BLOC1S4

Chr 4

biogenesis of lysosomal organelles complex 1 subunit 4

Also known as: BCAS4L, BLOS4, CNO

NCBI Gene: 55330ENSG00000186222UniProt: Q9NUP1

This protein is a component of the BLOC-1 complex required for biogenesis of lysosome-related organelles such as platelet dense granules and melanosomes, and targets membrane proteins into vesicles for delivery to neurites and nerve terminals. Mutations cause Hermansky-Pudlak syndrome, which involves bleeding disorders due to platelet dysfunction and oculocutaneous albinism. The condition follows autosomal recessive inheritance.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
0
Pubs (1 yr)
86
P/LP submissions
0%
P/LP missense
1.87
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— BLOC1S4
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.10) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
86 unique Pathogenic / Likely Pathogenic· 49 VUS of 137 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.87LOEUF
pLI 0.102
Z-score 0.17
OE 0.83 (0.24–1.87)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.05Z-score
OE missense 0.98 (0.83–1.17)
91 obs / 92.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.83 (0.24–1.87)
0≤0.351.4
Missense OE0.98 (0.83–1.17)
0≤0.61.4
Synonymous OE1.08
0≤1.21.6
LoF obs/exp: 1 / 1.2Missense obs/exp: 91 / 92.5Syn Z: -0.40
DN
0.6162th %ile
GOF
0.6638th %ile
LOF
0.3162th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

137 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic81
Likely Pathogenic5
VUS49
Likely Benign2
81
Pathogenic
5
Likely Pathogenic
49
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
81
0
81
Likely Pathogenic
0
0
5
0
5
VUS
0
46
3
0
49
Likely Benign
0
2
0
0
2
Benign
0
0
0
0
0
Total048890137

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BLOC1S4 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients