Gene Gene information from NCBI Gene database.
Entrez ID 3257
Gene name HPS1 biogenesis of lysosomal organelles complex 3 subunit 1
Gene symbol HPS1
Synonyms (NCBI Gene)
BLOC3S1HPS
Chromosome 10
Chromosome location 10q24.2
Summary 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 org
SNPs SNP information provided by dbSNP.
40
SNP ID Visualize variation Clinical significance Consequence
rs115265574 C>G,T Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity 5 prime UTR variant, non coding transcript variant, coding sequence variant, synonymous variant
rs121908385 C>A,T Pathogenic, likely-pathogenic Genic downstream transcript variant, missense variant, non coding transcript variant, stop gained, coding sequence variant
rs121908386 C>A,T Pathogenic 5 prime UTR variant, missense variant, non coding transcript variant, coding sequence variant, stop gained, intron variant
rs138771756 G>T Likely-pathogenic Genic downstream transcript variant, missense variant, non coding transcript variant, coding sequence variant
rs150444975 G>A,T Conflicting-interpretations-of-pathogenicity Missense variant, synonymous variant, coding sequence variant, non coding transcript variant, 5 prime UTR variant
miRNA miRNA information provided by mirtarbase database.
140
miRTarBase ID miRNA Experiments Reference
MIRT048904 hsa-miR-93-5p CLASH 23622248
MIRT043286 hsa-miR-331-3p CLASH 23622248
MIRT1054201 hsa-miR-1202 CLIP-seq
MIRT1054202 hsa-miR-3689d CLIP-seq
MIRT1054203 hsa-miR-3972 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
19
GO ID Ontology Definition Evidence Reference
GO:0005085 Function Guanyl-nucleotide exchange factor activity IBA
GO:0005085 Function Guanyl-nucleotide exchange factor activity IDA 23084991
GO:0005085 Function Guanyl-nucleotide exchange factor activity IEA
GO:0005515 Function Protein binding IPI 12756248, 20048159, 23084991
GO:0005737 Component Cytoplasm IDA 12756248
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
604982 5163 ENSG00000107521
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q92902
Protein name BLOC-3 complex member HPS1 (Hermansky-Pudlak syndrome 1 protein)
Protein function Component of the BLOC-3 complex, a complex that acts as a guanine exchange factor (GEF) for RAB32 and RAB38, promotes the exchange of GDP to GTP, converting them from an inactive GDP-bound form into an active GTP-bound form. The BLOC-3 complex p
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF19036 Fuz_longin_1 2 159 First Longin domain of FUZ, MON1 and HPS1 Domain
PF19037 Fuz_longin_2 204 405 Second Longin domain of FUZ, MON1 and HPS1 Domain
PF19038 Fuz_longin_3 540 695 Third Longin domain of FUZ, MON1 and HPS1 Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitous.
Sequence
Sequence length 700
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    RAB GEFs exchange GTP for GDP on RABs
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
599
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Hermansky-Pudlak syndrome Likely pathogenic; Pathogenic rs764927038, rs748888649, rs1185127836, rs748939090, rs758797992, rs769446880, rs1845534948, rs1330094451, rs281865163, rs121908385, rs281865082, rs281865077, rs2538792615, rs2538722919, rs281865084
View all (16 more)
RCV001826175
RCV001829291
RCV001829293
RCV001829295
RCV001829300
RCV001829311
RCV005614712
RCV003230766
RCV000614559
RCV000851731
RCV001273031
RCV003387717
RCV003226649
RCV004527060
RCV000851664
RCV001829292
RCV000851717
RCV004526896
RCV001275007
RCV001826482
RCV004699583
RCV001829294
RCV001829427
RCV001829480
RCV000851934
RCV000851267
RCV000851266
RCV001827370
RCV001828706
RCV001264552
RCV001264553
Hermansky-Pudlak syndrome 1 Likely pathogenic; Pathogenic rs1278834481, rs1938751649, rs2136083690, rs764927038, rs1846158787, rs2136197089, rs750909242, rs2136102397, rs758028806, rs1185127836, rs758797992, rs769446880, rs2136327710, rs962689701, rs972096803
View all (71 more)
RCV003475196
RCV001334305
RCV003469647
RCV003469730
RCV003473944
RCV001535829
RCV001782261
RCV001782262
RCV002503326
RCV003470937
RCV003470938
RCV003470939
RCV004571524
RCV003475168
RCV003470960
RCV002245363
RCV003465950
RCV003987398
RCV003465957
RCV005034817
RCV005034373
RCV000005595
RCV000005597
RCV000005598
RCV000005599
RCV000005600
RCV000005601
RCV005028125
RCV003146048
RCV001332268
RCV003476436
RCV003468357
RCV003476438
RCV003468358
RCV003468359
RCV003476439
RCV003468361
RCV003468362
RCV003468363
RCV003468364
RCV003476440
RCV003469784
RCV003476441
RCV003469785
RCV003476442
RCV003469786
RCV003476443
RCV003469787
RCV003476444
RCV003476445
RCV003476446
RCV003469788
RCV003476447
RCV003476448
RCV003476449
RCV003469789
RCV003469790
RCV003469791
RCV006275901
RCV004573369
RCV004573376
RCV000020181
RCV003475104
RCV002482892
RCV005025620
RCV000020193
RCV001804742
RCV003475214
RCV003475105
RCV004576721
RCV004576722
RCV004576723
RCV004576724
RCV000500361
RCV003470646
RCV002493407
RCV000851388
RCV000851390
RCV005036199
RCV000856814
RCV000856816
RCV003467767
RCV003469361
RCV003313990
RCV001780109
RCV003469434
RCV001290770
RCV001290771
Hermansky-Pudlak syndrome with pulmonary fibrosis Pathogenic rs2136156603 RCV001823204
HPS1-related disorder Likely pathogenic; Pathogenic rs2136083690, rs972096803, rs281865163, rs281865082, rs281865084, rs773323079, rs374689398 RCV004754745
RCV003426221
RCV004754244
RCV004754246
RCV004754268
RCV003419860
RCV003413557
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Cervical cancer Benign; Likely benign rs1801286, rs56378825 RCV005892308
RCV005908077
Cholangiocarcinoma Benign rs11591555 RCV005918377
Clear cell carcinoma of kidney Benign rs56378825 RCV005908078
Colorectal cancer Benign; Likely benign rs199874645 RCV005902652
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Albinism Associate 33808351, 35488210, 39457042
Albinism Oculocutaneous Associate 16093596, 19398212, 19865097, 30791930, 33124154, 35328057, 35870188
Albinism with hemorrhagic diathesis and pigmented reticuloendothelial cells Associate 11590544, 15982315, 19334085, 27459687, 29941477, 30634918, 30833808
Blood Platelet Disorders Associate 14510955
Carcinoma Pancreatic Ductal Associate 33801246
Crohn Disease Associate 36302964
Granuloma Associate 36302964
Hemorrhagic Disorders Associate 19398212
Hermanski Pudlak Syndrome Associate 11564171, 11590544, 14510955, 15020272, 15982315, 16093596, 16417222, 19334085, 19398212, 24583434, 25400188, 25468649, 29941477, 30791930, 31216486
View all (6 more)
Hypopigmentation Associate 19398212