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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	79803
Gene name	HPS6 biogenesis of lysosomal organelles complex 2 subunit 3
Gene symbol	HPS6
Synonyms (NCBI Gene)	BLOC2S3
Chromosome	10
Chromosome location	10q24.32
Summary	This intronless gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. This protein interacts with Hermansky-Pudlak syndrome 5 protein. Mutations in this gene are associated

Show/Hide all (23)

SNP ID	Visualize variation	Clinical significance	Consequence
rs139161525	G>A	Benign-likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs281865107	C>T	Pathogenic	Coding sequence variant, stop gained
rs281865108	->G	Conflicting-interpretations-of-pathogenicity, pathogenic	Coding sequence variant, frameshift variant
rs281865109	C>T	Pathogenic	Coding sequence variant, missense variant
rs281865110	C>T	Pathogenic	Coding sequence variant, stop gained
rs281865112	C>T	Pathogenic	Coding sequence variant, stop gained
rs281865113	CTGT>-	Pathogenic	Coding sequence variant, frameshift variant
rs281865114	TG>-	Pathogenic	Coding sequence variant, frameshift variant
rs756325364	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs756471925	TC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs763073715	A>C,G,T	Likely-pathogenic	Missense variant, initiator codon variant
rs1131692332	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1131692333	C>T	Pathogenic	Stop gained, coding sequence variant
rs1220869113	->AG	Pathogenic	Coding sequence variant, stop gained
rs1478574193	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1554903728	T>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1564899012	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1564899492	->G	Pathogenic	Frameshift variant, coding sequence variant
rs1564899951	CTGGAGCT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1590262288	CT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1590262450	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs1590263807	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1590263820	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (44)

miRTarBase ID	miRNA	Experiments	Reference
MIRT025655	hsa-miR-7-5p	Microarray	19073608
MIRT040541	hsa-miR-92b-3p	CLASH	23622248
MIRT1054365	hsa-miR-1245b-3p	CLIP-seq
MIRT1054366	hsa-miR-144	CLIP-seq
MIRT1054367	hsa-miR-153	CLIP-seq
MIRT1054368	hsa-miR-25	CLIP-seq
MIRT1054369	hsa-miR-32	CLIP-seq
MIRT1054370	hsa-miR-363	CLIP-seq
MIRT1054371	hsa-miR-367	CLIP-seq
MIRT1054372	hsa-miR-448	CLIP-seq
MIRT1054373	hsa-miR-4672	CLIP-seq
MIRT1054374	hsa-miR-4773	CLIP-seq
MIRT1054375	hsa-miR-92a	CLIP-seq
MIRT1054376	hsa-miR-92b	CLIP-seq
MIRT1054366	hsa-miR-144	CLIP-seq
MIRT1054367	hsa-miR-153	CLIP-seq
MIRT1054368	hsa-miR-25	CLIP-seq
MIRT1054369	hsa-miR-32	CLIP-seq
MIRT1054370	hsa-miR-363	CLIP-seq
MIRT1054371	hsa-miR-367	CLIP-seq
MIRT1054372	hsa-miR-448	CLIP-seq
MIRT1054373	hsa-miR-4672	CLIP-seq
MIRT1054374	hsa-miR-4773	CLIP-seq
MIRT1054375	hsa-miR-92a	CLIP-seq
MIRT1054376	hsa-miR-92b	CLIP-seq
MIRT1054366	hsa-miR-144	CLIP-seq
MIRT1054367	hsa-miR-153	CLIP-seq
MIRT1054368	hsa-miR-25	CLIP-seq
MIRT1054369	hsa-miR-32	CLIP-seq
MIRT1054370	hsa-miR-363	CLIP-seq
MIRT2244673	hsa-miR-3649	CLIP-seq
MIRT1054371	hsa-miR-367	CLIP-seq
MIRT2244674	hsa-miR-3691-3p	CLIP-seq
MIRT2244675	hsa-miR-3925-3p	CLIP-seq
MIRT1054372	hsa-miR-448	CLIP-seq
MIRT2244676	hsa-miR-4645-5p	CLIP-seq
MIRT1054373	hsa-miR-4672	CLIP-seq
MIRT2244677	hsa-miR-4673	CLIP-seq
MIRT1054374	hsa-miR-4773	CLIP-seq
MIRT2244678	hsa-miR-4802-3p	CLIP-seq
MIRT1054375	hsa-miR-92a	CLIP-seq
MIRT1054376	hsa-miR-92b	CLIP-seq
MIRT1054366	hsa-miR-144	CLIP-seq
MIRT1054374	hsa-miR-4773	CLIP-seq

