GOT1
glutamic-oxaloacetic transaminase 1
Basic information
Region (hg38): 10:99396870-99430624
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (2 variants)
- GOT1-related_disorder (2 variants)
- ASPARTATE_AMINOTRANSFERASE,_SERUM_LEVEL_OF,_QUANTITATIVE_TRAIT_LOCUS_1 (1 variants)
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. These statistics are base on transcript: NM_000002079.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 39 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 39 | 2 | 1 |
Highest pathogenic variant AF is 0.000334606
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
- Phenotype
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