HPS1

Chr 10

HPS1 biogenesis of lysosomal organelles complex 3 subunit 1

Also known as: BLOC3S1, HPS

NCBI Gene: 3257ENSG00000107521UniProt: Q92902

This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. The encoded protein is a component of three different protein complexes termed biogenesis of lysosome-related organelles complex (BLOC)-3, BLOC4, and BLOC5. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 1. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on chromosome 22. [provided by RefSeq, Aug 2015]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtHermansky-Pudlak syndrome 1

Clinical highlights

Gene-disease validity (ClinGen)
Hermansky-Pudlak syndrome 1 · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
13
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.69
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — HPS1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.69LOEUF
pLI 0.000
Z-score 3.07
OE 0.47 (0.32–0.69)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.12Z-score
OE missense 0.98 (0.91–1.07)
401 obs / 407.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.47 (0.32–0.69)
0≤0.351.4
Missense OE?0.98 (0.91–1.07)
0≤0.61.4
Synonymous OE?1.06
0≤1.21.6
LoF obs/exp: 18 / 38.6Missense obs/exp: 401 / 407.6Syn Z: -0.60

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

HPS1 · protein map & ClinVar variants

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

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