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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (7 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 7 | 7 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 1 |
Variants in RNPS1
This is a list of pathogenic ClinVar variants found in the RNPS1 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-2253989-C-T | Inborn genetic diseases | Uncertain significance (Feb 28, 2023) | ||
| 16-2254008-G-A | Inborn genetic diseases | Uncertain significance (Jun 02, 2023) | ||
| 16-2254040-G-A | Inborn genetic diseases | Uncertain significance (Sep 16, 2021) | ||
| 16-2254048-C-A | Inborn genetic diseases | Uncertain significance (Apr 14, 2022) | ||
| 16-2255624-G-A | Inborn genetic diseases | Uncertain significance (Feb 23, 2023) | ||
| 16-2255692-G-A | Benign (Mar 29, 2018) | |||
| 16-2262288-G-T | Inborn genetic diseases | Uncertain significance (Mar 20, 2023) | ||
| 16-2262332-C-T | Inborn genetic diseases | Uncertain significance (Oct 21, 2021) | ||
| 16-2262389-T-C | Inborn genetic diseases | Uncertain significance (Jan 18, 2022) | ||
| 16-2263132-C-G | Inborn genetic diseases | Uncertain significance (Mar 28, 2023) | ||
| 16-2263161-G-C | Inborn genetic diseases | Uncertain significance (Jun 24, 2022) | ||
| 16-2263162-C-G | Inborn genetic diseases | Uncertain significance (Apr 05, 2023) | ||
| 16-2263220-A-G | Inborn genetic diseases | Uncertain significance (Jul 28, 2021) | ||
| 16-2263249-G-C | Inborn genetic diseases | Uncertain significance (Feb 15, 2023) | ||
| 16-2264194-C-T | Inborn genetic diseases | Uncertain significance (Aug 02, 2023) | ||
| 16-2264298-T-A | Likely benign (Apr 16, 2018) | |||
| 16-2264312-G-A | Inborn genetic diseases | Uncertain significance (Jan 18, 2022) | ||
| 16-2264330-C-T | Inborn genetic diseases | Uncertain significance (Feb 22, 2023) |
GnomAD
Source:
| 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:
- 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
- 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