SNRPC
Basic information
Region (hg38): 6:34757504-34773857
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 SNRPC 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in SNRPC
This is a list of pathogenic ClinVar variants found in the SNRPC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-34767971-C-T | not specified | Uncertain significance (Jun 28, 2022) | ||
| 6-34767986-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
| 6-34770302-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 6-34770305-C-T | not specified | Uncertain significance (Dec 15, 2023) | ||
| 6-34773463-C-T | not specified | Uncertain significance (Jun 21, 2023) | ||
| 6-34773502-A-G | not specified | Uncertain significance (Mar 15, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNRPC | protein_coding | protein_coding | ENST00000244520 | 6 | 16389 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.723 | 0.274 | 125735 | 0 | 2 | 125737 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.55 | 31 | 104 | 0.297 | 0.00000552 | 1060 |
| Missense in Polyphen | 2 | 18.229 | 0.10972 | 234 | ||
| Synonymous | -1.39 | 35 | 26.0 | 1.35 | 0.00000128 | 286 |
| Loss of Function | 2.39 | 1 | 8.55 | 0.117 | 4.58e-7 | 98 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000620 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| 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. SNRPC/U1-C is directly involved in initial 5' splice-site recognition for both constitutive and regulated alternative splicing. The interaction with the 5' splice-site seems to precede base-pairing between the pre-mRNA and the U1 snRNA. Stimulates commitment or early (E) complex formation by stabilizing the base pairing of the 5' end of the U1 snRNA and the 5' splice-site region. {ECO:0000255|HAMAP- Rule:MF_03153, ECO:0000269|PubMed:1826349, ECO:0000269|PubMed:19325628, ECO:0000269|PubMed:2136774, ECO:0000269|PubMed:8798632}.;
- Pathway
- Spliceosome - Homo sapiens (human);spliceosomal assembly;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.0835
Intolerance Scores
- loftool
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.0917
- hipred
- Y
- hipred_score
- 0.804
- ghis
- 0.662
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.937
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snrpc
- Phenotype
Zebrafish Information Network
- Gene name
- snrpc
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- curved dorsal
Gene ontology
- Biological process
- spliceosomal snRNP assembly;mRNA 5'-splice site recognition;mRNA splicing, via spliceosome
- Cellular component
- nucleoplasm;U1 snRNP;Cajal body;U2-type prespliceosome
- Molecular function
- RNA binding;single-stranded RNA binding;mRNA binding;protein binding;zinc ion binding;U1 snRNA binding;pre-mRNA 5'-splice site binding;protein homodimerization activity;U1 snRNP binding