Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	3257
Gene name Gene Name - the full gene name approved by the HGNC.	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	HPS1
Synonyms (NCBI Gene) Gene synonyms aliases	BLOC3S1, HPS
Chromosome Chromosome number	10
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	10q24.2
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(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
rs281865073	TGA>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, inframe deletion
rs281865074	A>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, 5 prime UTR variant, intron variant
rs281865075	G>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, 5 prime UTR variant, intron variant
rs281865076	G>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, 5 prime UTR variant, intron variant
rs281865077	C>G,T	Pathogenic	Intron variant
rs281865078	C>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, frameshift variant
rs281865080	A>G	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, missense variant
rs281865081	C>-,CC	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant, 5 prime UTR variant
rs281865082	G>-,GG	Pathogenic-likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant, 5 prime UTR variant
rs281865084	G>-	Likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, frameshift variant
rs281865085	->T	Pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, frameshift variant
rs281865086	T>-	Pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, frameshift variant
rs281865087	T>-	Pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, frameshift variant
rs281865088	T>G	Likely-pathogenic, pathogenic	Genic downstream transcript variant, splice acceptor variant
rs281865089	C>G,T	Pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant, stop gained, non coding transcript variant
rs281865090	A>G	Pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, missense variant
rs281865091	C>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, frameshift variant
rs281865092	->G	Pathogenic	Frameshift variant, coding sequence variant, initiator codon variant, genic downstream transcript variant, non coding transcript variant
rs281865163	->CTCCCCTGCTGGGGGC	Pathogenic	Frameshift variant, downstream transcript variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs374689398	A>G	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs569192835	T>C	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, downstream transcript variant, missense variant
rs748106098	G>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant
rs773323079	ACAGGAAGTT>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant, non coding transcript variant
rs786205464	C>T	Likely-pathogenic	Stop gained, coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant
rs886077189	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs1260083432	C>T	Likely-pathogenic	Intron variant
rs1486224265	A>G	Pathogenic	Splice donor variant, intron variant
rs1591002808	G>A	Likely-pathogenic	Genic downstream transcript variant, stop gained, coding sequence variant, non coding transcript variant
rs1591003183	C>-	Likely-pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs1591031929	G>A	Pathogenic	Genic downstream transcript variant, stop gained, coding sequence variant, non coding transcript variant
rs1591045080	A>G	Likely-pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs1591055649	GTGGGGAACCAGTGTTTGGAGGGTGTCCTCTGCTATCTACAGAGGAAGAAGAGCTGCAGTGAGAGGTGGGATCCCTAAGT>A	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, splice acceptor variant, genic downstream transcript variant
rs1591082099	T>C	Likely-pathogenic	Intron variant, splice acceptor variant
rs1591109881	A>C	Likely-pathogenic	Synonymous variant, coding sequence variant, 5 prime UTR variant, splice donor variant, missense variant
rs1591120765	C>A	Pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant, non coding transcript variant

