SAT1
spermidine/spermine N1-acetyltransferase 1, the group of GCN5 related N-acetyltransferases
Basic information
Region (hg38): X:23783172-23786210
Previous symbols: [ "SAT" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAT1 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 1 | 1 |
Variants in SAT1
This is a list of pathogenic ClinVar variants found in the SAT1 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-23783890-C-T | Benign (May 07, 2018) | |||
| X-23785703-C-G | Likely benign (Jul 21, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SAT1 | protein_coding | protein_coding | ENST00000379270 | 6 | 3054 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.871 | 0.128 | 125713 | 0 | 1 | 125714 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.71 | 25 | 63.1 | 0.396 | 0.00000443 | 1137 |
| Missense in Polyphen | 4 | 16.583 | 0.24121 | 298 | ||
| Synonymous | -2.17 | 37 | 23.6 | 1.57 | 0.00000179 | 293 |
| Loss of Function | 2.40 | 0 | 6.68 | 0.00 | 4.22e-7 | 132 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000760 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Enzyme which catalyzes the acetylation of polyamines. Substrate specificity: norspermidine = spermidine >> spermine > N(1)-acetylspermine > putrescine. This highly regulated enzyme allows a fine attenuation of the intracellular concentration of polyamines. Also involved in the regulation of polyamine transport out of cells. Acts on 1,3-diaminopropane, 1,5-diaminopentane, putrescine, spermidine (forming N(1)- and N(8)-acetylspermidine), spermine, N(1)-acetylspermidine and N(8)-acetylspermidine. {ECO:0000269|PubMed:16455797, ECO:0000269|PubMed:17516632}.;
- Disease
- DISEASE: Keratosis follicularis spinulosa decalvans X-linked (KFSDX) [MIM:308800]: A rare disorder affecting the skin and the eye. Affected men show thickening of the skin of the neck, ears, and extremities, especially the palms and soles, loss of eyebrows, eyelashes and beard, thickening of the eyelids with blepharitis and ectropion, and corneal degeneration. {ECO:0000269|PubMed:12215835, ECO:0000269|PubMed:9341865}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
- Pathway
- Arginine and proline metabolism - Homo sapiens (human);Ferroptosis - Homo sapiens (human);NOTCH1 regulation of human endothelial cell calcification;Nucleotide Metabolism;Interconversion of polyamines;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Arginine Proline metabolism;spermine and spermidine degradation I;Alpha9 beta1 integrin signaling events;putrescine degradation III
(Consensus)
Recessive Scores
- pRec
- 0.0945
Intolerance Scores
- loftool
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.0686
- hipred
- Y
- hipred_score
- 0.543
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.969
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sat1
- Phenotype
- normal phenotype; reproductive system phenotype; neoplasm; liver/biliary system phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- sat1b
- Affected structure
- intersegmental vessel
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- angiogenesis;polyamine biosynthetic process;putrescine catabolic process;spermidine acetylation;regulation of cell population proliferation
- Cellular component
- cytosol
- Molecular function
- diamine N-acetyltransferase activity;protein binding;N-acetyltransferase activity;spermidine binding;identical protein binding