SATL1

Summary

SATL1 (spermidine/spermine N1-acetyl transferase like 1, HGNC:27992) is a protein-coding gene on chromosome Xq21.1, encoding Spermidine/spermine N(1)-acetyltransferase-like protein 1 (Q86VE3).

Predicted to enable spermidine binding activity. Predicted to be involved in spermidine acetylation.

Source: NCBI Gene 340562 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 111 total — 1 pathogenic
• MANE Select transcript: NM_001367857

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27992
Approved symbol	SATL1
Name	spermidine/spermine N1-acetyl transferase like 1
Location	Xq21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184788
Ensembl biotype	protein_coding
OMIM	301129
Entrez	340562

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000509231, ENST00000644105, ENST00000646118, ENST00000646235, ENST00000647304

RefSeq mRNA: 3 — MANE Select: NM_001367857 NM_001012980, NM_001367857, NM_001367858

CCDS: CCDS35343, CCDS94637, CCDS94638

Canonical transcript exons

ENST00000644105 — 8 exons

Exon	Start	End
ENSE00001318427	85094128	85094229
ENSE00001321490	85094916	85094996
ENSE00001332452	85103864	85103915
ENSE00001600301	85093185	85093225
ENSE00003821301	85092284	85092561
ENSE00003821692	85224205	85224326
ENSE00003825706	85107328	85109280
ENSE00003826987	85243588	85243779

Expression profiles

Bgee: expression breadth broad, 46 present calls, max score 79.62.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2788 / max 19.0966, expressed in 149 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199864	0.2788	149

Top tissues by expression

130 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.89	gold quality
ventricular zone	UBERON:0003053	65.04	gold quality
cortical plate	UBERON:0005343	62.86	gold quality
superior frontal gyrus	UBERON:0002661	59.13	gold quality
prefrontal cortex	UBERON:0000451	58.97	gold quality
ganglionic eminence	UBERON:0004023	57.91	gold quality
right adrenal gland cortex	UBERON:0035827	57.61	gold quality
right adrenal gland	UBERON:0001233	57.16	gold quality
frontal cortex	UBERON:0001870	56.60	gold quality
left adrenal gland cortex	UBERON:0035825	55.02	gold quality
left adrenal gland	UBERON:0001234	54.94	gold quality
adrenal gland	UBERON:0002369	54.19	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	53.60	gold quality
Brodmann (1909) area 9	UBERON:0013540	53.58	gold quality
cerebral cortex	UBERON:0000956	53.57	gold quality
right frontal lobe	UBERON:0002810	52.54	gold quality
primary visual cortex	UBERON:0002436	52.00	gold quality
adrenal tissue	UBERON:0018303	51.52	gold quality
anterior cingulate cortex	UBERON:0009835	51.41	gold quality
sural nerve	UBERON:0015488	50.11	gold quality
putamen	UBERON:0001874	49.94	gold quality
brain	UBERON:0000955	49.58	gold quality
testis	UBERON:0000473	48.98	gold quality
hypothalamus	UBERON:0001898	48.58	gold quality
nucleus accumbens	UBERON:0001882	48.29	gold quality
caudate nucleus	UBERON:0001873	48.00	gold quality
temporal lobe	UBERON:0001871	47.81	gold quality
amygdala	UBERON:0001876	47.77	gold quality
cerebellum	UBERON:0002037	46.88	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-81547	yes	95.23
E-MTAB-5061	yes	15.54
E-ANND-3	yes	4.55
E-MTAB-10137	no	33.12
E-GEOD-99795	no	13.81
E-ENAD-27	no	4.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting SATL1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-5193	100.00	67.26	1744
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-1244	99.33	68.38	832
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-6877-3P	98.98	65.83	560
HSA-MIR-6819-3P	98.95	65.57	572
HSA-MIR-218-1-3P	98.63	67.97	832
HSA-MIR-5187-5P	98.54	67.94	952
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-6847-5P	97.93	66.74	1808
HSA-MIR-6728-5P	97.79	66.33	891
HSA-MIR-665	97.60	65.64	1781
HSA-MIR-6500-3P	97.42	67.20	867
HSA-MIR-125A-3P	97.04	66.92	902
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-4703-3P	96.68	68.61	545
HSA-MIR-4749-3P	96.40	66.24	798
HSA-MIR-1298-5P	95.96	64.81	573
HSA-MIR-6769A-3P	94.91	61.36	412
HSA-MIR-764	94.16	64.85	656
HSA-MIR-6795-3P	91.86	63.00	218

