BLOC1S4

biogenesis of lysosomal organelles complex 1 subunit 4, the group of Biogenesis of lysosomal organelles complex 1 subunits

Basic information

Region (hg38): 4:6716174-6717664

Previous symbols: [ "CNO" ]

Links

ENSG00000186222 ∙ NCBI:55330 ∙ OMIM:605695 ∙ HGNC:24206 ∙ Uniprot:Q9NUP1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BLOC1S4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BLOC1S4 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in BLOC1S4

This is a list of pathogenic ClinVar variants found in the BLOC1S4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-6716229-A-T		not specified	Uncertain significance (Apr 25, 2023)
4-6716240-C-G		not specified	Uncertain significance (Aug 09, 2021)
4-6716241-T-C		not specified	Likely benign (May 24, 2024)
4-6716250-G-A		not specified	Uncertain significance (Jul 20, 2022)
4-6716282-G-C		not specified	Uncertain significance (Feb 28, 2023)
4-6716312-C-G		not specified	Uncertain significance (Jan 20, 2023)
4-6716337-C-T		not specified	Uncertain significance (May 27, 2022)
4-6716346-A-G		not specified	Uncertain significance (Aug 10, 2021)
4-6716357-G-C		not specified	Uncertain significance (Aug 07, 2024)
4-6716369-C-T		not specified	Uncertain significance (Apr 15, 2024)
4-6716370-C-T		not specified	Uncertain significance (Jul 11, 2023)
4-6716403-C-G		not specified	Uncertain significance (Jan 28, 2025)
4-6716435-G-A		not specified	Uncertain significance (Jan 31, 2022)
4-6716442-C-T		not specified	Uncertain significance (Sep 07, 2022)
4-6716445-G-T		not specified	Uncertain significance (Jun 24, 2022)
4-6716447-C-T		not specified	Uncertain significance (Aug 04, 2023)
4-6716466-A-G		not specified	Uncertain significance (Aug 15, 2023)
4-6716480-G-T		not specified	Uncertain significance (May 12, 2024)
4-6716538-C-T		not specified	Uncertain significance (Jun 06, 2023)
4-6716555-G-C		not specified	Uncertain significance (Jan 08, 2024)
4-6716567-C-A		not specified	Uncertain significance (Feb 10, 2022)
4-6716582-G-A		not specified	Uncertain significance (Dec 17, 2024)
4-6716597-C-T		not specified	Uncertain significance (Dec 12, 2024)
4-6716604-A-G		not specified	Uncertain significance (Feb 04, 2025)
4-6716637-G-C		not specified	Uncertain significance (Dec 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BLOC1S4	protein_coding	protein_coding	ENST00000320776	1	1546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.102	0.601	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0541	91	92.5	0.984	0.00000415	1382
Missense in Polyphen		28	31.216	0.89697		472
Synonymous	-0.403	46	42.6	1.08	0.00000200	463
Loss of Function	0.174	1	1.21	0.829	5.12e-8	31

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. 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. Plays a role in intracellular vesicle trafficking. {ECO:0000269|PubMed:17182842}.
• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Recessive Scores

• pRec: 0.119

Haploinsufficiency Scores

• pHI: 0.0725
• hipred: N
• hipred_score: 0.379
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bloc1s4
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; pigmentation phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; renal/urinary system phenotype; vision/eye phenotype

Gene ontology

• Biological process: anterograde axonal transport;neuron projection development;melanosome organization;anterograde synaptic vesicle transport;neuromuscular process controlling balance;platelet aggregation
• Cellular component: cytoplasm;cytosol;BLOC-1 complex;axon cytoplasm
• Molecular function: protein binding