SATL1

spermidine/spermine N1-acetyl transferase like 1, the group of GCN5 related N-acetyltransferases

Basic information

Region (hg38): X:85092284-85243911

Links

ENSG00000184788 ∙ NCBI:340562 ∙ ∙ HGNC:27992 ∙ Uniprot:Q86VE3 ∙ 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 SATL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SATL1 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				3	2	5
missense			30	3	2	35
nonsense				2	1	3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	30	8	5

Variants in SATL1

This is a list of pathogenic ClinVar variants found in the SATL1 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-85094152-A-G		not specified	Uncertain significance (Jan 27, 2022)
X-85094928-G-A		SATL1-related disorder	Likely benign (Jul 01, 2019)
X-85094935-G-A		SATL1-related disorder	Benign (Jan 20, 2020)
X-85094947-A-C		not specified	Uncertain significance (Jan 16, 2024)
X-85094987-C-G		not specified	Uncertain significance (Mar 20, 2023)
X-85095004-A-G		SATL1-related disorder	Benign (Oct 16, 2019)
X-85103858-C-T		SATL1-related disorder	Benign (Oct 16, 2019)
X-85103876-A-T		not specified	Uncertain significance (May 03, 2023)
X-85103880-C-T		not specified	Uncertain significance (Sep 26, 2023)
X-85107369-C-T		not specified	Uncertain significance (Jun 05, 2023)
X-85107525-A-G		not specified	Uncertain significance (Jun 13, 2024)
X-85107541-C-T		SATL1-related disorder	Benign (Jun 07, 2019)
X-85107555-T-A		SATL1-related disorder	Benign (Jul 11, 2019)
X-85107556-C-T		not specified	Uncertain significance (Nov 21, 2022)
X-85107561-C-T		not specified	Uncertain significance (Oct 26, 2021)
X-85107620-A-G		not specified	Uncertain significance (Jun 17, 2024)
X-85107624-G-C		not specified	Uncertain significance (Oct 12, 2021)
X-85107644-C-T		SATL1-related disorder	Benign (Nov 07, 2019)
X-85107812-A-G		not specified	Uncertain significance (Sep 22, 2022)
X-85107872-G-A		not specified	Uncertain significance (Jul 05, 2023)
X-85107884-C-T		not specified	Uncertain significance (Aug 02, 2021)
X-85107898-G-C		not specified	Uncertain significance (May 08, 2023)
X-85107918-G-C		not specified	Uncertain significance (Feb 21, 2024)
X-85108040-T-A		SATL1-related disorder	Likely benign (Aug 08, 2019)
X-85108062-G-A		SATL1-related disorder	Likely benign (May 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SATL1	protein_coding	protein_coding	ENST00000509231	5	16762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.00e-20	0.000407	125611	70	48	125729	0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.171	239	232	1.03	0.0000160	4234
Missense in Polyphen		55	50.394	1.0914		935
Synonymous	0.0944	83	84.1	0.987	0.00000636	1133
Loss of Function	-0.848	27	22.6	1.19	0.00000170	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000684	0.000577
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000261	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00608	0.00344
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 1.57
• rvis_percentile_EVS: 95.74

Haploinsufficiency Scores

• pHI: 0.0565
• hipred: N
• hipred_score: 0.123
• ghis: 0.387

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0180

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Satl1

Gene ontology

• Biological process: spermidine acetylation
• Cellular component: cytosol
• Molecular function: diamine N-acetyltransferase activity;N-acetyltransferase activity;spermidine binding