SNU13
Basic information
Region (hg38): 22:41673933-41690504
Previous symbols: [ "SSFA1", "NHP2L1" ]
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 SNU13 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 0 |
Variants in SNU13
This is a list of pathogenic ClinVar variants found in the SNU13 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-41680346-G-C | not specified | Uncertain significance (Sep 03, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNU13 | protein_coding | protein_coding | ENST00000401959 | 3 | 16575 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.748 | 0.242 | 125416 | 0 | 1 | 125417 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.20 | 21 | 74.6 | 0.282 | 0.00000425 | 818 |
| Missense in Polyphen | 0 | 15.445 | 0 | 211 | ||
| Synonymous | -0.157 | 34 | 32.9 | 1.03 | 0.00000198 | 265 |
| Loss of Function | 1.98 | 0 | 4.57 | 0.00 | 1.91e-7 | 61 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:28781166). Binds to the 5'-stem-loop of U4 snRNA and thereby contributes to spliceosome assembly (PubMed:10545122, PubMed:17412961). The protein undergoes a conformational change upon RNA-binding (PubMed:17412961). {ECO:0000269|PubMed:10545122, ECO:0000269|PubMed:17412961, ECO:0000269|PubMed:28781166}.;
- Pathway
- Ribosome biogenesis in eukaryotes - Homo sapiens (human);Spliceosome - Homo sapiens (human);mRNA Processing;rRNA processing;Metabolism of RNA;mRNA Splicing - Major Pathway;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- 0.347
- hipred
- Y
- hipred_score
- 0.672
- ghis
- 0.650
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Snu13
- Phenotype
Zebrafish Information Network
- Gene name
- snu13b
- Affected structure
- somite development
- Phenotype tag
- abnormal
- Phenotype quality
- disrupted
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;maturation of LSU-rRNA;box C/D snoRNP assembly;rRNA processing;single fertilization
- Cellular component
- dense fibrillar component;nucleus;nucleoplasm;U4atac snRNP;nucleolus;box C/D snoRNP complex;small-subunit processome;protein-containing complex;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome
- Molecular function
- RNA binding;protein binding;snoRNA binding;U4 snRNA binding;U4atac snRNA binding;U3 snoRNA binding;box C/D snoRNA binding;ATPase binding