SNUPN
Basic information
Region (hg38): 15:75598083-75626469
Previous symbols: [ "RNUT1" ]
Links
Phenotypes
GenCC
Source:
- muscular dystrophy, limb-girdle, autosomal recessive 29 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Muscular dystrophy, limb-girdle, autosomal recessive 29 | AR | 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 | Musculoskeletal; Neurologic; Ophthalmologic | 38366623; 38413582 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (40 variants)
- not_provided (2 variants)
- SNUPN_deficiency_muscular_dystrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNUPN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005701.4. 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 | 0 | |||||
| missense | 36 | 40 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 3 | 36 | 3 | 0 |
Highest pathogenic variant AF is 0.00016170103
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNUPN | protein_coding | protein_coding | ENST00000564644 | 8 | 28387 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.11e-14 | 0.0112 | 125659 | 0 | 88 | 125747 | 0.000350 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.608 | 175 | 199 | 0.879 | 0.0000104 | 2368 |
| Missense in Polyphen | 54 | 56.579 | 0.95442 | 634 | ||
| Synonymous | 1.09 | 63 | 75.0 | 0.840 | 0.00000393 | 661 |
| Loss of Function | -0.157 | 21 | 20.2 | 1.04 | 0.00000110 | 226 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000530 | 0.000530 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000273 | 0.000272 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000433 | 0.000431 |
| Middle Eastern | 0.000273 | 0.000272 |
| South Asian | 0.000556 | 0.000555 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs. {ECO:0000269|PubMed:10209022, ECO:0000269|PubMed:15920472, ECO:0000269|PubMed:16030253, ECO:0000269|PubMed:9670026}.;
- Pathway
- RNA transport - Homo sapiens (human);snRNP Assembly;Metabolism of RNA;Metabolism of non-coding RNA
(Consensus)
Intolerance Scores
- loftool
- 0.518
- rvis_EVS
- 0.6
- rvis_percentile_EVS
- 82.66
Haploinsufficiency Scores
- pHI
- 0.0938
- hipred
- Y
- hipred_score
- 0.515
- ghis
- 0.485
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.990
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snupn
- Phenotype
Gene ontology
- Biological process
- spliceosomal snRNP assembly;protein import into nucleus;import into nucleus;snRNA import into nucleus
- Cellular component
- nuclear pore;cytosol
- Molecular function
- RNA cap binding;protein binding;nuclear import signal receptor activity