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Satl1	ENSMUSG00000025527
rattus_norvegicus	Satl1	ENSRNOG00000022476
drosophila_melanogaster	CG4210	FBGN0038302
caenorhabditis_elegans		WBGENE00008408

Paralogs (2): SAT1 (ENSG00000130066), SAT2 (ENSG00000141504)

Protein

Protein identifiers

Spermidine/spermine N(1)-acetyltransferase-like protein 1 — Q86VE3 (reviewed: Q86VE3)

All UniProt accessions (2): Q86VE3, A0A2R8YFQ0

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the acetyltransferase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86VE3-1	1	yes
Q86VE3-2	2

RefSeq proteins (3): NP_001012998, NP_001354786, NP_001354787 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000182	GNAT_dom	Domain
IPR016181	Acyl_CoA_acyltransferase	Homologous_superfamily
IPR051016	Diverse_Substrate_AcTransf	Family

Pfam: PF00583

UniProt features (28 total): compositionally biased region 11, binding site 5, region of interest 4, sequence conflict 3, splice variant 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86VE3-F1	48.65	0.23

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (5): 552–553; 618–620; 626–631; 650–652; 676

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, GOBP_POLYAMINE_METABOLIC_PROCESS, GOMF_ACETYLTRANSFERASE_ACTIVITY, GOMF_AMINE_BINDING, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_N_ACYLTRANSFERASE_ACTIVITY, GOMF_N_ACETYLTRANSFERASE_ACTIVITY, STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP, chrXq21, GOBP_SPERMIDINE_METABOLIC_PROCESS, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP, MIR1244, MIR6728_5P, MIR4703_3P, DESCARTES_MAIN_FETAL_SLC26A4_PAEP_POSITIVE_CELLS

GO Biological Process (1): obsolete spermidine acetylation (GO:0032918)

GO Molecular Function (5): diamine N-acetyltransferase activity (GO:0004145), spermidine binding (GO:0019809), transferase activity (GO:0016740), acyltransferase activity (GO:0016746), acyltransferase activity, transferring groups other than amino-acyl groups (GO:0016747)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
N-acetyltransferase activity	1
polyamine binding	1
cation binding	1
catalytic activity	1
transferase activity	1
acyltransferase activity	1

Protein interactions and networks

STRING

550 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SATL1	POF1B	Q8WVV4	627
SATL1	APOOL	Q6UXV4	613
SATL1	SMCO3	A2RU48	608
SATL1	ZNF711	Q9Y462	601
SATL1	FAM47B	Q8NA70	594
SATL1	KLHL4	Q9C0H6	590
SATL1	DACH2	Q96NX9	590
SATL1	CPXCR1	Q8N123	583
SATL1	CYLC1	P35663	578
SATL1	OR1J4	Q8NGS1	544
SATL1	MAP7D3	Q8IWC1	517
SATL1	ARSF	P54793	504
SATL1	RPS6KA6	Q9UK32	495
SATL1	OR13A1	Q8NGR1	488
SATL1	C8orf74	Q6P047	479

IntAct

0 interactions, top by confidence:

BioGRID (2): SATL1 (Affinity Capture-MS), SATL1 (Synthetic Lethality)

ESM2 similar proteins: A0A087WUL8, A0A0J9YWL9, A0A0J9YY54, A0A0U1RQI7, A6NJ88, A6QL64, B4DH59, D3ZVV1, E9Q6E9, F1LWT0, O04492, O88799, P0DKJ7, P0DKJ8, P0DKL2, P0DPF3, P18583, P53353, Q08AG5, Q0P6D6, Q2EG98, Q3BBV2, Q4ZJZ1, Q5HY64, Q5JPF3, Q5QGU6, Q5TAG4, Q5TI25, Q5XHX6, Q6P3W6, Q6P902, Q6XPR3, Q6ZQX7, Q86T75, Q86VE3, Q86VQ3, Q8N2N9, Q8N660, Q8N693, Q96EQ9

Diamond homologs: P21673, P48026, P49431, Q01612, Q28999, Q3T0Q0, Q6P8J2, Q7PCJ8, Q7PCJ9, Q86VE3, Q8AXL1, Q96F10, Q9D5N8, Q9JHW6, D4FZ53, P39909, Q9ZV05, E3Q1H1, O17731, P08457, P79081, Q58604, O05517, O29729, P63423, P63424, Q57LQ8, Q5PI26, P43577, Q2NS89, Q9ZV06, Q44245

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

111 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	72
Likely benign	13
Benign	7

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4683035	GRCh37/hg19 Xq13.1-22.2(chrX:70460290-103312921)x3	Pathogenic

SpliceAI

716 predictions. Top by Δscore:

Variant	Effect	Δscore
X:85092558:CTAT:C	acceptor_gain	1.0000
X:85092559:TAT:T	acceptor_gain	1.0000
X:85092562:C:CC	acceptor_gain	1.0000
X:85092563:T:A	acceptor_loss	1.0000
X:85094126:A:C	donor_loss	1.0000
X:85094226:TTGC:T	acceptor_gain	1.0000
X:85094227:TGC:T	acceptor_gain	1.0000
X:85094227:TGCC:T	acceptor_loss	1.0000
X:85094228:GCC:G	acceptor_loss	1.0000
X:85094230:C:A	acceptor_loss	1.0000
X:85094230:C:CC	acceptor_gain	1.0000
X:85094231:T:G	acceptor_loss	1.0000
X:85092560:AT:A	acceptor_gain	0.9900
X:85094225:TTTGC:T	acceptor_gain	0.9900
X:85094228:GC:G	acceptor_gain	0.9900
X:85094229:CC:C	acceptor_gain	0.9900
X:85093182:TAC:T	donor_loss	0.9800
X:85093183:AC:A	donor_loss	0.9800
X:85093227:T:C	acceptor_gain	0.9800
X:85094128:C:G	donor_loss	0.9800
X:85094910:CTCTA:C	donor_loss	0.9800
X:85094911:TCTA:T	donor_loss	0.9800
X:85094912:CTACC:C	donor_loss	0.9800
X:85094913:TACCT:T	donor_loss	0.9800
X:85094914:ACCTG:A	donor_loss	0.9800
X:85094915:C:A	donor_loss	0.9800
X:85092512:C:CT	acceptor_gain	0.9700
X:85093225:CCTTT:C	acceptor_gain	0.9700
X:85094916:C:A	donor_loss	0.9700
X:85092507:GGTTC:G	acceptor_gain	0.9600

AlphaMissense

4683 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:85094210:A:C	F598L	0.989
X:85094210:A:T	F598L	0.989
X:85094212:A:G	F598L	0.989
X:85094977:A:C	F571L	0.986
X:85094977:A:T	F571L	0.986
X:85094979:A:G	F571L	0.986
X:85094959:G:C	F577L	0.985
X:85094959:G:T	F577L	0.985
X:85094961:A:G	F577L	0.985
X:85093188:A:C	S638R	0.983
X:85093188:A:T	S638R	0.983
X:85093190:T:G	S638R	0.983
X:85094993:A:G	L566S	0.982
X:85094946:C:G	A582P	0.977
X:85094951:A:G	L580P	0.977
X:85092557:G:T	A641D	0.976
X:85094208:G:T	A599D	0.976
X:85094214:C:T	G597E	0.975
X:85094209:C:G	A599P	0.973
X:85094953:G:C	C579W	0.973
X:85094211:A:G	F598S	0.972
X:85094955:A:G	C579R	0.972
X:85092436:G:C	F681L	0.968
X:85092436:G:T	F681L	0.968
X:85092438:A:G	F681L	0.968
X:85092558:C:G	A641P	0.968
X:85092437:A:G	F681S	0.967
X:85092431:A:G	F683S	0.966
X:85094203:A:C	Y601D	0.964
X:85094945:G:T	A582E	0.964

dbSNP variants (sampled 300 via entrez): RS1000001190 (X:85146041 C>A,T), RS1000048388 (X:85109783 T>G), RS1000048793 (X:85203746 T>C), RS1000058886 (X:85179478 T>C), RS1000134278 (X:85171538 T>A,G), RS1000191073 (X:85138135 C>G), RS1000195782 (X:85117634 A>G), RS1000231643 (X:85133043 G>A), RS1000244481 (X:85143110 T>A,C), RS1000250499 (X:85219531 C>A), RS1000274751 (X:85112037 G>C), RS1000307056 (X:85209660 T>A), RS1000331072 (X:85123471 T>C), RS1000363024 (X:85190078 T>C), RS1000377310 (X:85163865 C>T)

Disease associations

OMIM: gene MIM:301129 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
hydroxyhydroquinone	decreases expression	1
jinfukang	decreases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.