PSPC1

paraspeckle component 1, the group of RNA binding motif containing

Basic information

Region (hg38): 13:19674752-19783019

Links

ENSG00000121390 ∙ NCBI:55269 ∙ OMIM:612408 ∙ HGNC:20320 ∙ Uniprot:Q8WXF1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSPC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSPC1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PSPC1

This is a list of pathogenic ClinVar variants found in the PSPC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-19703194-T-C		not specified	Uncertain significance (May 27, 2022)
13-19703255-C-T		not specified	Uncertain significance (Jul 09, 2021)
13-19703321-C-T		not specified	Uncertain significance (May 02, 2024)
13-19703330-A-T		not specified	Uncertain significance (Dec 01, 2022)
13-19705700-T-C		not specified	Uncertain significance (Jan 02, 2024)
13-19705764-G-C		not specified	Uncertain significance (Jul 14, 2023)
13-19705808-C-T		not specified	Uncertain significance (Jun 17, 2024)
13-19705817-C-A		not specified	Uncertain significance (Jan 03, 2024)
13-19730292-G-C		not specified	Uncertain significance (May 24, 2023)
13-19730327-C-T		not specified	Uncertain significance (Aug 15, 2023)
13-19741638-G-A		not specified	Uncertain significance (Feb 10, 2022)
13-19751448-G-A		not specified	Uncertain significance (Aug 30, 2021)
13-19759410-C-T		not specified	Uncertain significance (Mar 22, 2023)
13-19772441-T-C		not specified	Uncertain significance (Mar 07, 2024)
13-19772450-C-T		not specified	Uncertain significance (Dec 13, 2022)
13-19772509-T-C		not specified	Uncertain significance (Jun 06, 2023)
13-19782410-G-C		not specified	Uncertain significance (Sep 07, 2022)
13-19782555-T-C		not specified	Uncertain significance (May 01, 2022)
13-19782586-C-T		not specified	Uncertain significance (Apr 25, 2022)
13-19782588-G-A		not specified	Uncertain significance (Oct 27, 2021)
13-19782671-G-T		not specified	Uncertain significance (Oct 18, 2021)
13-19782699-C-A		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSPC1	protein_coding	protein_coding	ENST00000338910	9	108247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00987	124549	0	2	124551	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.53	177	300	0.590	0.0000160	3390
Missense in Polyphen		21	56.888	0.36915		631
Synonymous	-0.934	112	100	1.12	0.00000488	1008
Loss of Function	4.03	2	22.7	0.0881	0.00000133	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000298	0.0000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates, cooperatively with NONO and SFPQ, androgen receptor-mediated gene transcription activity in Sertoli cell line (By similarity). Binds to poly(A), poly(G) and poly(U) RNA homopolymers. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer (By similarity). Together with NONO, required for the formation of nuclear paraspeckles. 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. {ECO:0000250|UniProtKB:Q8R326, ECO:0000269|PubMed:22416126, ECO:0000269|PubMed:28712728}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.259
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.151
• hipred: Y
• hipred_score: 0.816
• ghis: 0.705

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pspc1

Gene ontology

• Biological process: activation of innate immune response;regulation of transcription by RNA polymerase II;regulation of circadian rhythm;innate immune response;negative regulation of transcription, DNA-templated;rhythmic process
• Cellular component: fibrillar center;nucleus;nucleoplasm;cytoplasm;nuclear matrix;nuclear speck;paraspeckles
• Molecular function: transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA binding;protein binding;E-box binding