Menu
GeneBe

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

ENSG00000205937NCBI:10921OMIM:606447HGNC:10080Uniprot:Q15287AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNPS1 gene.

  • Inborn genetic diseases (16 variants)
  • not provided (2 variants)

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
clinvar
1
clinvar
2
missense
16
clinvar
16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 16 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 Inborn genetic diseases Uncertain significance (Feb 28, 2023)2455174
16-2254008-G-A Inborn genetic diseases Uncertain significance (Jun 02, 2023)2507801
16-2254040-G-A Inborn genetic diseases Uncertain significance (Sep 16, 2021)2250966
16-2254048-C-A Inborn genetic diseases Uncertain significance (Apr 14, 2022)2284386
16-2255624-G-A Inborn genetic diseases Uncertain significance (Feb 23, 2023)2463759
16-2255692-G-A Benign (Mar 29, 2018)770437
16-2262288-G-T Inborn genetic diseases Uncertain significance (Mar 20, 2023)2527186
16-2262332-C-T Inborn genetic diseases Uncertain significance (Oct 21, 2021)2256232
16-2262389-T-C Inborn genetic diseases Uncertain significance (Jan 18, 2022)2272135
16-2263132-C-G Inborn genetic diseases Uncertain significance (Mar 28, 2023)2530616
16-2263161-G-C Inborn genetic diseases Uncertain significance (Jun 24, 2022)2386358
16-2263162-C-G Inborn genetic diseases Uncertain significance (Apr 05, 2023)2532948
16-2263220-A-G Inborn genetic diseases Uncertain significance (Jul 28, 2021)2239860
16-2263249-G-C Inborn genetic diseases Uncertain significance (Feb 15, 2023)2484590
16-2264194-C-T Inborn genetic diseases Uncertain significance (Aug 02, 2023)2603584
16-2264298-T-A Likely benign (Apr 16, 2018)744292
16-2264312-G-A Inborn genetic diseases Uncertain significance (Jan 18, 2022)2358970
16-2264330-C-T Inborn genetic diseases Uncertain significance (Feb 22, 2023)2462319

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNPS1protein_codingprotein_codingENST00000565678 715297
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9800.0202125334041253380.0000160
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.191532010.7630.00001391985
Missense in Polyphen930.6760.29339349
Synonymous-0.6597669.01.100.00000409622
Loss of Function3.20011.90.005.86e-7162

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.00009940.0000993
East Asian0.000.00
Finnish0.00004640.0000464
European (Non-Finnish)0.00001770.0000177
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rnps1
Phenotype

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