RNPS1

RNA binding protein with serine rich domain 1, the group of ASAP complex|RNA binding motif containing

Basic information

Region (hg38): 16:2253115-2268397

Links

ENSG00000205937 ∙ NCBI:10921 ∙ OMIM:606447 ∙ HGNC:10080 ∙ Uniprot:Q15287 ∙ 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 RNPS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNPS1 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				1	1	2
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	1

Variants in RNPS1

This is a list of pathogenic ClinVar variants found in the RNPS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2253989-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-2254004-C-T		not specified	Uncertain significance (Dec 30, 2023)
16-2254007-C-T		not specified	Uncertain significance (Oct 20, 2023)
16-2254008-G-A		not specified	Uncertain significance (Jun 02, 2023)
16-2254040-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-2254048-C-A		not specified	Uncertain significance (Apr 14, 2022)
16-2255624-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-2255692-G-A			Benign (Mar 29, 2018)
16-2262288-G-T		not specified	Uncertain significance (Mar 20, 2023)
16-2262289-T-C		not specified	Uncertain significance (Feb 02, 2024)
16-2262332-C-T		not specified	Uncertain significance (Oct 21, 2021)
16-2262389-T-C		not specified	Uncertain significance (Jan 18, 2022)
16-2262840-G-C		not specified	Uncertain significance (Dec 26, 2023)
16-2263132-C-G		not specified	Uncertain significance (Mar 28, 2023)
16-2263139-G-A		not specified	Uncertain significance (Oct 25, 2023)
16-2263161-G-C		not specified	Uncertain significance (Jun 24, 2022)
16-2263162-C-G		not specified	Uncertain significance (Apr 05, 2023)
16-2263220-A-G		not specified	Uncertain significance (Jul 28, 2021)
16-2263249-G-C		not specified	Uncertain significance (Feb 15, 2023)
16-2264194-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-2264201-C-T		not specified	Uncertain significance (Sep 29, 2023)
16-2264298-T-A			Likely benign (Apr 16, 2018)
16-2264312-G-A		not specified	Uncertain significance (Mar 04, 2024)
16-2264330-C-T		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNPS1	protein_coding	protein_coding	ENST00000565678	7	15297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.980	0.0202	125334	0	4	125338	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	153	201	0.763	0.0000139	1985
Missense in Polyphen		9	30.676	0.29339		349
Synonymous	-0.659	76	69.0	1.10	0.00000409	622
Loss of Function	3.20	0	11.9	0.00	5.86e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of pre- and post-splicing multiprotein mRNP complexes. Auxiliary component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Component of the ASAP and PSAP complexes which bind RNA in a sequence-independent manner and are proposed to be recruited to the EJC prior to or during the splicing process and to regulate specific excision of introns in specific transcription subsets. The ASAP complex can inhibit RNA processing during in vitro splicing reactions. The ASAP complex promotes apoptosis and is disassembled after induction of apoptosis. Enhances the formation of the ATP-dependent A complex of the spliceosome. Involved in both constitutive splicing and, in association with SRP54 and TRA2B/SFRS10, in distinctive modulation of alternative splicing in a substrate-dependent manner. Involved in the splicing modulation of BCL2L1/Bcl-X (and probably other apoptotic genes); specifically inhibits formation of proapoptotic isoforms such as Bcl-X(S); the activity is different from the established EJC assembly and function. Participates in mRNA 3'-end cleavage. Involved in UPF2- dependent nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Also mediates increase of mRNA abundance and translational efficiency. Binds spliced mRNA 20-25 nt upstream of exon-exon junctions. {ECO:0000269|PubMed:10449421, ECO:0000269|PubMed:11546874, ECO:0000269|PubMed:12665594, ECO:0000269|PubMed:12944400, ECO:0000269|PubMed:14729963, ECO:0000269|PubMed:14752011, ECO:0000269|PubMed:15684395, ECO:0000269|PubMed:16209946, ECO:0000269|PubMed:17586820, ECO:0000269|PubMed:22203037}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Nonsense-Mediated Decay (NMD);Transport of Mature mRNA derived from an Intron-Containing Transcript;Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.331
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.404
• hipred: Y
• hipred_score: 0.783
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnps1

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;transcription, DNA-templated;RNA export from nucleus;mRNA export from nucleus;RNA splicing;mRNA 3'-end processing;positive regulation of apoptotic process;negative regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;nuclear speck;exon-exon junction complex;ASAP complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding