GCAT
protein-codingglycine C-acetyltransferase
Gene summary
The degradation of L-threonine to glycine consists of a two-step biochemical pathway involving the enzymes L-threonine dehydrogenase and 2-amino-3-ketobutyrate coenzyme A ligase. L-Threonine is first converted into 2-amino-3-ketobutyrate by L-threonine dehydrogenase. This gene encodes the second enzyme in this pathway, which then catalyzes the reaction between 2-amino-3-ketobutyrate and coenzyme A to form glycine and acetyl-CoA. The encoded enzyme is considered a class II pyridoxal-phosphate-dependent aminotransferase. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 14. [provided by RefSeq, Jan 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GCAT variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014291.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 78 | 1 | 79 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 85 | 1 | 0 | 86 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055106.1 | 9 | MANE Select | |
| Ensembl | ENSP00000248924.6 | 9 | MANE Select | |
| RefSeq | NP_001165161.1 | 9 | Standard | |
| Ensembl | ENSP00000371110.3 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycine, serine and threonine metabolism - Homo sapiens (human)
- 3-Phosphoglycerate dehydrogenase deficiency
- Non Ketotic Hyperglycinemia
- Glycine and Serine Metabolism
- Dimethylglycine Dehydrogenase Deficiency
Biological Process
- cellular amino acid metabolic process
- biosynthetic process
- L-threonine catabolic process to glycine
Molecular Function
- glycine C-acetyltransferase activity
- pyridoxal phosphate binding
Cellular Component
- nucleoplasm
- mitochondrion
- mitochondrial inner membrane
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000323205
- Coding exons
- 9
- Length
- 9272
- Individuals with no LoFs
- 125501
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 245
- Defined
- 125748
- p
- 0.000983
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.164 | 281 | 273 | 1.03 | 0.0000166 | 2814 |
| Missense (PolyPhen) | 95 | 108.19 | 0.87811 | 1158 | ||
| Synonymous | 1.68 | 92 | 115 | 0.800 | 0.00000693 | 958 |
| Loss of Function | 0.814 | 14 | 17.7 | 0.791 | 8.37e-7 | 205 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0069 | 0.0069 | notable |
| Latino/Admixed American | 0.00061 | 0.00061 | rare |
| Ashkenazi Jewish | 0.00050 | 0.00050 | rare |
| East Asian | 0.0037 | 0.0037 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00023 | 0.00023 | rare |
| South Asian | 0.00020 | 0.00016 | rare |
| Other | 0.0016 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.150
Intolerance Scores
- LoFtool
- 0.0849
- RVIS EVS
- 0.85
- RVIS percentile EVS
- 88.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.996
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |