SNRNP40
Basic information
Region (hg38): 1:31259568-31296788
Previous symbols: [ "WDR57" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP40 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 | 0 | |||||
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 | 0 | 0 |
Variants in SNRNP40
This is a list of pathogenic ClinVar variants found in the SNRNP40 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-31261561-T-C | not specified | Uncertain significance (Oct 01, 2024) | ||
1-31261574-C-T | not specified | Uncertain significance (Sep 08, 2024) | ||
1-31261589-T-C | not specified | Uncertain significance (Feb 08, 2023) | ||
1-31267877-G-A | not specified | Uncertain significance (Jan 07, 2025) | ||
1-31267911-A-C | not specified | Uncertain significance (Jan 30, 2024) | ||
1-31271416-T-G | not specified | Uncertain significance (Dec 15, 2022) | ||
1-31271453-T-C | not specified | Uncertain significance (Jul 19, 2023) | ||
1-31281423-T-C | not specified | Uncertain significance (Apr 05, 2023) | ||
1-31281445-G-T | not specified | Uncertain significance (Feb 23, 2023) | ||
1-31281450-G-A | not specified | Uncertain significance (Mar 24, 2023) | ||
1-31281467-G-C | not specified | Uncertain significance (Nov 10, 2022) | ||
1-31291925-T-C | not specified | Uncertain significance (May 23, 2023) | ||
1-31291951-A-T | not specified | Uncertain significance (Jun 07, 2024) | ||
1-31291991-T-C | not specified | Uncertain significance (Sep 20, 2024) | ||
1-31293225-G-C | not specified | Uncertain significance (Aug 17, 2022) | ||
1-31293329-G-A | not specified | Uncertain significance (Oct 12, 2022) | ||
1-31293341-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
1-31296612-G-A | not specified | Uncertain significance (Dec 31, 2023) | ||
1-31296618-A-G | not specified | Uncertain significance (Dec 31, 2023) | ||
1-31296649-C-G | not specified | Uncertain significance (Apr 11, 2023) | ||
1-31296669-G-A | not specified | Uncertain significance (Apr 20, 2023) | ||
1-31296714-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
1-31296732-C-A | not specified | Uncertain significance (Dec 13, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SNRNP40 | protein_coding | protein_coding | ENST00000263694 | 10 | 37246 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.853 | 0.147 | 125724 | 0 | 22 | 125746 | 0.0000875 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.55 | 136 | 197 | 0.690 | 0.00000968 | 2324 |
Missense in Polyphen | 33 | 73.027 | 0.45189 | 871 | ||
Synonymous | 0.0589 | 76 | 76.7 | 0.991 | 0.00000395 | 696 |
Loss of Function | 3.46 | 3 | 19.5 | 0.154 | 9.09e-7 | 237 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000883 | 0.0000883 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000168 | 0.000167 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs. {ECO:0000269|PubMed:9774689}.;
- Pathway
- Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- loftool
- 0.320
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.63
Haploinsufficiency Scores
- pHI
- 0.290
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.692
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.149
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snrnp40
- Phenotype
Gene ontology
- Biological process
- RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;RNA processing;RNA splicing
- Cellular component
- nucleoplasm;U5 snRNP;small nucleolar ribonucleoprotein complex;cytosol;nuclear speck;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
- Molecular function
- RNA binding;protein binding