GOT1

glutamic-oxaloacetic transaminase 1

Basic information

Region (hg38): 10:99396870-99430624

Links

ENSG00000120053 ∙ NCBI:2805 ∙ OMIM:138180 ∙ HGNC:4432 ∙ Uniprot:P17174 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GOT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOT1 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						0
missense			24		1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	24	0	1

Variants in GOT1

This is a list of pathogenic ClinVar variants found in the GOT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-99397564-C-G		not specified	Uncertain significance (Aug 17, 2021)
10-99397576-T-A		not specified	Uncertain significance (Jan 20, 2025)
10-99397621-CGTT-C		ASPARTATE AMINOTRANSFERASE, SERUM LEVEL OF, QUANTITATIVE TRAIT LOCUS 1	Pathogenic (Nov 01, 2011)
10-99402625-G-A		not specified	Uncertain significance (Aug 08, 2023)
10-99402646-T-C		not specified	Uncertain significance (Oct 22, 2021)
10-99402682-T-C		not specified	Uncertain significance (Jul 02, 2024)
10-99403483-C-G		not specified	Uncertain significance (Feb 05, 2024)
10-99403514-C-T		not specified	Uncertain significance (Mar 12, 2024)
10-99403554-C-T		not specified	Uncertain significance (Jun 27, 2022)
10-99403596-G-A		not specified	Uncertain significance (Jul 17, 2024)
10-99403599-C-G		not specified	Uncertain significance (May 01, 2024)
10-99403748-A-C		not specified	Uncertain significance (Dec 09, 2023)
10-99403870-C-T		not specified	Uncertain significance (Oct 13, 2021)
10-99403879-G-A			Benign/Likely benign (Feb 01, 2024)
10-99405767-A-C		not specified	Uncertain significance (Oct 17, 2024)
10-99405801-A-C		not specified	Uncertain significance (Sep 25, 2023)
10-99405828-G-A		GOT1-related disorder	Likely benign (Sep 09, 2019)
10-99405850-T-C			Benign (Jul 11, 2018)
10-99406195-C-T		GOT1-related disorder	Likely benign (Nov 30, 2020)
10-99406753-G-A		not specified	Uncertain significance (Dec 31, 2024)
10-99406785-C-T		not specified	Uncertain significance (May 01, 2024)
10-99406786-G-A		not specified	Uncertain significance (Nov 10, 2022)
10-99406787-C-T		GOT1-related disorder	Benign (Oct 23, 2019)
10-99420667-C-T		not specified	Uncertain significance (Jul 21, 2021)
10-99420668-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOT1	protein_coding	protein_coding	ENST00000370508	9	33755

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00116	0.997	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	158	244	0.649	0.0000137	2691
Missense in Polyphen		65	108.82	0.59732		1171
Synonymous	0.806	82	91.8	0.893	0.00000507	838
Loss of Function	2.73	9	23.2	0.389	0.00000141	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Biosynthesis of L-glutamate from L-aspartate or L- cysteine. Important regulator of levels of glutamate, the major excitatory neurotransmitter of the vertebrate central nervous system. Acts as a scavenger of glutamate in brain neuroprotection. The aspartate aminotransferase activity is involved in hepatic glucose synthesis during development and in adipocyte glyceroneogenesis. Using L-cysteine as substrate, regulates levels of mercaptopyruvate, an important source of hydrogen sulfide. Mercaptopyruvate is converted into H(2)S via the action of 3- mercaptopyruvate sulfurtransferase (3MST). Hydrogen sulfide is an important synaptic modulator and neuroprotectant in the brain. {ECO:0000269|PubMed:16039064}.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Arginine and proline metabolism - Homo sapiens (human);Phenylalanine metabolism - Homo sapiens (human);Phenylalanine, tyrosine and tryptophan biosynthesis - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Tyrosine metabolism - Homo sapiens (human);Arginine biosynthesis - Homo sapiens (human);Valproic Acid Pathway, Pharmacodynamics;Pathway_PA165964473;Tyrosinemia, transient, of the newborn;Beta-mercaptolactate-cysteine disulfiduria;Dopamine beta-hydroxylase deficiency;Disulfiram Action Pathway;Hyperornithinemia with gyrate atrophy (HOGA);Creatine deficiency, guanidinoacetate methyltransferase deficiency;L-arginine:glycine amidinotransferase deficiency;Hyperornithinemia-hyperammonemia-homocitrullinuria [HHH-syndrome];Guanidinoacetate Methyltransferase Deficiency (GAMT Deficiency);Phenylalanine and Tyrosine Metabolism;Tyrosine Metabolism;Alkaptonuria;Monoamine oxidase-a deficiency (MAO-A);Hawkinsinuria;Tyrosinemia Type I;Cysteine Metabolism;Prolinemia Type II;Phenylketonuria;Prolidase Deficiency (PD);Arginine and Proline Metabolism;Cystinosis, ocular nonnephropathic;Tyrosinemia Type 3 (TYRO3);Hyperprolinemia Type I;Hyperprolinemia Type II;Ornithine Aminotransferase Deficiency (OAT Deficiency);Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency);Tyrosinemia Type 2 (or Richner-Hanhart syndrome);Alanine and aspartate metabolism;Trans-sulfuration pathway;Amino Acid metabolism;Glycolysis and Gluconeogenesis;Metabolism of carbohydrates;Alanine Aspartate Asparagine metabolism;Metabolism of polyamines;Metabolism of amino acids and derivatives;Methionine salvage pathway;malate-aspartate shuttle;Glycine Serine metabolism;L-cysteine degradation II;L-cysteine degradation I;asparagine biosynthesis;Metabolism;aspartate biosynthesis;Methionine Cysteine metabolism;Phenylalanine degradation;asparagine degradation;Arginine Proline metabolism;Gluconeogenesis;Glucose metabolism;Sulfur amino acid metabolism;superpathway of methionine degradation;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.599

Intolerance Scores

• loftool: 0.383
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.216
• hipred: Y
• hipred_score: 0.663
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Got1

Gene ontology

• Biological process: gluconeogenesis;2-oxoglutarate metabolic process;oxaloacetate metabolic process;glycerol biosynthetic process;aspartate metabolic process;aspartate biosynthetic process;aspartate catabolic process;glutamate metabolic process;Notch signaling pathway;cellular amino acid biosynthetic process;response to carbohydrate;glutamate catabolic process to aspartate;glutamate catabolic process to 2-oxoglutarate;positive regulation of transforming growth factor beta receptor signaling pathway;cellular response to insulin stimulus;negative regulation of collagen biosynthetic process;response to immobilization stress;response to cadmium ion;response to glucocorticoid;negative regulation of cytosolic calcium ion concentration;negative regulation of mitochondrial depolarization;fatty acid homeostasis;transdifferentiation;cellular response to mechanical stimulus;response to transition metal nanoparticle
• Cellular component: nucleus;nucleoplasm;cytoplasm;lysosome;cytosol;axon terminus;extracellular exosome
• Molecular function: L-aspartate:2-oxoglutarate aminotransferase activity;phosphatidylserine decarboxylase activity;pyridoxal phosphate binding;carboxylic acid binding;L-cysteine:2-oxoglutarate aminotransferase activity