SAT2

spermidine/spermine N1-acetyltransferase family member 2, the group of GCN5 related N-acetyltransferases

Basic information

Region (hg38): 17:7626233-7627876

Links

ENSG00000141504 ∙ NCBI:112483 ∙ OMIM:611463 ∙ HGNC:23160 ∙ Uniprot:Q96F10 ∙ 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 SAT2 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAT2 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						0
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in SAT2

This is a list of pathogenic ClinVar variants found in the SAT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-7626488-A-C		not specified	Uncertain significance (Dec 19, 2022)
17-7626549-C-T		not specified	Likely benign (Aug 16, 2022)
17-7626764-T-G		not specified	Uncertain significance (Mar 23, 2022)
17-7626945-C-G		not specified	Uncertain significance (Jan 09, 2024)
17-7627198-A-T		not specified	Uncertain significance (Oct 26, 2021)
17-7627571-C-A		not specified	Uncertain significance (Nov 15, 2023)
17-7627574-A-C		not specified	Uncertain significance (Aug 02, 2022)
17-7627610-G-T		not specified	Uncertain significance (Dec 02, 2021)
17-7627611-C-T		not specified	Uncertain significance (Jan 31, 2023)
17-7627623-G-A		not specified	Uncertain significance (Sep 29, 2023)
17-7627626-C-T		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAT2	protein_coding	protein_coding	ENST00000269298	6	1643

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000278	0.327	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.469	84	97.0	0.866	0.00000494	1095
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000594	0.000594
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enzyme which catalyzes the acetylation of polyamines. Substrate specificity: norspermidine > spermidine = spermine >> N(1)acetylspermine = putrescine.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);Ferroptosis - Homo sapiens (human);spermine and spermidine degradation I;putrescine degradation III (Consensus)

Recessive Scores

• pRec: 0.0994

Intolerance Scores

• loftool: 0.635
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.0827
• hipred: N
• hipred_score: 0.457
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000543

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sat2

Gene ontology

• Biological process: putrescine catabolic process;spermidine acetylation;spermine acetylation;putrescine acetylation;nor-spermidine metabolic process
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: diamine N-acetyltransferase activity;protein binding;N-acetyltransferase activity;spermidine binding;identical protein binding