Show/Hide all (31)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25189619, 33961781
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IBA
GO:0005765	Component	Lysosomal membrane	IDA	25189619
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	NAS	23247405
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0007596	Process	Blood coagulation	IEA
GO:0009306	Process	Protein secretion	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0030742	Function	GTP-dependent protein binding	IPI	22511774
GO:0031084	Component	BLOC-2 complex	IBA
GO:0031084	Component	BLOC-2 complex	IPI	15030569
GO:0031267	Function	Small GTPase binding	IPI	22511774
GO:0031901	Component	Early endosome membrane	IEA
GO:0032418	Process	Lysosome localization	IBA
GO:0032418	Process	Lysosome localization	IEA
GO:0032418	Process	Lysosome localization	IMP	25189619
GO:0043473	Process	Pigmentation	IEA
GO:0055088	Process	Lipid homeostasis	IEA
GO:0060155	Process	Platelet dense granule organization	NAS	23247405
GO:0072657	Process	Protein localization to membrane	IBA
GO:0072657	Process	Protein localization to membrane	IMP	22511774
GO:1903232	Process	Melanosome assembly	NAS	23247405

MIM	HGNC	e!Ensembl
607522	18817	ENSG00000166189

Q86YV9

Protein name

BLOC-2 complex member HPS6 (Hermansky-Pudlak syndrome 6 protein) (Ruby-eye protein homolog) (Ru)

Protein function

May regulate the synthesis and function of lysosomes and of highly specialized organelles, such as melanosomes and platelet dense granules (PubMed:17041891). Acts as a cargo adapter for the dynein-dynactin motor complex to mediate the transport

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF15702	HPS6	1 → 773	Hermansky-Pudlak syndrome 6 protein	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous.

Sequence

MKRSGTLRLLSDLSAFGGAARLRELVAGDSAVRVRGSPDGRHLLLLRPPGAVAPQLLVAS
RGPGAELERAWPAGQPSPLDAFFLPWPARPALVLVWESGLAEVWGAGVGPGWRPLQSTEL
CPGGGARVVAVAALRGRLVWCEERQARAEGPSGSPAAAFSHCVCVRTLEPSGEASTSLGR
THVLLHHCPAFGLLASCRQLFLVPTATTWPGVAHVLLIWSPGKGKVMVAAPRLGLSYSKS
LNPGRGDTWDFRTLLRGLPGLLSPREPLAVHTWAPTPQGLLLLDFGGTVSLLQSHGGTRA
VGTLQEAPVGPWGSAALGTFQGTLACVLGSTLELLDMGSGQLLERKVLSTDRVHLLEPPA
PGMEDEEELETRGNLRLLSALGLFCVGWEAPQGVELPSAKDLVFEEACGYYQRRSLRGAQ
LTPEELRHSSTFRAPQALASILQGHLPPSALLTMLRTELRDYRGLEQLKAQLVAGDDEEA
GWTELAEQEVARLLRTELIGDQLAQLNTVFQALPTAAWGATLRALQLQLDGNGKLRSQAP
PDVWKKVLGGITAGKEPPNGILPPFELLCQCLCQLEPRWLPPFVELAQQQGGPGWGAGGP
GLPLYRRALAVLGEEGTRPEALELELLLSSGRPKAVLQAVGQLVQKEQWDRALDAGLALG
PSSPLLRSEIFKLLLAEFAQHRRLDAHLPLLCRLCPPELAPAELLLLLRTYLPDEVGPPT
PFPEPGAEPPLTVGLLKALLEQTGAQGWLSGPVLSPYEDILWDPSTPPPTPPRDL

