PSPC1

Summary

PSPC1 (paraspeckle component 1, HGNC:20320) is a protein-coding gene on chromosome 13q12.11, encoding Paraspeckle component 1 (Q8WXF1). RNA-binding protein required for the formation of nuclear paraspeckles. It is a selective cancer dependency (DepMap: 15.1% of cell lines).

This gene encodes a nucleolar protein that localizes to punctate subnuclear structures that occur close to splicing speckles, known as paraspeckles. These paraspeckles are composed of RNA-protein structures that include a non-coding RNA, NEAT1/Men epsilon/beta, and the Drosophila Behavior Human Splicing family of proteins, which include the product of this gene and the P54NRB/NONO and PSF/SFPQ proteins. Paraspeckles may function in the control of gene expression via an RNA nuclear retention mechanism. The protein encoded by this gene is found in paraspeckles in transcriptionally active cells, but it localizes to unique cap structures at the nucleolar periphery when RNA polymerase II transcription is inhibited, or during telophase. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene, which is also located on chromosome 13, has been identified.

Source: NCBI Gene 55269 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 79 total
• Druggable target: yes
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• Cancer dependency (DepMap): dependent in 15.1% of screened cell lines
• MANE Select transcript: NM_001354909

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20320
Approved symbol	PSPC1
Name	paraspeckle component 1
Location	13q12.11
Locus type	gene with protein product
Status	Approved
Aliases	PSP1, FLJ10955
Ensembl gene	ENSG00000121390
Ensembl biotype	protein_coding
OMIM	612408
Entrez	55269

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000338910, ENST00000427943, ENST00000471658, ENST00000492741, ENST00000497722, ENST00000619300, ENST00000635251, ENST00000635562, ENST00000885045, ENST00000885046, ENST00000885047, ENST00000937572, ENST00000946081

RefSeq mRNA: 4 — MANE Select: NM_001354909 NM_001042414, NM_001354908, NM_001354909, NM_001363660

CCDS: CCDS41870, CCDS86343

Canonical transcript exons

ENST00000338910 — 9 exons

Exon	Start	End
ENSE00000822387	19741565	19741649
ENSE00000822388	19751271	19751467
ENSE00000822389	19759323	19759418
ENSE00001093320	19730239	19730344
ENSE00001093324	19772242	19772543
ENSE00001374935	19702500	19703360
ENSE00001596908	19709542	19709599
ENSE00001705148	19705662	19705831
ENSE00003892974	19782386	19782945

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 97.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.4521 / max 660.4083, expressed in 1814 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136318	33.4976	1813
136319	1.9546	1131

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	97.16	gold quality
ganglionic eminence	UBERON:0004023	96.03	gold quality
sural nerve	UBERON:0015488	95.85	gold quality
cortical plate	UBERON:0005343	95.50	gold quality
right testis	UBERON:0004534	94.55	gold quality
left testis	UBERON:0004533	94.32	gold quality
granulocyte	CL:0000094	93.53	gold quality
calcaneal tendon	UBERON:0003701	93.17	gold quality
monocyte	CL:0000576	93.07	gold quality
mononuclear cell	CL:0000842	92.87	gold quality
leukocyte	CL:0000738	92.82	gold quality
cerebellar hemisphere	UBERON:0002245	92.77	gold quality
cerebellar cortex	UBERON:0002129	92.68	gold quality
gastrocnemius	UBERON:0001388	92.40	gold quality
endocervix	UBERON:0000458	92.34	gold quality
anterior cingulate cortex	UBERON:0009835	92.24	gold quality
left ovary	UBERON:0002119	92.17	gold quality
cingulate cortex	UBERON:0003027	92.17	gold quality
testis	UBERON:0000473	92.16	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.15	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.05	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.02	gold quality
right uterine tube	UBERON:0001302	91.89	gold quality
body of uterus	UBERON:0009853	91.86	gold quality
left uterine tube	UBERON:0001303	91.85	gold quality
right ovary	UBERON:0002118	91.83	gold quality
ectocervix	UBERON:0012249	91.77	gold quality
muscle of leg	UBERON:0001383	91.74	gold quality
prefrontal cortex	UBERON:0000451	91.65	gold quality
adenohypophysis	UBERON:0002196	91.62	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

65 targeting PSPC1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 17)

• We map the domain within PSP1 that is mediating this interaction and show it is required for the correct localization of PSP1 to paraspeckles. This interaction is necessary but not sufficient for paraspeckle targeting by PSP1 (PMID:16148043)
• downregulated were the a protein coding gene PSPC1 in breast and ovarian cancer cells (PMID:21532345)
• crystal of PSPC1-NONO contained one heterodimer in the asymmetric unit and diffracted to 1.9 A resolution using synchrotron radiation (PMID:22102035)
• The crystal structure of the heterodimer of the multidomain conserved region of the Drosophila behavior/human splicing proteins, PSPC1 and NONO, is described. (PMID:22416126)
• Development of a pipeline for automated, high-throughput analysis of PSPC1 paraspeckle protein isoforms reveals specific roles for IMPa2, IMPa4 and IMPa6 proteins. (PMID:28240251)
• PSPC1 and TET2 contribute to ERVL and ERVL-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of RNAs through 5hmC modification. (PMID:29483655)
• Analytical ultracentrifugation to estimate the dimerization equilibrium of the SFPQ-containing dimers revealed that the SFPQ-containing dimers dissociate at low micromolar concentrations and that the heterodimers have higher affinities than the homodimer. Moreover, we observed that the apparent dissociation constant for the SFPQ/PSPC1 heterodimer was over 6-fold lower than that of the SFPQ/NONO heterodimer. (PMID:29530979)
• PSPC1 increases transforming growth factor-beta1 (TGF-beta1) secretion through an interaction with phosphorylated and nuclear Smad2/3 to potentiate TGF-beta1 autocrine signaling, promoting epithelial mesenchymal transformation, stemness and metastasis. (PMID:29593326)
• This study determined that Hepatitis Delta Virus replication induces the delocalization of PSP1 to cytoplasmic foci containing PABP and increases NEAT1 level causing an enlargement of NEAT1 foci. (PMID:29662142)
• PSPC1, a nuclear substrate of PTK6, sequesters PTK6 in the nucleus and loses its metastasis driving capability in hepatocellular carcinoma. Conversely, PSPC1 upregulation or PSPC1-Y523F mutation promotes epithelial-mesenchymal transition, stemness, and metastasis via cytoplasmic translocation of active PTK6 and nuclear translocation of beta-catenin, which interacts with PSPC1 to augment Wnt3a autocrine signaling. (PMID:31844057)
• PSPC1 Potentiates IGF1R Expression to Augment Cell Adhesion and Motility. (PMID:32570949)
• Paraspeckle components NONO and PSPC1 are not mislocalized from motor neuron nuclei in sporadic ALS. (PMID:32844195)
• Nuclear receptor 4A1 (NR4A1) antagonists target paraspeckle component 1 (PSPC1) in cancer cells. (PMID:34699643)
• PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2. (PMID:35681031)
• Obstructive sleep apnoea is related to melanoma aggressiveness through paraspeckle protein-1 upregulation. (PMID:36265878)
• Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer. (PMID:37209920)
• PSPC1 Binds to HCV IRES and Prevents Ribosomal Protein S5 Binding, Inhibiting Viral RNA Translation. (PMID:38793620)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	pspc1	ENSDARG00000006621
mus_musculus	Pspc1	ENSMUSG00000021938
rattus_norvegicus	Pspc1	ENSRNOG00000020782

Paralogs (7): SPEN (ENSG00000065526), SFPQ (ENSG00000116560), NONO (ENSG00000147140), RAVER1 (ENSG00000161847), RAVER2 (ENSG00000162437), RBM15 (ENSG00000162775), RBM15B (ENSG00000259956)

Protein

Protein identifiers

Paraspeckle component 1 — Q8WXF1 (reviewed: Q8WXF1)

Alternative names: Paraspeckle protein 1

All UniProt accessions (3): A0A0U1RQF9, Q8WXF1, X6RDA4

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein required for the formation of nuclear paraspeckles. Binds to poly(A), poly(G) and poly(U) RNA homopolymers. Regulates, cooperatively with NONO and SFPQ, androgen receptor-mediated gene transcription activity in Sertoli cell line. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-BMAL1 heterodimer. Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway.

Subunit / interactions. Forms heterodimers with NONO; this involves formation of a coiled coil domain by helices from both proteins. Found in a RNP complex with CAT2 transcribed nuclear RNA (CTN-RNA). Interaction with NONO is required for its targeting to paraspeckles and perinucleolar caps. Interacts with SFPQ. Part of the HDP-RNP complex composed of at least HEXIM1, PRKDC, XRCC5, XRCC6, paraspeckle proteins (SFPQ, NONO, PSPC1, RBM14, and MATR3) and NEAT1 RNA. Interacts with ALKBH5 (when acetylated); interaction with acetylated ALKBH5 facilitates recognition of N(6)-methyladenosine (m6A) RNAs.

