AGXT2

alanine--glyoxylate aminotransferase 2

Basic information

Region (hg38): 5:34998100-35048135

Links

ENSG00000113492 ∙ NCBI:64902 ∙ OMIM:612471 ∙ HGNC:14412 ∙ Uniprot:Q9BYV1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Beta-aminoisobutyric aciduria	AR	General	The clinical significance is unclear	Biochemical	21572414

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGXT2 gene.

• Inborn genetic diseases (28 variants)
• not provided (6 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGXT2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			28		3	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				1		1
non coding						0
Total	0	0	28	2	4

Variants in AGXT2

This is a list of pathogenic ClinVar variants found in the AGXT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-34998760-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-34998807-G-A		not specified	Uncertain significance (Nov 03, 2023)
5-34998813-G-A		not specified	Uncertain significance (Apr 12, 2023)
5-35003789-C-A		not specified	Uncertain significance (Jun 29, 2023)
5-35003845-A-G		not specified	Uncertain significance (Nov 21, 2023)
5-35003869-T-C			Likely benign (Dec 12, 2017)
5-35010005-C-T		not specified	Uncertain significance (Feb 06, 2023)
5-35010047-C-T		not specified	Uncertain significance (Apr 08, 2022)
5-35010055-A-G		not specified	Uncertain significance (Feb 23, 2023)
5-35010067-T-A		not specified	Uncertain significance (Oct 21, 2021)
5-35010145-A-G		not specified	Uncertain significance (Jul 12, 2023)
5-35012953-C-T		not specified	Benign/Likely benign (Feb 20, 2017)
5-35013036-T-C		not specified	Uncertain significance (Dec 19, 2023)
5-35014004-G-A		not specified	Uncertain significance (Mar 24, 2023)
5-35014010-A-G		not specified	Uncertain significance (Jul 21, 2021)
5-35014039-C-T		not specified	Uncertain significance (Jan 11, 2023)
5-35014083-A-G		not specified	Uncertain significance (Jan 25, 2023)
5-35014103-C-A		not specified	Uncertain significance (Aug 13, 2021)
5-35025809-G-C		not specified	Uncertain significance (Feb 06, 2024)
5-35025825-C-T		not specified	Uncertain significance (Jun 13, 2023)
5-35026456-G-A		not specified	Uncertain significance (Jun 02, 2023)
5-35026465-G-C		not specified	Uncertain significance (Apr 19, 2023)
5-35026465-G-GT		Beta-aminoisobutyric acid, urinary excretion of	Uncertain significance (Apr 04, 2024)
5-35026486-T-C		not specified	Uncertain significance (May 11, 2022)
5-35032776-C-T			Benign (Jun 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGXT2	protein_coding	protein_coding	ENST00000231420	14	49993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.71e-28	0.00000464	125600	0	148	125748	0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.661	315	284	1.11	0.0000155	3362
Missense in Polyphen		110	92.657	1.1872		1161
Synonymous	-1.07	114	100	1.14	0.00000557	984
Loss of Function	-1.45	37	28.7	1.29	0.00000165	315

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00256	0.00256
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000326	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000390	0.000387
Middle Eastern	0.000326	0.000326
South Asian	0.00121	0.00121
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can metabolize asymmetric dimethylarginine (ADMA) via transamination to alpha-keto-delta-(NN-dimethylguanidino) valeric acid (DMGV). ADMA is a potent inhibitor of nitric-oxide (NO) synthase, and this activity provides mechanism through which the kidney regulates blood pressure. {ECO:0000269|PubMed:20018850, ECO:0000269|PubMed:23023372, ECO:0000269|PubMed:24586340}.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);One carbon metabolism and related pathways;Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Alanine Aspartate Asparagine metabolism;Metabolism of amino acids and derivatives;glycine biosynthesis;Glycolysis Gluconeogenesis;Glycine Serine metabolism;Metabolism;Glyoxylate metabolism and glycine degradation (Consensus)

Recessive Scores

• pRec: 0.184

Intolerance Scores

• loftool: 0.339
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.27

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.216

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.337

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Agxt2
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: glyoxylate catabolic process;glycine biosynthetic process, by transamination of glyoxylate;L-alanine catabolic process, by transamination;positive regulation of nitric oxide biosynthetic process;glyoxylate metabolic process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: alanine-glyoxylate transaminase activity;pyridoxal phosphate binding;(R)-3-amino-2-methylpropionate-pyruvate transaminase activity