SNRNP200
small nuclear ribonucleoprotein U5 subunit 200, the group of Spliceosomal Bact complex|Spliceosomal P complex|Spliceosomal C complex|U5 small nuclear ribonucleoprotein|RNA helicases
Basic information
Region (hg38): 2:96274338-96321271
Previous symbols: [ "ASCC3L1", "RP33" ]
Links
Phenotypes
GenCC
Source:
- retinitis pigmentosa 33 (Definitive), mode of inheritance: AD
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- retinitis pigmentosa 33 (Strong), mode of inheritance: AD
- retinitis pigmentosa 33 (Definitive), mode of inheritance: AD
- SNRNP200-related dominant retinopathy (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Retinitis pigmentosa 33 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Ophthalmologic | 16612614; 19878916; 21618346; 23029027 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (1188 variants)
- Retinal_dystrophy (108 variants)
- Inborn_genetic_diseases (96 variants)
- Retinitis_pigmentosa (96 variants)
- Retinitis_pigmentosa_33 (41 variants)
- SNRNP200-related_disorder (35 variants)
- not_specified (12 variants)
- Autosomal_dominant_retinitis_pigmentosa (2 variants)
- Rod-cone_dystrophy (2 variants)
- Stargardt_disease (1 variants)
- Cone-rod_dystrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP200 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014014.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 22 | 354 | 15 | 391 | ||
| missense | 21 | 472 | 57 | 560 | ||
| nonsense | 4 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 7 | |||||
| splice donor/acceptor (+/-2bp) | 6 | |||||
| Total | 5 | 23 | 510 | 411 | 20 |
Highest pathogenic variant AF is 0.0000830305
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNRNP200 | protein_coding | protein_coding | ENST00000323853 | 45 | 31224 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 9.46e-16 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 5.94 | 610 | 1.19e+3 | 0.515 | 0.0000774 | 14073 |
| Missense in Polyphen | 168 | 472.67 | 0.35543 | 5603 | ||
| Synonymous | 0.769 | 436 | 457 | 0.954 | 0.0000282 | 4148 |
| Loss of Function | 9.44 | 4 | 112 | 0.0358 | 0.00000703 | 1269 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000904 | 0.0000904 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. Involved in spliceosome assembly, activation and disassembly. Mediates changes in the dynamic network of RNA-RNA interactions in the spliceosome. Catalyzes the ATP-dependent unwinding of U4/U6 RNA duplices, an essential step in the assembly of a catalytically active spliceosome. {ECO:0000269|PubMed:16723661, ECO:0000269|PubMed:23045696, ECO:0000269|PubMed:8670905, ECO:0000269|PubMed:9539711}.;
- Disease
- DISEASE: Retinitis pigmentosa 33 (RP33) [MIM:610359]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:16723661, ECO:0000269|PubMed:19710410, ECO:0000269|PubMed:19878916, ECO:0000269|PubMed:21618346, ECO:0000269|PubMed:23029027, ECO:0000269|PubMed:23045696, ECO:0000269|PubMed:23887765, ECO:0000269|PubMed:24319334}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- loftool
- 0.112
- rvis_EVS
- -2.34
- rvis_percentile_EVS
- 1.17
Haploinsufficiency Scores
- pHI
- 0.370
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.650
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.913
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snrnp200
- Phenotype
- limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- snrnp200
- Affected structure
- retinal rod cell
- Phenotype tag
- abnormal
- Phenotype quality
- physical object quality
Gene ontology
- Biological process
- cis assembly of pre-catalytic spliceosome;spliceosome conformational change to release U4 (or U4atac) and U1 (or U11);mRNA splicing, via spliceosome;osteoblast differentiation
- Cellular component
- nucleus;nucleoplasm;spliceosomal complex;U5 snRNP;membrane;U4/U6 x U5 tri-snRNP complex;catalytic step 2 spliceosome;post-mRNA release spliceosomal complex
- Molecular function
- RNA binding;ATP-dependent RNA helicase activity;protein binding;ATP binding;ATP-dependent helicase activity;identical protein binding