Sequence length

775

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hermansky-Pudlak syndrome	Pathogenic; Likely pathogenic	rs776754431, rs2136334244, rs752399257, rs2136333814, rs2540988146, rs2540988872, rs199891110, rs2067964335, rs2540988736, rs2136333690, rs1220869113, rs1564899012, rs1590262450, rs756471925, rs1478574193 View all (3 more)	RCV004801068 RCV003226503 RCV003226509 RCV002222931 RCV002282925 View all (13 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hermansky-Pudlak syndrome 6	Likely pathogenic; Pathogenic	rs2136333791, rs2067971306, rs1590263662, rs1462863412, rs760452661, rs281865113, rs753804000, rs199891110, rs2540986756, rs2540987646, rs1383241620, rs2540985942, rs764867254, rs1412405724, rs2136334341 View all (16 more)	RCV001358142 RCV001580271 RCV001783431 RCV002243490 RCV002254224 View all (26 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HPS6-related disorder	Pathogenic; Likely pathogenic	rs752399257, rs749791114, rs1564899888, rs756471925	RCV003426265 RCV003419167 RCV004750918 RCV003411709	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Abnormal bleeding	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HERMANSKI-PUDLAK SYNDROME	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HERMANSKY-PUDLAK SYNDROME DUE TO BLOC-2 DEFICIENCY	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HERMANSKY-PUDLAK SYNDROME WITHOUT PULMONARY FIBROSIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Storage pool disease of platelets	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thrombocytopenia	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
VASCULAR DEMENTIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (24)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Albinism	Albinism	Pubtator	33808351, 35488210, 39457042	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Albinism	Albinism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Albinism Ocular	Ocular albinism	Pubtator	38091959	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Albinism Oculocutaneous	Oculocutaneous albinism	Pubtator	19843503, 27641950, 30369044	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Albinism, Ocular	Ocular albinism	BEFREE	27225848		★★★★★ ★☆☆☆☆ Found in Text Mining only
Albinism, Ocular	Ocular albinism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Albinism, Oculocutaneous	Oculocutaneous albinism	BEFREE	27593200, 27641950, 27917594, 30369044		★★★★★ ★☆☆☆☆ Found in Text Mining only
Blood Coagulation Disorders	Blood Coagulation Disorders	BEFREE	27641950		★★★★★ ★☆☆☆☆ Found in Text Mining only
Blood Coagulation Disorders Inherited	Blood coagulation disorder	Pubtator	27641950	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	30947698	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemophilia B	Hemophilia	BEFREE	27641950		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemophilia B	Hemophilia b	Pubtator	27641950	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemorrhage	Hemorrhage	Pubtator	30369044	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemorrhagic Disorders	Hemorrhagic disease	Pubtator	19843503	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hermanski-Pudlak Syndrome	Hermansky-Pudlak Syndrome	BEFREE	27917594		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hermanski-Pudlak Syndrome	Hermansky-Pudlak Syndrome	CLINVAR_DG	31064749		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hermanski-Pudlak Syndrome	Hermansky-Pudlak Syndrome	GENOMICS_ENGLAND_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hermanski-Pudlak Syndrome	Hermansky-Pudlak Syndrome	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HERMANSKY-PUDLAK SYNDROME 6	Hermansky-Pudlak Syndrome	CLINVAR_DG	12548288, 17041891, 19843503		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HERMANSKY-PUDLAK SYNDROME 6	Hermansky-Pudlak Syndrome	GENOMICS_ENGLAND_DG	19843503		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hermansky-Pudlak syndrome without pulmonary fibrosis	Hermansky-Pudlak Syndrome Without Pulmonary Fibrosis	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inflammatory Bowel Diseases	Inflammatory bowel disease	Pubtator	33423334	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

HPS6 (HPS6 biogenesis of lysosomal organelles complex 2 subunit 3)