SLX9

Summary

SLX9 (SLX9 ribosome biogenesis factor, HGNC:15811) is a protein-coding gene on chromosome 21q22.3, encoding Ribosome biogenesis protein SLX9 homolog (Q9NSI2). May be involved in ribosome biogenesis. It is a selective cancer dependency (DepMap: 39.9% of cell lines).

Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleolus. Predicted to be part of 90S preribosome and preribosome, small subunit precursor.

Source: NCBI Gene 85395 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 60 total
• Cancer dependency (DepMap): dependent in 39.9% of screened cell lines
• MANE Select transcript: NM_058190

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15811
Approved symbol	SLX9
Name	SLX9 ribosome biogenesis factor
Location	21q22.3
Locus type	gene with protein product
Status	Approved
Aliases	PRED56
Ensembl gene	ENSG00000160256
Ensembl biotype	protein_coding
Entrez	85395

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000291634, ENST00000397826, ENST00000458015, ENST00000479127, ENST00000485207, ENST00000873999, ENST00000874000, ENST00000874001, ENST00000874002, ENST00000874003, ENST00000874004, ENST00000915546, ENST00000915547, ENST00000943396

RefSeq mRNA: 7 — MANE Select: NM_058190 NM_001316983, NM_001316984, NM_001316985, NM_001316986, NM_001316987, NM_001316988, NM_058190

CCDS: CCDS13718, CCDS82682

Canonical transcript exons

ENST00000291634 — 6 exons

Exon	Start	End
ENSE00001050957	44943684	44943837
ENSE00001878719	44940029	44940186
ENSE00003504383	44973197	44973265
ENSE00003550369	44967034	44967181
ENSE00003668740	44960100	44960168
ENSE00003850908	44976680	44976973

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 97.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.4075 / max 168.7018, expressed in 1807 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
189520	25.5128	1805
189519	0.8947	513

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
popliteal artery	UBERON:0002250	97.37	gold quality
tibial artery	UBERON:0007610	97.37	gold quality
apex of heart	UBERON:0002098	96.28	gold quality
aorta	UBERON:0000947	92.82	gold quality
heart left ventricle	UBERON:0002084	92.75	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.70	gold quality
lower esophagus	UBERON:0013473	92.67	gold quality
left coronary artery	UBERON:0001626	92.13	gold quality
cardiac ventricle	UBERON:0002082	92.13	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	91.65	gold quality
mucosa of stomach	UBERON:0001199	91.63	gold quality
gastrocnemius	UBERON:0001388	91.50	gold quality
muscle layer of sigmoid colon	UBERON:0035805	91.04	gold quality
coronary artery	UBERON:0001621	90.42	gold quality
right coronary artery	UBERON:0001625	90.37	gold quality
muscle of leg	UBERON:0001383	90.10	gold quality
mucosa of transverse colon	UBERON:0004991	89.72	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.46	gold quality
heart	UBERON:0000948	89.09	gold quality
skin of leg	UBERON:0001511	89.07	gold quality
right atrium auricular region	UBERON:0006631	88.75	gold quality
right lobe of liver	UBERON:0001114	88.64	gold quality
left testis	UBERON:0004533	88.63	gold quality
right testis	UBERON:0004534	88.43	gold quality
body of stomach	UBERON:0001161	88.26	gold quality
esophagus	UBERON:0001043	88.22	gold quality
skin of abdomen	UBERON:0001416	87.85	gold quality
right adrenal gland	UBERON:0001233	87.81	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.73	gold quality
left adrenal gland	UBERON:0001234	87.46	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting SLX9, 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-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-4660	97.79	67.44	1328
HSA-MIR-1225-3P	97.29	64.60	876

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 39.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• FAM207A/C21orf70 is a putative trans-acting factor involved in biogenesis of the 40S ribosomal subunit. (PMID:21097556)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	slx9	ENSDARG00000071500
mus_musculus	Slx9	ENSMUSG00000032977
rattus_norvegicus	Slx9	ENSRNOG00000001225

Protein

Protein identifiers

Ribosome biogenesis protein SLX9 homolog — Q9NSI2 (reviewed: Q9NSI2)

All UniProt accessions (2): Q9NSI2, C9JJU7

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in ribosome biogenesis.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Not detected in any tested tissue.

Similarity. Belongs to the SLX9 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NSI2-1	A	yes
Q9NSI2-2	B

RefSeq proteins (7): NP_001303912, NP_001303913, NP_001303914, NP_001303915, NP_001303916, NP_001303917, NP_478070* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028160	Slx9-like	Family

Pfam: PF15341

UniProt features (15 total): helix 3, compositionally biased region 3, region of interest 2, modified residue 2, chain 1, strand 1, turn 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
7WTU	ELECTRON MICROSCOPY	3
7WTT	ELECTRON MICROSCOPY	3.1
7WTS	ELECTRON MICROSCOPY	3.2
7WTW	ELECTRON MICROSCOPY	3.2
7WTV	ELECTRON MICROSCOPY	3.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NSI2-F1	72.55	0.33

Functional residue map

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

Post-translational modifications (2): 34, 203

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, GOBP_RIBOSOME_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, chr21q22, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOCC_90S_PRERIBOSOME, GOCC_PRERIBOSOME, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX, BHAT_ESR1_TARGETS_VIA_AKT1_UP

GO Biological Process (1): maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): nucleolus (GO:0005730), 90S preribosome (GO:0030686), preribosome, small subunit precursor (GO:0030688), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
preribosome	2
maturation of SSU-rRNA	1
binding	1
nuclear lumen	1
intracellular membraneless organelle	1
t-UTP complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

802 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLX9	NOC4L	Q9BVI4	506
SLX9	CCDC71	Q8IV32	491
SLX9	TSPEAR	Q8WU66	482
SLX9	RIOK2	Q9BVS4	480
SLX9	RRP12	Q5JTH9	479
SLX9	LTV1	Q96GA3	478
SLX9	KRTAP12-2	P59991	460
SLX9	PEX39	Q5I0X4	444
SLX9	KRTAP10-8	P60410	440
SLX9	CCDC102A	Q96A19	435
SLX9	BYSL	Q13895	430
SLX9	KRTAP10-2	P60368	419
SLX9	SLF2	Q8IX21	409
SLX9	DENND10	Q8TCE6	395
SLX9	TSR1	Q2NL82	374

IntAct

74 interactions, top by confidence:

A	B	Type	Score
SLX9	GOLGA2	psi-mi:“MI:0915”(physical association)	0.670
GOLGA2	SLX9	psi-mi:“MI:0915”(physical association)	0.670
BYSL	PARN	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
IFT81	NDC80	psi-mi:“MI:0914”(association)	0.640
PICK1	SLX9	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	SLX9	psi-mi:“MI:0915”(physical association)	0.560
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
APLNR	SLC33A1	psi-mi:“MI:0914”(association)	0.530
KRR1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
SLX9	ZDHHC17	psi-mi:“MI:0915”(physical association)	0.370
ZDHHC17	SLX9	psi-mi:“MI:0915”(physical association)	0.370
FOXQ1	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
KSR1	FBLL1	psi-mi:“MI:0914”(association)	0.350
KSR1	DDX39A	psi-mi:“MI:0914”(association)	0.350
KSR1		psi-mi:“MI:0914”(association)	0.350
EZR	MACROD2	psi-mi:“MI:0914”(association)	0.350
FGD1	MECP2	psi-mi:“MI:0914”(association)	0.350
ARHGEF25	ARPC1B	psi-mi:“MI:0914”(association)	0.350
MAST1	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
CASP8	CCN1	psi-mi:“MI:0914”(association)	0.350
BYSL	RPS3A	psi-mi:“MI:0914”(association)	0.350
SLX9	BUD23	psi-mi:“MI:0914”(association)	0.350
RPS11	SCAMP1	psi-mi:“MI:0914”(association)	0.350

BioGRID (227): FAM207A (Two-hybrid), FAM207A (Two-hybrid), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Proximity Label-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS), FAM207A (Affinity Capture-MS)

ESM2 similar proteins: A1A4P4, A1CH36, A2ALW5, A5AAL8, B0BN56, O42911, O70279, P0C2B7, P58468, P83565, Q0CLE8, Q1ECT8, Q290P4, Q2GVC2, Q3SZ86, Q4G0I0, Q4V7Q1, Q5B4U6, Q5BJW9, Q5RFR4, Q5XJW2, Q61733, Q6RUT7, Q753F1, Q7SDU5, Q7SHR9, Q80ZS3, Q86TS9, Q8BGX2, Q8BK72, Q8CHP5, Q8SPE7, Q8TAE8, Q8VD26, Q8WUQ7, Q96AN5, Q96DF8, Q9BRP8, Q9BSF4, Q9BYN8

Diamond homologs: P58468, Q9NSI2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 108 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
SARS-CoV-1 modulates host translation machinery	5	18.2×	7e-04
rRNA processing in the nucleus and cytosol	8	15.1×	3e-05
SARS-CoV-1-host interactions	7	14.5×	1e-04
rRNA processing	8	13.8×	3e-05
SARS-CoV-1 Infection	6	10.1×	2e-03
Cellular response to starvation	5	9.7×	9e-03
Major pathway of rRNA processing in the nucleolus and cytosol	10	7.3×	2e-04
Metabolism of RNA	11	5.4×	7e-04

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal small subunit biogenesis	7	16.3×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2738 predictions. Top by Δscore:

Variant	Effect	Δscore
21:44960167:GA:G	donor_gain	1.0000
21:44960169:G:GG	donor_gain	1.0000
21:44967030:TTAG:T	acceptor_loss	1.0000
21:44967031:TAGA:T	acceptor_loss	1.0000
21:44967032:A:AG	acceptor_gain	1.0000
21:44967032:A:AT	acceptor_loss	1.0000
21:44967033:G:GG	acceptor_gain	1.0000
21:44967033:G:GT	acceptor_loss	1.0000
21:44967033:GA:G	acceptor_gain	1.0000
21:44967033:GAA:G	acceptor_gain	1.0000
21:44967180:AGG:A	donor_loss	1.0000
21:44967182:GTGA:G	donor_loss	1.0000
21:44973266:G:GG	donor_gain	1.0000
21:44976678:A:AG	acceptor_gain	1.0000
21:44976679:G:GG	acceptor_gain	1.0000
21:44976679:GC:G	acceptor_gain	1.0000
21:44976679:GCGA:G	acceptor_gain	1.0000
21:44940184:AAG:A	donor_loss	0.9900
21:44940185:AGG:A	donor_loss	0.9900
21:44940186:GGT:G	donor_loss	0.9900
21:44940188:T:A	donor_loss	0.9900
21:44943672:T:TA	acceptor_gain	0.9900
21:44943673:G:A	acceptor_gain	0.9900
21:44960095:CTCA:C	acceptor_loss	0.9900
21:44960096:TCAG:T	acceptor_loss	0.9900
21:44960098:A:AT	acceptor_loss	0.9900
21:44960162:TTGCA:T	donor_gain	0.9900
21:44961187:GGCT:G	donor_gain	0.9900
21:44961188:GCTG:G	donor_gain	0.9900
21:44967033:GAAA:G	acceptor_gain	0.9900

AlphaMissense

1478 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:44943711:T:C	F53L	0.986
21:44943713:T:A	F53L	0.986
21:44943713:T:G	F53L	0.986
21:44960149:G:C	R111S	0.986
21:44960149:G:T	R111S	0.986
21:44960159:T:A	W115R	0.982
21:44960159:T:C	W115R	0.982
21:44960128:G:C	K104N	0.978
21:44960128:G:T	K104N	0.978
21:44960148:G:C	R111T	0.977
21:44976699:T:C	F197L	0.976
21:44976701:T:A	F197L	0.976
21:44976701:T:G	F197L	0.976
21:44967121:T:A	L147H	0.975
21:44940061:G:A	G2R	0.973
21:44940061:G:C	G2R	0.973
21:44976700:T:C	F197S	0.973
21:44960160:G:C	W115S	0.971
21:44960161:G:C	W115C	0.971
21:44960161:G:T	W115C	0.971
21:44967034:A:T	K118I	0.968
21:44943727:T:A	I58K	0.967
21:44940091:C:G	H12D	0.966
21:44960151:G:C	R112P	0.966
21:44943712:T:C	F53S	0.965
21:44940101:C:A	A15D	0.964
21:44943712:T:G	F53C	0.964
21:44940071:G:T	R5M	0.962
21:44976751:T:A	I214N	0.962
21:44940061:G:T	G2W	0.961

dbSNP variants (sampled 300 via entrez): RS1000072434 (21:44959698 G>A), RS1000146787 (21:44939340 A>C,G), RS1000181678 (21:44957955 G>C), RS1000298841 (21:44955651 C>T), RS1000337633 (21:44951678 A>C,T), RS1000355878 (21:44962391 T>C), RS1000382721 (21:44971971 A>G), RS1000387360 (21:44938670 C>T), RS1000427190 (21:44967680 C>T), RS1000473428 (21:44951492 C>T), RS1000566694 (21:44959046 C>G), RS1000584152 (21:44963918 C>T), RS1000650725 (21:44962663 C>T), RS1000707603 (21:44968256 C>T), RS1000765341 (21:44938135 T>C)

Disease associations

OMIM: gene `` | 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

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
TAK-243	increases sumoylation	1
bisphenol A	decreases methylation	1
butyraldehyde	increases expression	1
zinc chromate	decreases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
aflatoxin B2	increases methylation	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
chromium hexavalent ion	decreases expression, increases abundance	1
abrine	decreases expression	1
jinfukang	increases expression	1
Caffeine	decreases phosphorylation	1
Methapyrilene	increases methylation	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Lactic Acid	decreases expression	1
Vitamin K 3	affects expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B3HM	Abcam HEK293T SLX9 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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