BLOC1S2
biogenesis of lysosomal organelles complex 1 subunit 2, the group of BLOC-1 related complex subunits|Biogenesis of lysosomal organelles complex 1 subunits
Basic information
Region (hg38): 10:100273280-100286680
Links
Phenotypes
GenCC
Source:
No genCC data.
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 BLOC1S2 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in BLOC1S2
This is a list of pathogenic ClinVar variants found in the BLOC1S2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-100280150-T-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 10-100286104-T-A | not specified | Uncertain significance (Apr 19, 2024) | ||
| 10-100286646-G-A | not specified | Uncertain significance (Jan 04, 2022) | ||
| 10-100286649-G-A | not specified | Uncertain significance (Aug 17, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BLOC1S2 | protein_coding | protein_coding | ENST00000370372 | 5 | 12757 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0119 | 0.860 | 125690 | 0 | 49 | 125739 | 0.000195 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.00 | 50 | 74.3 | 0.673 | 0.00000330 | 920 |
| Missense in Polyphen | 3 | 19.947 | 0.1504 | 291 | ||
| Synonymous | -1.40 | 38 | 28.5 | 1.33 | 0.00000127 | 257 |
| Loss of Function | 1.25 | 4 | 7.75 | 0.516 | 3.29e-7 | 104 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000579 | 0.0000579 |
| Ashkenazi Jewish | 0.000695 | 0.000695 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000343 | 0.000343 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the BLOC-1 complex, a complex that is required for normal biogenesis of lysosome-related organelles (LRO), such as platelet dense granules and melanosomes (PubMed:15102850, PubMed:17182842). In concert with the AP-3 complex, the BLOC-1 complex is required to target membrane protein cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals. The BLOC-1 complex, in association with SNARE proteins, is also proposed to be involved in neurite extension (By similarity). As part of the BORC complex may play a role in lysosomes movement and localization at the cell periphery. Associated with the cytosolic face of lysosomes, the BORC complex may recruit ARL8B and couple lysosomes to microtubule plus-end- directed kinesin motor (PubMed:25898167). May play a role in cell proliferation (PubMed:15381421). {ECO:0000250|UniProtKB:Q9CWG9, ECO:0000269|PubMed:15102850, ECO:0000269|PubMed:15381421, ECO:0000269|PubMed:17182842, ECO:0000269|PubMed:25898167}.;
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- loftool
- 0.357
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.11
Haploinsufficiency Scores
- pHI
- 0.163
- hipred
- Y
- hipred_score
- 0.514
- ghis
- 0.558
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.435
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bloc1s2
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype; embryo phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- bloc1s2
- Affected structure
- erythroid lineage cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased occurrence
Gene ontology
- Biological process
- anterograde axonal transport;extrinsic apoptotic signaling pathway via death domain receptors;endosomal transport;neuron projection development;lysosome localization;melanosome organization;anterograde synaptic vesicle transport;platelet dense granule organization;mitochondrial outer membrane permeabilization
- Cellular component
- gamma-tubulin complex;mitochondrion;lysosomal membrane;BLOC-1 complex;BORC complex;axon cytoplasm
- Molecular function
- protein binding;gamma-tubulin binding