Show/Hide all(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
MIRT1054204	hsa-miR-4459	CLIP-seq
MIRT1054205	hsa-miR-4755-3p	CLIP-seq
MIRT1054206	hsa-miR-665	CLIP-seq
MIRT1054207	hsa-miR-3613-3p	CLIP-seq
MIRT1054208	hsa-miR-3646	CLIP-seq
MIRT1054209	hsa-miR-4251	CLIP-seq
MIRT1054210	hsa-miR-4329	CLIP-seq
MIRT1054211	hsa-miR-520d-5p	CLIP-seq
MIRT1054212	hsa-miR-524-5p	CLIP-seq
MIRT1054213	hsa-miR-580	CLIP-seq
MIRT1054214	hsa-miR-627	CLIP-seq
MIRT1054215	hsa-miR-924	CLIP-seq
MIRT2012306	hsa-miR-3154	CLIP-seq
MIRT2012307	hsa-miR-4417	CLIP-seq
MIRT2012308	hsa-miR-4437	CLIP-seq
MIRT2012309	hsa-miR-4674	CLIP-seq
MIRT2012310	hsa-miR-4715-3p	CLIP-seq
MIRT2012311	hsa-miR-541	CLIP-seq
MIRT2012312	hsa-miR-654-5p	CLIP-seq
MIRT2244654	hsa-miR-1976	CLIP-seq
MIRT2244655	hsa-miR-2467-5p	CLIP-seq
MIRT2012310	hsa-miR-4715-3p	CLIP-seq
MIRT2389156	hsa-miR-1293	CLIP-seq
MIRT2389157	hsa-miR-3184	CLIP-seq
MIRT2389158	hsa-miR-3622a-3p	CLIP-seq
MIRT2389159	hsa-miR-3622b-3p	CLIP-seq
MIRT2389160	hsa-miR-423-5p	CLIP-seq
MIRT2012307	hsa-miR-4417	CLIP-seq
MIRT2389161	hsa-miR-4483	CLIP-seq
MIRT2389162	hsa-miR-4691-5p	CLIP-seq
MIRT2389163	hsa-miR-4704-3p	CLIP-seq
MIRT2389164	hsa-miR-4731-5p	CLIP-seq
MIRT2389165	hsa-miR-516a-3p	CLIP-seq
MIRT2012311	hsa-miR-541	CLIP-seq
MIRT2389166	hsa-miR-544b	CLIP-seq
MIRT2012312	hsa-miR-654-5p	CLIP-seq
MIRT2547520	hsa-miR-1182	CLIP-seq
MIRT2547521	hsa-miR-1228	CLIP-seq
MIRT2547522	hsa-miR-1236	CLIP-seq
MIRT2547523	hsa-miR-1285	CLIP-seq
MIRT2389156	hsa-miR-1293	CLIP-seq
MIRT2547524	hsa-miR-1324	CLIP-seq
MIRT2547525	hsa-miR-1587	CLIP-seq
MIRT2547526	hsa-miR-184	CLIP-seq
MIRT2547527	hsa-miR-1913	CLIP-seq
MIRT2547528	hsa-miR-2110	CLIP-seq
MIRT2547529	hsa-miR-2392	CLIP-seq
MIRT2244655	hsa-miR-2467-5p	CLIP-seq
MIRT2547530	hsa-miR-3147	CLIP-seq
MIRT2012306	hsa-miR-3154	CLIP-seq
MIRT2547531	hsa-miR-3157-3p	CLIP-seq
MIRT2547532	hsa-miR-3158-5p	CLIP-seq
MIRT2547533	hsa-miR-3166	CLIP-seq
MIRT2547534	hsa-miR-3170	CLIP-seq
MIRT2547535	hsa-miR-3187-5p	CLIP-seq
MIRT2547536	hsa-miR-323-5p	CLIP-seq
MIRT2547537	hsa-miR-324-3p	CLIP-seq
MIRT2547538	hsa-miR-3620	CLIP-seq
MIRT2547539	hsa-miR-3664-3p	CLIP-seq
MIRT1054202	hsa-miR-3689d	CLIP-seq
MIRT2547540	hsa-miR-378g	CLIP-seq
MIRT2547541	hsa-miR-4252	CLIP-seq
MIRT2547542	hsa-miR-4271	CLIP-seq
MIRT2547543	hsa-miR-4276	CLIP-seq
MIRT2547544	hsa-miR-4292	CLIP-seq
MIRT2547545	hsa-miR-4315	CLIP-seq
MIRT2547546	hsa-miR-4418	CLIP-seq
