GLYATL2
protein-codingglycine-N-acyltransferase like 2
Gene summary
Enables glycine N-acyltransferase activity. Involved in long-chain fatty acid catabolic process; medium-chain fatty acid catabolic process; and monounsaturated fatty acid catabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~70.2 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 GLYATL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145016.4. 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 | 0 | |||||
| missense | 57 | 4 | 61 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 57 | 4 | 0 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_659453.3 | 5 | MANE Select | |
| Ensembl | ENSP00000287275.1 | 5 | MANE Select | |
| Ensembl | ENSP00000434277.1 | 5 | Standard | |
| Ensembl | ENSP00000434277.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Amino acid conjugation of benzoic acid
- Metapathway biotransformation Phase I and II
- Conjugation of benzoate with glycine
- Conjugation of salicylate with glycine
- Conjugation of carboxylic acids
Biological Process
- long-chain fatty acid catabolic process
- medium-chain fatty acid catabolic process
- monounsaturated fatty acid catabolic process
Molecular Function
- glycine N-acyltransferase activity
Cellular Component
- mitochondrion
- endoplasmic reticulum
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000287275
- Coding exons
- 5
- Length
- 70147
- Individuals with no LoFs
- 124733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 45
- Defined
- 124778
- p
- 0.000180
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.467 | 165 | 149 | 1.11 | 0.00000694 | 1959 |
| Missense (PolyPhen) | 41 | 40.519 | 1.0119 | 557 | ||
| Synonymous | 1.26 | 42 | 53.7 | 0.782 | 0.00000256 | 495 |
| Loss of Function | 0.0849 | 9 | 9.28 | 0.970 | 3.91e-7 | 119 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00088 | 0.00087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000071 | 0.000071 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00050 | 0.00050 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mitochondrial acyltransferase which transfers the acyl group to the N-terminus of glycine. Conjugates numerous substrates, such as arachidonoyl-CoA and saturated medium and long-chain acyl-CoAs ranging from chain-length C8:0-CoA to C18:0- CoA, to form a variety of N-acylglycines. Shows a preference for monounsaturated fatty acid oleoyl-CoA (C18:1-CoA) as an acyl donor. Does not exhibit any activity toward C22:6-CoA and chenodeoxycholoyl-CoA, nor toward serine or alanine. {ECO:0000269|PubMed:20305126}.;
Intolerance Scores
- LoFtool
- 0.903
- RVIS EVS
- 0.95
- RVIS percentile EVS
- 90.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.177
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |