FSAF1

Summary

FSAF1 (40S small subunit processome assembly factor 1, HGNC:25332) is a protein-coding gene on chromosome 1q42.2, encoding 40S small subunit processome assembly factor 1 (Q8NDD1). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. It is a selective cancer dependency (DepMap: 77.6% of cell lines).

Enables RNA binding activity. Involved in ribosomal small subunit biogenesis. Located in chromosome. Part of small-subunit processome.

Source: NCBI Gene 128061 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 19 total
• Cancer dependency (DepMap): dependent in 77.6% of screened cell lines
• MANE Select transcript: NM_152379

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25332
Approved symbol	FSAF1
Name	40S small subunit processome assembly factor 1
Location	1q42.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp547B1713
Ensembl gene	ENSG00000143633
Ensembl biotype	protein_coding
Entrez	128061

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000318906, ENST00000366649, ENST00000366651, ENST00000451322, ENST00000462669, ENST00000471936, ENST00000486384, ENST00000495795, ENST00000925188

RefSeq mRNA: 2 — MANE Select: NM_152379 NM_001300830, NM_152379

CCDS: CCDS1591, CCDS73049

Canonical transcript exons

ENST00000366649 — 7 exons

Exon	Start	End
ENSE00001070058	231238857	231239188
ENSE00001442252	231225471	231225523
ENSE00001952878	231241024	231241175
ENSE00003474360	231229150	231229209
ENSE00003659670	231226973	231227068
ENSE00003676600	231226739	231226825
ENSE00003848472	231223765	231224414

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 95.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.3195 / max 243.7578, expressed in 1780 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
17976	10.6208	1769
17974	0.5347	214
17975	0.1641	78

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	95.18	gold quality
secondary oocyte	CL:0000655	93.96	gold quality
tibia	UBERON:0000979	92.05	gold quality
oocyte	CL:0000023	91.59	gold quality
duodenum	UBERON:0002114	90.45	gold quality
mucosa of transverse colon	UBERON:0004991	89.94	gold quality
epithelial cell of pancreas	CL:0000083	89.83	gold quality
jejunal mucosa	UBERON:0000399	89.34	gold quality
rectum	UBERON:0001052	89.02	gold quality
parietal pleura	UBERON:0002400	88.29	gold quality
endothelial cell	CL:0000115	87.54	gold quality
germinal epithelium of ovary	UBERON:0001304	87.46	gold quality
colonic mucosa	UBERON:0000317	87.39	gold quality
tibialis anterior	UBERON:0001385	87.36	silver quality
palpebral conjunctiva	UBERON:0001812	87.24	gold quality
small intestine Peyer’s patch	UBERON:0003454	87.22	gold quality
right uterine tube	UBERON:0001302	87.06	gold quality
minor salivary gland	UBERON:0001830	86.98	gold quality
monocyte	CL:0000576	86.86	gold quality
pancreatic ductal cell	CL:0002079	86.82	gold quality
leukocyte	CL:0000738	86.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.72	gold quality
small intestine	UBERON:0002108	86.66	gold quality
calcaneal tendon	UBERON:0003701	86.65	gold quality
upper arm skin	UBERON:0004263	86.55	silver quality
right lobe of liver	UBERON:0001114	86.54	gold quality
granulocyte	CL:0000094	86.38	gold quality
right adrenal gland cortex	UBERON:0035827	86.38	gold quality
transverse colon	UBERON:0001157	86.31	gold quality
body of pancreas	UBERON:0001150	86.27	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.83
E-GEOD-100618	no	163.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting FSAF1, 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-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-501-3P	99.33	66.12	651
HSA-MIR-502-3P	99.33	66.12	651
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-4274	98.59	66.10	630
HSA-MIR-144-5P	97.66	69.90	531
HSA-MIR-194-3P	97.36	65.96	1027
HSA-MIR-376A-2-5P	96.43	68.06	715
HSA-MIR-2861	95.24	65.47	1056

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• The Nucleolar Protein C1orf131 Is a Novel Gene Involved in the Progression of Lung Adenocarcinoma Cells through the AKT Signalling Pathway. (PMID:38928092)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fsaf1	ENSDARG00000078606
mus_musculus	Fsaf1	ENSMUSG00000031984
rattus_norvegicus	C19h1orf131	ENSRNOG00000019169
drosophila_melanogaster	CG1738	FBGN0030291

Protein

Protein identifiers

40S small subunit processome assembly factor 1 — Q8NDD1 (reviewed: Q8NDD1)

All UniProt accessions (3): Q8NDD1, Q5TBH9, Q5TBI2

UniProt curated annotations — full annotation on UniProt →

Function. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome. Prevents helicase DHX37 to be recruited before post-A1 state.

Subunit / interactions. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3.

Subcellular location. Chromosome. Nucleus. Nucleolus.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8NDD1-1	1	yes
Q8NDD1-5	2
Q8NDD1-6	3
Q8NDD1-7	4

RefSeq proteins (2): NP_001287759, NP_689592* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027973	FSAF1-like	Family
IPR052852	SSU_Processome_Comp	Family

Pfam: PF15375

UniProt features (21 total): modified residue 6, region of interest 5, splice variant 4, compositionally biased region 3, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7MQ8	ELECTRON MICROSCOPY	3.6
7MQ9	ELECTRON MICROSCOPY	3.87

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NDD1-F1	69.00	0.25

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 (6): 78, 86, 163, 185, 279, 73

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 86 (showing top): GOBP_RIBOSOME_BIOGENESIS, GGGNRMNNYCAT_UNKNOWN, GOBP_MATURATION_OF_SSU_RRNA, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, ACEVEDO_LIVER_CANCER_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, NUYTTEN_EZH2_TARGETS_DN, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN, GOCC_PRERIBOSOME, GOCC_SMALL_SUBUNIT_PROCESSOME

GO Biological Process (1): ribosomal small subunit biogenesis (GO:0042274)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): chromosome (GO:0005694), small-subunit processome (GO:0032040), nucleus (GO:0005634), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	2
ribonucleoprotein complex biogenesis	1
ribosome biogenesis	1
nucleic acid binding	1
binding	1
nucleolus	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1

Protein interactions and networks

STRING

434 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FSAF1	ANKRD18B	A2A2Z9	541
FSAF1	FAM72B	Q86X60	447
FSAF1	CCDC137	Q6PK04	444
FSAF1	C9orf78	Q9NZ63	420
FSAF1	CWC27	Q6UX04	397
FSAF1	SREK1	Q8WXA9	369
FSAF1	DCAF13	Q9NV06	368
FSAF1	SIPA1L2	Q9P2F8	366
FSAF1	ZC3H11A	O75152	356
FSAF1	MPHOSPH10	O00566	354
FSAF1	ZNF326	Q5BKZ1	353
FSAF1	PUM3	Q15397	350
FSAF1	DDX27	Q96GQ7	349
FSAF1	UTP4	Q969X6	348
FSAF1	CLPSL2	Q6UWE3	348

IntAct

23 interactions, top by confidence:

A	B	Type	Score
SREK1IP1	KPNA5	psi-mi:“MI:0914”(association)	0.530
SNN	MTDH	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
CDC73	SCAMP3	psi-mi:“MI:0914”(association)	0.350
Naa50	WDR46	psi-mi:“MI:0914”(association)	0.350
Ppp2ca	DKFZP586J0619	psi-mi:“MI:0914”(association)	0.350
Gtf3c2	PAPD5	psi-mi:“MI:0914”(association)	0.350
KRAS		psi-mi:“MI:0914”(association)	0.350
JUN		psi-mi:“MI:0914”(association)	0.350
ID2	CLASP2	psi-mi:“MI:0914”(association)	0.350
DUSP23	DNM1L	psi-mi:“MI:0914”(association)	0.350
INPP5K	PES1	psi-mi:“MI:0914”(association)	0.350
LMNB1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
SNRPC	DDX39A	psi-mi:“MI:0914”(association)	0.350
EMB	RLBP1	psi-mi:“MI:0914”(association)	0.350
NAT10	DIS3L2	psi-mi:“MI:0914”(association)	0.350
PRR3	POLRMT	psi-mi:“MI:0914”(association)	0.350
CEP164	RBFOX2	psi-mi:“MI:2364”(proximity)	0.270
ZNF800	MED19	psi-mi:“MI:2364”(proximity)	0.270
NPM1	SBNO1	psi-mi:“MI:2364”(proximity)	0.270
	FSAF1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (66): C1orf131 (Reconstituted Complex), C1orf131 (Proximity Label-MS), C1orf131 (Proximity Label-MS), C1orf131 (Affinity Capture-MS), C1orf131 (Affinity Capture-MS), C1orf131 (Affinity Capture-MS), C1orf131 (Affinity Capture-MS), C1orf131 (Affinity Capture-MS), C1orf131 (Affinity Capture-MS), RARS (Affinity Capture-MS), EIF5B (Affinity Capture-MS), IARS (Affinity Capture-MS), KARS (Affinity Capture-MS), MYBBP1A (Affinity Capture-MS), PPP2R1A (Affinity Capture-MS)

ESM2 similar proteins: A5PJN1, O57594, O75683, P0DPK0, P53352, P70279, Q05B65, Q0VCY3, Q17QR4, Q2KIV0, Q2TBX7, Q3KRF3, Q3U155, Q3ZCI6, Q58CQ0, Q5D1Z3, Q5NVE2, Q5R939, Q5RGP9, Q5XIB5, Q5XIG5, Q5ZIH9, Q5ZMG5, Q640V3, Q641W3, Q66H19, Q6NS45, Q6PK04, Q7ZWE7, Q8BG17, Q8BK35, Q8C6C7, Q8CIL4, Q8NDD1, Q8NEF9, Q8R0K4, Q8R2N0, Q8TF30, Q96J88, Q9CR02

Diamond homologs: Q3KRF3, Q8CIL4, Q8NDD1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1178 predictions. Top by Δscore:

Variant	Effect	Δscore
1:231225531:C:CT	acceptor_gain	1.0000
1:231226734:CCTA:C	donor_loss	1.0000
1:231226735:CTACC:C	donor_loss	1.0000
1:231226736:TACC:T	donor_loss	1.0000
1:231226738:C:CG	donor_loss	1.0000
1:231226738:CCAGT:C	donor_gain	1.0000
1:231226821:GGAGG:G	acceptor_gain	1.0000
1:231226822:GAGG:G	acceptor_gain	1.0000
1:231226823:AGG:A	acceptor_gain	1.0000
1:231226824:GG:G	acceptor_gain	1.0000
1:231226825:GCT:G	acceptor_loss	1.0000
1:231226826:C:CC	acceptor_gain	1.0000
1:231226826:C:CG	acceptor_loss	1.0000
1:231226827:T:A	acceptor_loss	1.0000
1:231226831:A:AC	acceptor_gain	1.0000
1:231226967:CCTCA:C	donor_loss	1.0000
1:231226968:CTCAC:C	donor_loss	1.0000
1:231226969:TCA:T	donor_loss	1.0000
1:231226970:CA:C	donor_loss	1.0000
1:231226971:A:C	donor_loss	1.0000
1:231226972:C:A	donor_loss	1.0000
1:231226976:AGCG:A	donor_gain	1.0000
1:231227064:CGAGC:C	acceptor_gain	1.0000
1:231227067:GC:G	acceptor_gain	1.0000
1:231227067:GCC:G	acceptor_loss	1.0000
1:231227068:CC:C	acceptor_gain	1.0000
1:231227069:C:CC	acceptor_gain	1.0000
1:231227069:CT:C	acceptor_loss	1.0000
1:231227070:T:C	acceptor_loss	1.0000
1:231229148:A:AC	donor_gain	1.0000

AlphaMissense

1921 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:231226995:C:G	R195P	0.997
1:231226993:C:G	A196P	0.996
1:231226996:G:T	R195S	0.995
1:231226992:G:T	A196D	0.994
1:231227053:G:C	H176D	0.994
1:231238908:A:C	F133L	0.994
1:231238908:A:T	F133L	0.994
1:231238910:A:G	F133L	0.994
1:231226978:C:G	A201P	0.993
1:231227043:C:T	G179D	0.993
1:231224328:A:T	L278Q	0.992
1:231227003:T:A	E192D	0.992
1:231227003:T:G	E192D	0.992
1:231227049:C:G	R177P	0.992
1:231227064:C:G	R172P	0.992
1:231224334:A:G	L276P	0.991
1:231226983:A:G	L199P	0.991
1:231224348:G:C	F271L	0.989
1:231224348:G:T	F271L	0.989
1:231224350:A:G	F271L	0.989
1:231226980:C:A	G200V	0.989
1:231226983:A:T	L199Q	0.989
1:231227068:C:G	A171P	0.989
1:231226977:G:T	A201D	0.988
1:231227012:T:A	R189S	0.987
1:231227012:T:G	R189S	0.987
1:231227046:A:G	F178S	0.987
1:231224355:C:T	G269E	0.986
1:231226980:C:T	G200D	0.985
1:231226981:C:G	G200R	0.985

dbSNP variants (sampled 300 via entrez): RS1000162775 (1:231240337 A>C), RS1000216146 (1:231228060 C>T), RS1000298223 (1:231233317 C>T), RS1000452504 (1:231226601 C>G,T), RS1000586116 (1:231227194 C>A,G), RS1000619601 (1:231239895 C>T), RS1000902862 (1:231228386 G>C), RS1000960746 (1:231240326 G>A), RS1001048492 (1:231232837 T>C), RS1001297786 (1:231238690 A>G), RS1001498192 (1:231231657 G>A), RS1001514239 (1:231233622 G>A,C), RS1002224292 (1:231225625 T>C), RS1002255519 (1:231225851 G>A), RS1002594048 (1:231224658 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

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	2
Acetaminophen	decreases expression	2
Cyclosporine	decreases expression	2
FR900359	decreases phosphorylation	1
dicrotophos	decreases expression	1
kojic acid	decreases expression	1
trichostatin A	affects expression	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
manganese chloride	increases expression, increases abundance	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
Temozolomide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Azathioprine	decreases expression	1
Coal	increases abundance, increases expression	1
Dimethyl Sulfoxide	increases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Manganese	increases expression, increases abundance	1
Ribonucleotides	affects binding	1
Smoke	increases abundance, increases expression	1
Thiram	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
Zinc	decreases expression	1
Aflatoxin B1	increases methylation	1
Sodium Selenite	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1LS	Abcam HeLa C1orf131 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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