SNAPC5
Basic information
Region (hg38): 15:66490135-66497780
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 SNAPC5 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 | 7 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 7 | 0 | 0 |
Variants in SNAPC5
This is a list of pathogenic ClinVar variants found in the SNAPC5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-66490357-C-T | Likely benign (Dec 04, 2019) | |||
15-66490358-C-T | Benign (Jan 12, 2020) | |||
15-66490360-C-G | Likely benign (Feb 23, 2021) | |||
15-66490389-C-T | Benign (Dec 07, 2019) | |||
15-66490485-C-T | RASopathy | Likely benign (Nov 04, 2023) | ||
15-66490486-G-A | not specified • RASopathy | Benign (Jan 27, 2024) | ||
15-66490490-C-A | RASopathy | Likely benign (Aug 27, 2023) | ||
15-66490491-C-A | RASopathy | Likely benign (Nov 01, 2022) | ||
15-66490494-A-T | RASopathy | Likely benign (Jul 25, 2023) | ||
15-66490494-AC-A | RASopathy | Likely benign (Nov 25, 2022) | ||
15-66490496-A-G | RASopathy | Likely benign (Jan 22, 2023) | ||
15-66490499-C-T | RASopathy | Uncertain significance (Nov 27, 2023) | ||
15-66490505-C-T | Noonan syndrome • RASopathy | Uncertain significance (Jul 07, 2023) | ||
15-66490514-ATCA-G | Uncertain significance (Nov 09, 2022) | |||
15-66490519-G-A | RASopathy | Likely benign (Nov 17, 2022) | ||
15-66490524-C-A | Cardiovascular phenotype | Uncertain significance (May 17, 2024) | ||
15-66490524-C-T | Uncertain significance (Jul 27, 2022) | |||
15-66490531-T-C | RASopathy • Cardiovascular phenotype | Likely benign (May 09, 2017) | ||
15-66490534-G-A | RASopathy | Likely benign (Mar 26, 2023) | ||
15-66490540-G-A | RASopathy | Likely benign (Nov 24, 2023) | ||
15-66490543-T-C | RASopathy | Likely benign (Jul 19, 2022) | ||
15-66490546-T-G | RASopathy | Uncertain significance (Jul 07, 2023) | ||
15-66490548-C-T | RASopathy | Uncertain significance (Jul 29, 2023) | ||
15-66490549-A-T | RASopathy | Likely benign (Sep 22, 2023) | ||
15-66490552-T-C | Cardiovascular phenotype | Likely benign (Jul 30, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SNAPC5 | protein_coding | protein_coding | ENST00000316634 | 3 | 7679 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000201 | 0.300 | 125726 | 0 | 20 | 125746 | 0.0000795 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.724 | 66 | 51.4 | 1.28 | 0.00000230 | 636 |
Missense in Polyphen | 20 | 14.729 | 1.3579 | 189 | ||
Synonymous | -1.12 | 29 | 22.3 | 1.30 | 0.00000106 | 189 |
Loss of Function | -0.433 | 5 | 4.06 | 1.23 | 1.70e-7 | 53 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000322 | 0.000322 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000326 | 0.000326 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000264 | 0.0000264 |
Middle Eastern | 0.000326 | 0.000326 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box.;
- Pathway
- Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.511
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.0822
- hipred
- N
- hipred_score
- 0.338
- ghis
- 0.639
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snapc5
- Phenotype
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;transcription by RNA polymerase II;transcription initiation from RNA polymerase III promoter;snRNA transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;nucleolus;nuclear body
- Molecular function
- DNA-binding transcription factor activity;protein binding