SAT1

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

Basic information

Region (hg38): X:23783172-23786210

Previous symbols: [ "SAT" ]

Links

ENSG00000130066

∙ NCBI:6303 ∙ OMIM:313020 ∙ HGNC:10540 ∙ Uniprot:P21673 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			2 clinvar			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	Phenotype	Significance	ClinVar
X-23783385-G-A		Likely benign (Jun 01, 2024)	3250627
X-23783386-C-A	not specified	Conflicting classifications of pathogenicity (Jun 01, 2024)	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

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: 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

	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