SNRNP70
Basic information
Region (hg38): 19:49085419-49108605
Previous symbols: [ "RNPU1Z", "RPU1", "SNRP70" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (37 variants)
- not_provided (1 variants)
- Global_developmental_delay (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP70 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003089.6. 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 | 1 | |||||
| missense | 38 | 38 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNRNP70 | protein_coding | protein_coding | ENST00000598441 | 9 | 23187 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000743 | 114584 | 0 | 1 | 114585 | 0.00000436 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.45 | 137 | 307 | 0.446 | 0.0000242 | 2753 |
| Missense in Polyphen | 16 | 89.045 | 0.17968 | 846 | ||
| Synonymous | -0.956 | 129 | 116 | 1.11 | 0.00000799 | 898 |
| Loss of Function | 4.47 | 1 | 25.2 | 0.0396 | 0.00000200 | 225 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000753 | 0.0000753 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. SNRNP70 binds to the loop I region of U1-snRNA. The truncated isoforms cannot bind U1-snRNA.;
- Pathway
- Spliceosome - Homo sapiens (human);mRNA Processing;spliceosomal assembly;Metabolism of RNA;TCR;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.250
Haploinsufficiency Scores
- pHI
- 0.548
- hipred
- Y
- hipred_score
- 0.840
- ghis
- 0.595
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.830
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snrnp70
- Phenotype
Zebrafish Information Network
- Gene name
- snrnp70
- Affected structure
- motor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- truncated
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;regulation of ATPase activity;regulation of RNA splicing;positive regulation of mRNA splicing, via spliceosome;negative regulation of protein refolding;negative regulation of chaperone-mediated autophagy
- Cellular component
- nucleus;nucleoplasm;spliceosomal complex;U1 snRNP;nuclear speck
- Molecular function
- RNA binding;mRNA binding;protein binding;U1 snRNA binding