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

ENSG00000196072 ∙ NCBI:282991 ∙ OMIM:609768 ∙ HGNC:20984 ∙ Uniprot:Q6QNY1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 18.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_173809.5	NP_776170.2	5	yes	-
ENST00000370372.7	ENSP00000359398.2	5	yes	-
NM_001001342.2	NP_001001342.1	4	-	-
NM_001282436.2	NP_001269365.1	4	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BLOC1S2 gene.

• not_specified (8 variants)

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. These statistics are base on transcript: NM_173809.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5			5
Total	0	0	15	0	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

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

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