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GeneBe

SAT1

spermidine/spermine N1-acetyltransferase 1, the group of GCN5 related N-acetyltransferases

Basic information

Region (hg38): X:23783172-23786210

Previous symbols: [ "SAT" ]

Links

ENSG00000130066NCBI:6303OMIM:313020HGNC:10540Uniprot:P21673AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAT1 gene.

  • 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.

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
clinvar
1
missense
0
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 0 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-23783386-C-A not specified Uncertain significance (Nov 16, 2022)3157918
X-23783890-C-T Benign (May 07, 2018)747117
X-23785703-C-G Likely benign (Jul 21, 2018)713838
X-23785725-G-A not specified Uncertain significance (Jan 03, 2024)3157919

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAT1protein_codingprotein_codingENST00000379270 63054
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8710.128125713011257140.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.712563.10.3960.000004431137
Missense in Polyphen416.5830.24121298
Synonymous-2.173723.61.570.00000179293
Loss of Function2.4006.680.004.22e-7132

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00007600.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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