MIRT2547547	hsa-miR-4425	CLIP-seq
MIRT1054204	hsa-miR-4459	CLIP-seq
MIRT2389161	hsa-miR-4483	CLIP-seq
MIRT2012309	hsa-miR-4674	CLIP-seq
MIRT2547548	hsa-miR-4695-5p	CLIP-seq
MIRT2547549	hsa-miR-4700-3p	CLIP-seq
MIRT2547550	hsa-miR-4701-5p	CLIP-seq
MIRT2012310	hsa-miR-4715-3p	CLIP-seq
MIRT2547551	hsa-miR-4725-3p	CLIP-seq
MIRT2547552	hsa-miR-4771	CLIP-seq
MIRT2547553	hsa-miR-4781-3p	CLIP-seq
MIRT2547554	hsa-miR-4790-5p	CLIP-seq
MIRT2547555	hsa-miR-4802-3p	CLIP-seq
MIRT2547556	hsa-miR-4802-5p	CLIP-seq
MIRT2547557	hsa-miR-491-5p	CLIP-seq
MIRT2547558	hsa-miR-509-3-5p	CLIP-seq
MIRT2547559	hsa-miR-509-5p	CLIP-seq
MIRT1054211	hsa-miR-520d-5p	CLIP-seq
MIRT1054212	hsa-miR-524-5p	CLIP-seq
MIRT2547560	hsa-miR-588	CLIP-seq
MIRT2547561	hsa-miR-601	CLIP-seq
MIRT2547562	hsa-miR-612	CLIP-seq
MIRT2547563	hsa-miR-642a	CLIP-seq
MIRT1054201	hsa-miR-1202	CLIP-seq
MIRT2547521	hsa-miR-1228	CLIP-seq
MIRT2547523	hsa-miR-1285	CLIP-seq
MIRT2389156	hsa-miR-1293	CLIP-seq
MIRT2547524	hsa-miR-1324	CLIP-seq
MIRT2547526	hsa-miR-184	CLIP-seq
MIRT2547527	hsa-miR-1913	CLIP-seq
MIRT2547528	hsa-miR-2110	CLIP-seq
MIRT2547529	hsa-miR-2392	CLIP-seq
MIRT2682454	hsa-miR-2467-3p	CLIP-seq
MIRT2244655	hsa-miR-2467-5p	CLIP-seq
MIRT2547531	hsa-miR-3157-3p	CLIP-seq
MIRT2547532	hsa-miR-3158-5p	CLIP-seq
MIRT2547533	hsa-miR-3166	CLIP-seq
MIRT2547534	hsa-miR-3170	CLIP-seq
MIRT2547535	hsa-miR-3187-5p	CLIP-seq
MIRT2547536	hsa-miR-323-5p	CLIP-seq
MIRT2547537	hsa-miR-324-3p	CLIP-seq
MIRT2547538	hsa-miR-3620	CLIP-seq
MIRT2547539	hsa-miR-3664-3p	CLIP-seq
MIRT2682455	hsa-miR-3678-3p	CLIP-seq
MIRT1054202	hsa-miR-3689d	CLIP-seq
MIRT1054203	hsa-miR-3972	CLIP-seq
MIRT2547541	hsa-miR-4252	CLIP-seq
MIRT2547542	hsa-miR-4271	CLIP-seq
MIRT2547544	hsa-miR-4292	CLIP-seq
MIRT2547545	hsa-miR-4315	CLIP-seq
MIRT2547546	hsa-miR-4418	CLIP-seq
MIRT1054204	hsa-miR-4459	CLIP-seq
MIRT2389161	hsa-miR-4483	CLIP-seq
MIRT2547548	hsa-miR-4695-5p	CLIP-seq
MIRT2547550	hsa-miR-4701-5p	CLIP-seq
MIRT2547551	hsa-miR-4725-3p	CLIP-seq
MIRT1054205	hsa-miR-4755-3p	CLIP-seq
MIRT2547552	hsa-miR-4771	CLIP-seq
MIRT2547554	hsa-miR-4790-5p	CLIP-seq
MIRT2547555	hsa-miR-4802-3p	CLIP-seq
MIRT2547556	hsa-miR-4802-5p	CLIP-seq
MIRT2547557	hsa-miR-491-5p	CLIP-seq
MIRT2547558	hsa-miR-509-3-5p	CLIP-seq
MIRT2547559	hsa-miR-509-5p	CLIP-seq
MIRT2547560	hsa-miR-588	CLIP-seq
MIRT2547561	hsa-miR-601	CLIP-seq
MIRT2547562	hsa-miR-612	CLIP-seq
MIRT1054206	hsa-miR-665	CLIP-seq

