BLOC1S1
biogenesis of lysosomal organelles complex 1 subunit 1, the group of BLOC-1 related complex subunits|Biogenesis of lysosomal organelles complex 1 subunits
Basic information
Region (hg38): 12:55716038-55720087
Previous symbols: [ "GCN5L1" ]
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AR
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 BLOC1S1 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 | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 0 |
Variants in BLOC1S1
This is a list of pathogenic ClinVar variants found in the BLOC1S1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-55716055-G-C | not specified | Uncertain significance (Apr 12, 2024) | ||
| 12-55716068-G-C | not specified | Uncertain significance (May 15, 2024) | ||
| 12-55716071-G-A | not specified | Uncertain significance (Feb 17, 2024) | ||
| 12-55716077-G-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 12-55716088-C-T | not specified | Uncertain significance (May 16, 2024) | ||
| 12-55716099-G-C | not specified | Uncertain significance (Dec 04, 2024) | ||
| 12-55716123-G-T | not specified | Uncertain significance (Mar 29, 2023) | ||
| 12-55716125-C-T | not specified | Uncertain significance (Jun 18, 2021) | ||
| 12-55716177-T-G | not specified | Uncertain significance (Sep 03, 2024) | ||
| 12-55716939-G-A | not specified | Uncertain significance (Feb 01, 2023) | ||
| 12-55716951-C-T | not specified | Uncertain significance (May 18, 2022) | ||
| 12-55719215-G-T | not specified | Uncertain significance (Feb 17, 2022) | ||
| 12-55719527-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 12-55719547-C-T | not specified | Uncertain significance (Aug 14, 2024) | ||
| 12-55719548-G-A | not specified | Uncertain significance (May 15, 2024) | ||
| 12-55719554-T-C | not specified | Uncertain significance (Oct 28, 2024) | ||
| 12-55719563-C-A | not specified | Uncertain significance (Feb 05, 2025) | ||
| 12-55719589-C-G | not specified | Uncertain significance (Jul 25, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BLOC1S1 | protein_coding | protein_coding | ENST00000548925 | 4 | 4052 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0708 | 0.878 | 125740 | 0 | 6 | 125746 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0339 | 86 | 85.1 | 1.01 | 0.00000420 | 982 |
| Missense in Polyphen | 16 | 22.481 | 0.71172 | 318 | ||
| Synonymous | -0.558 | 38 | 33.9 | 1.12 | 0.00000162 | 303 |
| Loss of Function | 1.65 | 3 | 8.05 | 0.373 | 3.90e-7 | 80 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000910 | 0.0000909 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000274 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| 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. 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 (PubMed:17182842). 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). {ECO:0000269|PubMed:17182842, ECO:0000269|PubMed:25898167}.;
- Pathway
- Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.452
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.163
- hipred
- N
- hipred_score
- 0.174
- ghis
- 0.487
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Bloc1s1
- Phenotype
- vision/eye phenotype; pigmentation 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); homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- bloc1s1
- Affected structure
- iridophore
- Phenotype tag
- abnormal
- Phenotype quality
- lacks all parts of type
Gene ontology
- Biological process
- anterograde axonal transport;aerobic respiration;endosomal transport;peptidyl-lysine acetylation;neuron projection development;lysosome localization;melanosome organization;anterograde synaptic vesicle transport;platelet dense granule organization
- Cellular component
- extracellular space;mitochondrial intermembrane space;mitochondrial matrix;lysosomal membrane;cytosol;BLOC-1 complex;BORC complex;axon cytoplasm
- Molecular function
- protein binding