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

180

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
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 RCV002283419 RCV003155512 RCV003155847 RCV003155883 RCV006269925 RCV002282184 RCV000851760 RCV000851709 RCV000852193 RCV000852216 RCV000852046 RCV000852050 RCV000851270
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 RCV000003301 RCV003225774 RCV004796764 RCV006275897 RCV003146056 RCV003146064 RCV005030068 RCV005030277 RCV005030308 RCV003988756 RCV004579653 RCV000023648 RCV000023649 RCV000023650 RCV000023653 RCV000023654 RCV000496090 RCV000496087 RCV000503617 RCV000500537 RCV000761514 RCV005029419 RCV005029422 RCV001290773 RCV001290774 RCV001290772
HPS6-related disorder	Pathogenic; Likely pathogenic	rs752399257, rs749791114, rs1564899888, rs756471925	RCV003426265 RCV003419167 RCV004750918 RCV003411709

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Abnormal bleeding	Uncertain significance	rs1208203730	RCV001270599
Storage pool disease of platelets	Uncertain significance	rs754025975, rs772000976	RCV000851859 RCV000851628
Thrombocytopenia	Uncertain significance	rs1208203730	RCV001270599

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Albinism	Associate	33808351, 35488210, 39457042
Albinism Ocular	Associate	38091959
Albinism Oculocutaneous	Associate	19843503, 27641950, 30369044
Blood Coagulation Disorders Inherited	Associate	27641950
Breast Neoplasms	Associate	30947698
Hemophilia B	Associate	27641950
Hemorrhage	Associate	30369044
Hemorrhagic Disorders	Associate	19843503
Hermanski Pudlak Syndrome	Associate	15030569, 19843503, 27641950, 30369044, 30990103, 34608437, 38091959
Hypopigmentation	Associate	19843503
Inflammatory Bowel Diseases	Associate	33423334
Neoplastic Syndromes Hereditary	Associate	30947698

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