Subcellular location. Nucleus speckle. Nucleus. Nucleolus. Nucleus matrix. Cytoplasm.

Tissue specificity. Expressed in pancreas, kidney, skeletal muscle, liver, lung, placenta, brain and heart.

Similarity. Belongs to the PSPC family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WXF1-1	1, PSP1-alpha	yes
Q8WXF1-2	2, PSP1-beta

RefSeq proteins (4): NP_001035879, NP_001341837, NP_001341838, NP_001350589 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR012975	NOPS	Domain
IPR034522	PSP1_RRM1	Domain
IPR034523	PSP1_RRM2	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076, PF08075

UniProt features (47 total): strand 13, helix 10, modified residue 6, mutagenesis site 6, region of interest 3, domain 2, splice variant 2, compositionally biased region 2, chain 1, turn 1, coiled-coil region 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
3SDE	X-RAY DIFFRACTION	1.9
5WPA	X-RAY DIFFRACTION	2.29
5IFN	X-RAY DIFFRACTION	3.17

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WXF1-F1	74.41	0.51

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): 409, 473, 477, 507, 509, 1

Mutagenesis-validated functional residues (6):

Position	Phenotype
119	abolishes accumulation in paraspeckles, but not in perinucleolar caps; when associated with a-121; a-198 and a-200.
121	abolishes accumulation in paraspeckles, but not in perinucleolar caps; when associated with a-119; a-198 and a-200.
198	abolishes accumulation in paraspeckles, but not in perinucleolar caps; when associated with a-119; a-121 and a-200.
200	abolishes accumulation in paraspeckles, but not in perinucleolar caps; when associated with a-119; a-121 and a-198.
275	abolishes interaction with nono and localization in nuclear paraspeckles; when associated with a-279.
279	abolishes interaction with nono and localization in nuclear paraspeckles; when associated with a-275.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 156 (showing top): GOBP_CIRCADIAN_RHYTHM, TGCGCANK_UNKNOWN, CHANDRAN_METASTASIS_DN, GOBP_REGULATION_OF_CIRCADIAN_RHYTHM, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, ONKEN_UVEAL_MELANOMA_UP, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, LE_EGR2_TARGETS_UP, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_ORGANELLE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_RESPONSE_TO_BIOTIC_STIMULUS

GO Biological Process (8): activation of innate immune response (GO:0002218), regulation of DNA-templated transcription (GO:0006355), regulation of circadian rhythm (GO:0042752), innate immune response (GO:0045087), negative regulation of DNA-templated transcription (GO:0045892), rhythmic process (GO:0048511), membraneless organelle assembly (GO:0140694), immune system process (GO:0002376)

GO Molecular Function (3): RNA binding (GO:0003723), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (8): fibrillar center (GO:0001650), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear matrix (GO:0016363), nuclear speck (GO:0016607), paraspeckles (GO:0042382), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
nuclear lumen	3
DNA-templated transcription	2
biological_process	2
binding	2
nuclear ribonucleoprotein granule	2
activation of immune response	1
positive regulation of innate immune response	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
circadian rhythm	1
regulation of biological process	1
immune response	1
defense response to symbiont	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
organelle assembly	1
nucleic acid binding	1
nucleolus	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1524 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PSPC1	RBM14	Q96PK6	991
PSPC1	A0A0A6YYI9	A0A0A6YYI9	990
PSPC1	NONO	P30807	983
PSPC1	SFPQ	P23246	982
PSPC1	MATR3	P43243	921
PSPC1	FUS	P35637	835
PSPC1	TARDBP	Q13148	723
PSPC1	CPSF6	Q16630	636
PSPC1	HDAC1	Q13547	610
PSPC1	SRSF1	Q07955	560
PSPC1	HEXIM1	O94992	550
PSPC1	TET2	Q6N021	527
PSPC1	XRCC5	P13010	496
PSPC1	RNF14	Q9UBS8	490
PSPC1	DDX3X	O00571	490
PSPC1	SS18	Q15532	490

IntAct

138 interactions, top by confidence:

