronic kidney disease	4.000000e-48
GCST009733_220	Urinary metabolite levels in chronic kidney disease	6.000000e-50
GCST009733_71	Urinary metabolite levels in chronic kidney disease	2.000000e-24
GCST009733_79	Urinary metabolite levels in chronic kidney disease	9.000000e-56
GCST009733_83	Urinary metabolite levels in chronic kidney disease	1.000000e-22
GCST009735_43	Urinary metabolite modules (eigenmetabolites) in chronic kidney disease	1.000000e-96
GCST012020_293	Serum metabolite levels	1.000000e-36
GCST012020_294	Serum metabolite levels	4.000000e-91
GCST012020_295	Serum metabolite levels	3.000000e-185
GCST012020_296	Serum metabolite levels	8.000000e-58

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004725	metabolite measurement
EFO:0005116	urinary metabolite measurement
EFO:0006523	symmetrical dimethylarginine measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C565904	Beta-Aminoisobutyric Acid, Urinary Excretion of (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs114286107	AGXT2		0.00	0

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	3
Aflatoxin B1	affects expression, decreases expression, decreases methylation	3
Acetaminophen	decreases expression	2
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression, affects expression	2
Cyclosporine	decreases expression	2
perfluorodecanesulfonic acid	increases expression	1
methyleugenol	decreases expression	1
bisphenol A	increases expression	1
titanium dioxide	decreases expression	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
Rosiglitazone	decreases expression	1
Troglitazone	decreases expression	1
Chenodeoxycholic Acid	affects cotreatment, decreases expression	1
Deoxycholic Acid	affects cotreatment, decreases expression	1
Endosulfan	affects cotreatment, decreases expression	1
Estradiol	decreases expression	1
Glycochenodeoxycholic Acid	affects cotreatment, decreases expression	1
Glycocholic Acid	affects cotreatment, decreases expression	1
Glycodeoxycholic Acid	affects cotreatment, decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Fenofibrate	decreases expression	1
Valproic Acid	decreases expression	1
Palmitic Acid	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.