SAT2
protein-codingspermidine/spermine N1-acetyltransferase family member 2, the group of GCN5 related N-acetyltransferases
Gene summary
Enables diamine N-acetyltransferase activity and identical protein binding activity. Involved in polyamine metabolic process. Located in extracellular exosome. [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 ~1.6 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 SAT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_133491.5. 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 | 18 | 3 | 21 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 20 | 3 | 0 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_597998.1 | 6 | MANE Select | |
| Ensembl | ENSP00000269298.5 | 6 | MANE Select | |
| RefSeq | NP_001307774.1 | 6 | Standard | |
| RefSeq | NP_001307775.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Arginine and proline metabolism - Homo sapiens (human)
- Ferroptosis - Homo sapiens (human)
- spermine and spermidine degradation I
- putrescine degradation III
Biological Process
- putrescine catabolic process
- spermidine acetylation
- spermine acetylation
- putrescine acetylation
- nor-spermidine metabolic process
Molecular Function
- diamine N-acetyltransferase activity
- protein binding
- N-acetyltransferase activity
- spermidine binding
- identical protein binding
Cellular Component
- cytoplasm
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000269298
- Coding exons
- 6
- Length
- 1643
- Individuals with no LoFs
- 125720
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 28
- Defined
- 125748
- p
- 0.000111
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.469 | 84 | 97.0 | 0.866 | 0.00000494 | 1095 |
| Missense (PolyPhen) | 24 | 27.894 | 0.86039 | 289 | ||
| Synonymous | 0.510 | 33 | 36.9 | 0.893 | 0.00000190 | 318 |
| Loss of Function | 0.300 | 9 | 10.0 | 0.898 | 4.27e-7 | 122 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000079 | 0.000079 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Enzyme which catalyzes the acetylation of polyamines. Substrate specificity: norspermidine > spermidine = spermine >> N(1)acetylspermine = putrescine.;
Recessive Scores
- pRec
- 0.0994
Intolerance Scores
- LoFtool
- 0.635
- RVIS EVS
- 0.28
- RVIS percentile EVS
- 71.08
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0000543
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |