SATL1

protein-coding

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

Gene summary

Predicted to enable diamine N-acetyltransferase activity and spermidine binding activity. Predicted to be involved in spermidine acetylation. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001367857.2

Inheritance

—

ClinVar variants

U:93B:18

Top phenotype

SATL1-related disorder

gnomAD constraint

pLI —, LoF o/e 1.19

Max pathogenic AF

—

Genomic locus

chrX:85,092,284-85,243,911

External References & Databases

Ensembl (ENSG00000184788)

Transcript & Mutation Effects

hg38 • Region Span ~151.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SATL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 80

SATL1-related disorderTotal: 9

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367857.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	3 clinvar	1 clinvar	9
missense			80 clinvar	10 clinvar	1 clinvar	91
nonsense			4 clinvar	2 clinvar	1 clinvar	7
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	93	15	3	111

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367857.2	RefSeq	NP_001354786.1	6	MANE Select
ENST00000644105.2	Ensembl	ENSP00000494345.1	6	MANE Select
NM_001012980.2	RefSeq	NP_001012998.2	5	Standard
NM_001367858.2	RefSeq	NP_001354787.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermidine acetylation

Molecular Function

diamine N-acetyltransferase activity
N-acetyltransferase activity
spermidine binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000509231
Coding exons: 5
Length: 16762
Individuals with no LoFs: 125611
Homozygous LoFs: 70
Heterozygous LoFs: 48
Defined: 125729
p: 0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.171	239	232	1.03	0.0000160	4234
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00054	0.00043	rare
Latino/Admixed American	0.00015	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000018	rare
South Asian	0.0061	0.0034	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.932
RVIS EVS: 1.57
RVIS percentile EVS: 95.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0180

Gene Damage Prediction

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