Show/Hide all(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
GO:0005737	Component	Cytoplasm	TAS	10625677
GO:0005764	Component	Lysosome	TAS	10625677
GO:0005829	Component	Cytosol	TAS
GO:0007040	Process	Lysosome organization	TAS	10625677
GO:0007601	Process	Visual perception	IEA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0031085	Component	BLOC-3 complex	IBA
GO:0031085	Component	BLOC-3 complex	IPI	12756248, 20048159, 23084991
GO:0031410	Component	Cytoplasmic vesicle	IDA	11836498
GO:0046983	Function	Protein dimerization activity	IPI	12663659
GO:0060155	Process	Platelet dense granule organization	NAS	20048159
GO:1903232	Process	Melanosome assembly	IBA
GO:1903232	Process	Melanosome assembly	IDA	23084991
GO:1903232	Process	Melanosome assembly	NAS	23174301

MIM	HGNC	e!Ensembl
604982	5163	ENSG00000107521

Protein

UniProt ID

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

MKCVLVATEGAEVLFYWTDQEFEESLRLKFGQSENEEEELPALEDQLSTLLAPVIISSMT
MLEKLSDTYTCFSTENGNFLYVLHLFGECLFIAINGDHTESEGDLRRKLYVLKYLFEVHF
GLVTVDGHLIRKELRPPDLAQRVQLWEHFQSLLWTYSRLREQEQCFAVEALERLIHPQLC
ELCIEALERHVIQAVNTSPERGGEEALHAFLLVHSKLLAFYSSHSASSLRPADLLALILL
VQDLYPSESTAEDDIQPSPRRARSSQNIPVQQAWSPHSTGPTGGSSAETETDSFSLPEEY
FTPAPSPGDQSSGSTIWLEGGTPPMDALQIAEDTLQTLVPHCPVPSGPRRIFLDANVKES
YCPLVPHTMYCLPLWQGINLVLLTRSPSAPLALVLSQLMDGFSMLEKKLKEGPEPGASLR
SQPLVGDLRQRMDKFVKNRGAQEIQSTWLEFKAKAFSKSEPGSSWELLQACGKLKRQLCA
IYRLNFLTTAPSRGGPHLPQHLQDQVQRLMREKLTDWKDFLLVKSRRNITMVSYLEDFPG
LVHFIYVDRTTGQMVAPSLNCSQKTSSELGKGPLAAFVKTKVWSLIQLARRYLQKGYTTL
LFQEGDFYCSYFLWFENDMGYKLQMIEVPVLSDDSVPIGMLGGDYYRKLLRYYSKNRPTE
AVRCYELLALHLSVIPTDLLVQQAGQLARRLWEASRIPLL

Sequence length

700

Interactions

View interactions

	Reactome
			RAB GEFs exchange GTP for GDP on RABs

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Hermansky-Pudlak Syndrome	Hermansky-Pudlak syndrome 1	rs121908385, rs281865086, rs886077189, rs281865081, rs1591120765, rs281865082, rs281865088, rs786205464, rs1260083432, rs1591055649, rs1591092841, rs121908386, rs281865090, rs773323079, rs281865075 View all (10 more)	N/A
hermansky-pudlak syndrome	Hermansky-Pudlak syndrome	rs1453977337, rs281865086, rs281865080, rs886077189, rs281865081, rs121908385, rs281865088, rs281865082, rs281865090, rs1591002808, rs773323079, rs1591045080, rs281865075, rs1486224265, rs281865077 View all (4 more)	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Hermansky-Pudlak Syndrome With Pulmonary Fibrosis	Hermansky-Pudlak syndrome with pulmonary fibrosis	N/A	N/A	GenCC
Oligodendroglioma	Oligodendroglioma	N/A	N/A	GWAS

Show/Hide Text Mining Associations (31)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
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
Inflammation	Associate	36302964
Inflammatory Bowel Diseases	Associate	33423334
Iris Diseases	Associate	34362826
Lung Diseases	Associate	9562579
Lung Diseases Interstitial	Associate	24583434
Lung Injury	Associate	25400188
Lysosomal Storage Diseases	Associate	16093596
Melanoma	Associate	11564171
Menorrhagia	Stimulate	30659653
Metabolic Diseases	Associate	36302964
Microphthalmia Isolated With Corectopia	Associate	34362826
Neoplasms	Associate	33801246
Nevus	Associate	15982315
Nevus Pigmented	Associate	15982315
Nystagmus Pathologic	Associate	19398212
Pigmentation Disorders	Associate	23084991, 9562579
Platelet granule deficiency disorder	Associate	15020272
Pulmonary Fibrosis	Associate	19398212, 29941477, 31619213
Pulmonary Fibrosis	Stimulate	33536261
Stroke	Associate	19023099
Vision Disorders	Associate	11590544, 19398212

HPS1 (HPS1 biogenesis of lysosomal organelles complex 3 subunit 1)