GOT2
Basic information
Region (hg38): 16:58707131-58734342
Links
Phenotypes
GenCC
Source:
- developmental and epileptic encephalopathy, 82 (Limited), mode of inheritance: AR
- developmental and epileptic encephalopathy, 82 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Developmental and epileptic encephalopathy 82 | AR | Neurologic | The condition can involve early-onset metabolic encephalopathy, and treatment with combined pyridoxine and serine has been described asresulting in improvement in seizures and mild developmental progress | Biochemical; Neurologic | 31422819 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOT2 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 | 11 | 20 | ||||
missense | 46 | 58 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 3 | 2 | 6 | ||
non coding | 15 | 19 | ||||
Total | 0 | 4 | 48 | 29 | 18 |
Variants in GOT2
This is a list of pathogenic ClinVar variants found in the GOT2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-58708186-G-A | Likely benign (Oct 13, 2023) | |||
16-58708208-C-T | Developmental and epileptic encephalopathy, 82 | Uncertain significance (Mar 18, 2021) | ||
16-58708213-G-A | Likely benign (Dec 11, 2023) | |||
16-58708216-G-A | Benign (Jan 08, 2024) | |||
16-58708220-G-C | not specified | Uncertain significance (Jun 13, 2023) | ||
16-58708225-G-A | Likely benign (Feb 21, 2023) | |||
16-58708250-T-C | Uncertain significance (Nov 15, 2022) | |||
16-58708284-G-A | Likely benign (Oct 27, 2023) | |||
16-58708286-C-T | Likely benign (Oct 03, 2023) | |||
16-58708287-G-A | Likely benign (Jun 08, 2021) | |||
16-58708301-G-C | Benign (Nov 02, 2023) | |||
16-58708308-G-T | Likely benign (Feb 18, 2023) | |||
16-58708310-A-C | Likely benign (Jul 25, 2023) | |||
16-58709407-A-C | Likely benign (Jun 21, 2023) | |||
16-58709417-C-T | Uncertain significance (Oct 24, 2022) | |||
16-58709436-G-A | Uncertain significance (Dec 09, 2021) | |||
16-58709456-T-G | not specified | Uncertain significance (May 23, 2024) | ||
16-58709461-C-T | Uncertain significance (Jun 18, 2022) | |||
16-58709462-G-A | Benign (Jan 22, 2024) | |||
16-58709472-T-C | not specified | Uncertain significance (Nov 17, 2022) | ||
16-58709490-C-A | Early infantile epileptic encephalopathy with suppression bursts • Developmental and epileptic encephalopathy, 82 | Likely pathogenic (May 29, 2020) | ||
16-58709497-T-C | Benign (Jul 17, 2023) | |||
16-58709503-G-A | Developmental and epileptic encephalopathy, 82 | Uncertain significance (May 03, 2023) | ||
16-58709505-T-C | Uncertain significance (Oct 12, 2021) | |||
16-58709518-G-C | GOT2-related disorder | Conflicting classifications of pathogenicity (Jan 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GOT2 | protein_coding | protein_coding | ENST00000245206 | 10 | 27227 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0142 | 0.985 | 125733 | 0 | 13 | 125746 | 0.0000517 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.39 | 190 | 252 | 0.754 | 0.0000144 | 2808 |
Missense in Polyphen | 41 | 70.613 | 0.58063 | 846 | ||
Synonymous | 1.93 | 68 | 91.5 | 0.743 | 0.00000523 | 846 |
Loss of Function | 2.84 | 7 | 21.1 | 0.332 | 9.78e-7 | 243 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000211 | 0.000208 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.0000541 | 0.0000527 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the irreversible transamination of the L- tryptophan metabolite L-kynurenine to form kynurenic acid (KA). Plays a key role in amino acid metabolism. Important for metabolite exchange between mitochondria and cytosol. Facilitates cellular uptake of long-chain free fatty acids. {ECO:0000269|PubMed:9537447}.;
- Pathway
- Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Arginine and proline metabolism - Homo sapiens (human);Phenylalanine metabolism - Homo sapiens (human);Fat digestion and absorption - 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;Argininemia;2-Hydroxyglutric Aciduria (D And L Form);Citrullinemia Type I;Carbamoyl Phosphate Synthetase Deficiency;Argininosuccinic Aciduria;Malate-Aspartate Shuttle;Urea Cycle;Glutaminolysis and Cancer;Homocarnosinosis;Hyperinsulinism-Hyperammonemia Syndrome;Succinic semialdehyde dehydrogenase deficiency;Ornithine Transcarbamylase Deficiency (OTC Deficiency);4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency;Glutamate Metabolism;Alanine and aspartate metabolism;Amino Acid metabolism;Glycolysis and Gluconeogenesis;Metabolism of carbohydrates;Alanine Aspartate Asparagine metabolism;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;malate-aspartate shuttle;Glycine Serine metabolism;Tyrosine metabolism;Metabolism;Methionine Cysteine metabolism;Phenylalanine degradation;L-kynurenine degradation;4-hydroxyproline degradation;Methionine and cysteine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Glyoxylate metabolism and glycine degradation;Arginine Proline metabolism;Gluconeogenesis;Glucose metabolism;Sulfur amino acid metabolism;Amino acid synthesis and interconversion (transamination)
(Consensus)
Recessive Scores
- pRec
- 0.975
Intolerance Scores
- loftool
- 0.107
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.6
Haploinsufficiency Scores
- pHI
- 0.231
- hipred
- Y
- hipred_score
- 0.794
- ghis
- 0.460
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.370
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Got2
- Phenotype
Gene ontology
- Biological process
- gluconeogenesis;2-oxoglutarate metabolic process;oxaloacetate metabolic process;aspartate metabolic process;aspartate biosynthetic process;aspartate catabolic process;glutamate metabolic process;female pregnancy;lactation;cellular amino acid biosynthetic process;response to muscle activity;fatty acid transport;4-hydroxyproline catabolic process;glutamate catabolic process to aspartate;glutamate catabolic process to 2-oxoglutarate;response to insulin;response to morphine;response to ethanol;glyoxylate metabolic process;L-kynurenine metabolic process
- Cellular component
- mitochondrion;mitochondrial inner membrane;mitochondrial matrix;plasma membrane;cell surface;T-tubule;protein-containing complex;perikaryon;myelin sheath;extracellular exosome
- Molecular function
- RNA binding;L-aspartate:2-oxoglutarate aminotransferase activity;phospholipid binding;kynurenine-oxoglutarate transaminase activity;amino acid binding;enzyme binding;pyridoxal phosphate binding;protein homodimerization activity;4-hydroxyglutamate transaminase activity