BCAS2
Basic information
Region (hg38): 1:114567557-114581629
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 BCAS2 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 | 8 | |||||
| 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 | 1 |
Variants in BCAS2
This is a list of pathogenic ClinVar variants found in the BCAS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-114568143-C-T | not specified | Uncertain significance (Jun 01, 2023) | ||
| 1-114568156-T-C | not specified | Uncertain significance (May 09, 2024) | ||
| 1-114570066-A-C | not specified | Uncertain significance (Jun 16, 2023) | ||
| 1-114570067-T-C | not specified | Uncertain significance (Dec 30, 2023) | ||
| 1-114570746-G-C | not specified | Uncertain significance (Feb 19, 2025) | ||
| 1-114575611-T-C | not specified | Uncertain significance (Apr 25, 2022) | ||
| 1-114575630-T-C | not specified | Uncertain significance (Mar 13, 2023) | ||
| 1-114575641-T-G | not specified | Uncertain significance (Jan 23, 2025) | ||
| 1-114576718-C-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 1-114581533-T-C | not specified | Uncertain significance (Jan 07, 2025) | ||
| 1-114581582-T-C | Benign (Jun 14, 2017) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BCAS2 | protein_coding | protein_coding | ENST00000369541 | 7 | 14083 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.78e-8 | 0.302 | 125712 | 0 | 33 | 125745 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.515 | 101 | 117 | 0.866 | 0.00000548 | 1466 |
| Missense in Polyphen | 10 | 21.404 | 0.46721 | 311 | ||
| Synonymous | 0.0388 | 41 | 41.3 | 0.992 | 0.00000188 | 398 |
| Loss of Function | 0.599 | 13 | 15.5 | 0.836 | 8.19e-7 | 178 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000339 | 0.000334 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000385 | 0.000381 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.000385 | 0.000381 |
| South Asian | 0.000197 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. May have a scaffolding role in the spliceosome assembly as it contacts all other components of the core complex. The PRP19-CDC5L complex may also play a role in the response to DNA damage (DDR). {ECO:0000269|PubMed:24332808}.;
- Pathway
- Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.562
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 62.74
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.489
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bcas2
- Phenotype
- cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype;
Gene ontology
- Biological process
- RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;RNA splicing
- Cellular component
- Prp19 complex;nucleoplasm;DNA replication factor A complex;spliceosomal complex;nucleolus;centrosome;nuclear speck;U2-type catalytic step 2 spliceosome
- Molecular function
- protein binding