A	B	Type	Score
PSPC1	NONO	psi-mi:“MI:0915”(physical association)	0.940
NONO	PSPC1	psi-mi:“MI:0915”(physical association)	0.940
NONO	SFPQ	psi-mi:“MI:0914”(association)	0.900
CCDC22	VPS26C	psi-mi:“MI:0914”(association)	0.790
SFPQ	PSPC1	psi-mi:“MI:0403”(colocalization)	0.700
SFPQ	PSPC1	psi-mi:“MI:0915”(physical association)	0.700
NONO	PSPC1	psi-mi:“MI:0915”(physical association)	0.560
	PSPC1	psi-mi:“MI:0915”(physical association)	0.560
PSPC1	KRT31	psi-mi:“MI:0915”(physical association)	0.560
KRT31	PSPC1	psi-mi:“MI:0915”(physical association)	0.560
PSPC1		psi-mi:“MI:0915”(physical association)	0.560
PSPC1	FXR1	psi-mi:“MI:0915”(physical association)	0.550
NONO	SERPINB7	psi-mi:“MI:0914”(association)	0.530
CCDC22	ZWINT	psi-mi:“MI:0914”(association)	0.530
PSPC1		psi-mi:“MI:0915”(physical association)	0.400
SMAD2	FAM83G	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (605): PSPC1 (Affinity Capture-MS), PSPC1 (Two-hybrid), PSPC1 (Two-hybrid), KRTAP13-1 (Two-hybrid), PSPC1 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS), PSPC1 (Reconstituted Complex), PSPC1 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS), DNAJB4 (Co-fractionation)

ESM2 similar proteins: A0A8M1NHK4, A0AV96, B3M3R5, B4KX02, O22173, O43347, P86049, Q05196, Q15233, Q1LZD9, Q32NN2, Q3UEB3, Q4KLH4, Q5R469, Q5R5P4, Q5R9H4, Q5RFL9, Q5W9D5, Q5W9D6, Q5W9D7, Q5YD48, Q61474, Q66H68, Q6DEY7, Q6GR16, Q6IRN2, Q6P0D0, Q7JJZ8, Q8GZ26, Q8K3P4, Q8MSV2, Q8R326, Q8TBY0, Q8WXF1, Q91WT8, Q91XU1, Q920Q6, Q923K9, Q96DH6, Q96PU8

Diamond homologs: A0A0D1DWZ5, A0A2R8Y4L2, A1CRM1, A1D4K4, A2A5N3, A2Q848, A3LXL0, A4QUF0, A5DM21, A5DW14, F1QB54, F4HT49, O01671, O04319, O14102, O17310, O22173, O61374, O64380, O97018, P04147, P09867, P0CB38, P0CP46, P0CP47, P11940, P17130, P19339, P20965, P21187, P29341, P31209, P32588, P39684, P41891, P42731, P49313, P60047, P60048, P60049

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
PSPC1	“form complex”	“LMX1B/SFPQ/PSPC1 complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 123 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
mRNA 3’-end processing	6	13.9×	6e-04
mRNA Polyadenylation	10	10.3×	8e-06
SARS-CoV-1-host interactions	5	10.3×	9e-03
mRNA Splicing	6	7.8×	9e-03
Processing of Capped Intron-Containing Pre-mRNA	8	7.7×	1e-03
mRNA Splicing - Major Pathway	12	7.7×	8e-06
Dengue Virus-Host Interactions	13	7.0×	8e-06
Metabolism of RNA	9	4.4×	1e-02

GO biological processes:

GO term	Partners	Fold	FDR
translational initiation	5	16.6×	2e-03
mRNA transport	5	12.2×	6e-03
regulation of alternative mRNA splicing, via spliceosome	5	11.3×	8e-03
negative regulation of translation	6	10.9×	3e-03
positive regulation of translation	5	10.5×	9e-03
RNA splicing	10	8.2×	2e-04
mRNA processing	11	8.0×	1e-04
mRNA splicing, via spliceosome	9	7.6×	9e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — LUSC.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2602 predictions. Top by Δscore:

Variant	Effect	Δscore
13:19703499:C:CT	acceptor_gain	1.0000
13:19703500:A:AC	acceptor_gain	1.0000
13:19703500:A:C	acceptor_gain	1.0000
13:19730235:TTA:T	donor_loss	1.0000
13:19730236:TA:T	donor_loss	1.0000
13:19730237:A:AC	donor_gain	1.0000
13:19730238:C:CG	donor_gain	1.0000
13:19730238:CA:C	donor_gain	1.0000
13:19730238:CAT:C	donor_gain	1.0000
13:19730238:CATT:C	donor_gain	1.0000
13:19730238:CATTT:C	donor_gain	1.0000
13:19730260:AAAGC:A	donor_gain	1.0000
13:19730340:CATGT:C	acceptor_gain	1.0000
13:19730341:ATGT:A	acceptor_gain	1.0000
13:19730342:TGT:T	acceptor_gain	1.0000
13:19730343:GT:G	acceptor_gain	1.0000
13:19730344:TC:T	acceptor_loss	1.0000
13:19730345:C:CC	acceptor_gain	1.0000
13:19730345:CTGAA:C	acceptor_loss	1.0000
13:19730351:A:AC	acceptor_gain	1.0000
13:19730351:A:C	acceptor_gain	1.0000
13:19730352:T:C	acceptor_gain	1.0000
13:19730352:T:TC	acceptor_gain	1.0000
13:19730353:T:C	acceptor_gain	1.0000
13:19741560:TTTAC:T	donor_loss	1.0000
13:19741561:TTACC:T	donor_loss	1.0000
13:19741562:TACC:T	donor_loss	1.0000
13:19741563:ACCTT:A	donor_loss	1.0000
13:19741564:CC:C	donor_loss	1.0000
13:19741581:T:TA	donor_gain	1.0000

