SAT1
Basic information
Region (hg38): X:23783172-23786210
Previous symbols: [ "SAT" ]
Links
Phenotypes
GenCC
Source:
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 SAT1 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 | 1 | |||||
missense | 2 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 1 | 1 | ||||
non coding ? | 0 | |||||
Total | 0 | 0 | 2 | 1 | 0 |
Variants in SAT1
This is a list of pathogenic ClinVar variants found in the SAT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-23783385-G-A | Likely benign (Jun 01, 2024) | |||
X-23783386-C-A | not specified | Conflicting classifications of pathogenicity (Jun 01, 2024) | ||
X-23783890-C-T | Benign (May 07, 2018) | |||
X-23785703-C-G | Likely benign (Jul 21, 2018) | |||
X-23785725-G-A | not specified | Uncertain significance (Jan 03, 2024) |
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