AlphaMissense

3469 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:19741619:C:G	R333P	1.000
13:19741625:A:G	L331P	1.000
13:19741634:T:G	Q328P	1.000
13:19741646:A:G	L324P	1.000
13:19751276:C:A	R321M	1.000
13:19751282:A:G	L319P	1.000
13:19751307:C:G	A311P	1.000
13:19751327:A:G	L304P	1.000
13:19751340:C:G	A300P	1.000
13:19751369:C:G	R290P	1.000
13:19751393:A:G	L282P	1.000
13:19751393:A:T	L282H	1.000
13:19751397:C:G	A281P	1.000
13:19751403:A:G	W279R	1.000
13:19751403:A:T	W279R	1.000
13:19751405:C:G	R278P	1.000
13:19751441:G:T	A266D	1.000
13:19751461:T:A	R259S	1.000
13:19751461:T:G	R259S	1.000
13:19759365:C:T	G243D	1.000
13:19759366:C:G	G243R	1.000
13:19759404:A:T	V230D	1.000
13:19772300:T:C	K206E	1.000
13:19772308:A:G	F203S	1.000
13:19772314:A:T	V201E	1.000
13:19772320:C:T	G199D	1.000
13:19772321:C:G	G199R	1.000
13:19772377:C:T	G180D	1.000
13:19772378:C:G	G180R	1.000
13:19772389:A:G	F176S	1.000

dbSNP variants (sampled 300 via entrez): RS1000045119 (13:19757199 G>A), RS1000057496 (13:19678403 C>T), RS1000077422 (13:19672533 T>A,C), RS1000081399 (13:19713107 T>G), RS1000113272 (13:19714812 T>C,G), RS1000129313 (13:19694048 G>A), RS1000160605 (13:19693894 T>C,G), RS1000183141 (13:19713567 A>G,T), RS1000185582 (13:19726472 C>T), RS1000208717 (13:19763305 G>A,C), RS1000255800 (13:19682977 A>T), RS1000297182 (13:19757733 A>T), RS1000306232 (13:19756855 C>A), RS1000373924 (13:19732278 A>AC), RS1000385939 (13:19769967 T>G)

Disease associations

OMIM: gene MIM:612408 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008161_96	Waist circumference adjusted for body mass index	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725161 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.59	Kd	2586	nM	CHEMBL5653589
5.59	ED50	2586	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 8 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149137: Binding affinity to human PSPC1 incubated for 45 mins by Kinobead based pull down assay	kd	2.5863	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	3
Cadmium Chloride	decreases expression	3
bisphenol A	decreases expression, affects cotreatment, affects expression, increases abundance	2
deoxynivalenol	increases expression	2
sodium arsenite	affects binding, increases reaction, decreases expression, increases activity	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	2
Doxorubicin	decreases expression, decreases response to substance	2
Cyclosporine	decreases expression	2
Asbestos, Crocidolite	increases expression	2
bisphenol F	increases expression	1
ginger extract	affects cotreatment, affects expression, increases abundance	1
2,4,6-tribromophenol	decreases expression	1
chloroacetaldehyde	decreases expression	1
daidzein	affects cotreatment, increases expression	1
decabromobiphenyl ether	decreases expression	1
daidzin	affects cotreatment, increases expression	1
beta-lapachone	decreases expression	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	decreases expression	1
benzo(e)pyrene	decreases methylation	1
nivalenol	increases expression	1
genistin	affects cotreatment, increases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
glycitein	affects cotreatment, increases expression	1
glycitin	affects cotreatment, increases expression	1
ICG 001	affects expression	1
bisphenol B	increases expression	1
14-deoxy-11,12-didehydroandrographolide	decreases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652179	Binding	Binding affinity to human PSPC1 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TH38	HAP1 PSPC1 (-) 1	Cancer cell line	Male
CVCL_XS01	HAP1 PSPC1 (-) 2	Cancer cell line	Male
CVCL_XS02	HAP1 PSPC1 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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