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

Gene

• Entrez ID: 79803
• Gene name: HPS6 biogenesis of lysosomal organelles complex 2 subunit 3
• Gene symbol: HPS6
• Synonyms: 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

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25189619
GO:0005765	Component	Lysosomal membrane	IBA	21873635
GO:0005765	Component	Lysosomal membrane	IDA	25189619
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0006996	Process	Organelle organization	IBA	21873635
GO:0007596	Process	Blood coagulation	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0030318	Process	Melanocyte differentiation	IBA	21873635
GO:0030742	Function	GTP-dependent protein binding	IPI	22511774
GO:0031084	Component	BLOC-2 complex	IBA	21873635
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	21873635
GO:0032418	Process	Lysosome localization	IMP	25189619
GO:0072657	Process	Protein localization to membrane	IBA	21873635
GO:0072657	Process	Protein localization to membrane	IMP	22511774

Other IDs

• MIM: 607522
• HGNC: 18817
• e!Ensembl: ENSG00000166189

Protein

• UniProt ID: 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

• Sequence:

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

• Sequence length: 775

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Albinism	Albinism	rs28940876, rs387906560, rs62635045, rs140365820, rs141949212, rs1384042381, rs62635042
Hermansky-pudlak syndrome	Hermanski-Pudlak Syndrome, HERMANSKY-PUDLAK SYNDROME 6	rs281865116, rs281865113, rs281865103, rs104893945, rs119471021, rs281865100, rs281865097, rs119471022, rs119471023, rs119471024, rs119471025, rs201227603, rs281865093, rs397507168, rs281865095, rs121908316, rs281865163, rs281865082, rs121908385, rs121908386, rs281865081, rs281865077, rs121908904, rs1000881595, rs121908905, rs121908906, rs121908907, rs281865084, rs281865086, rs281865088, rs281865090, rs281865075, rs281865076, rs281865080, rs281865104, rs281865105, rs397507169, rs281865101, rs201348482, rs1564899492, rs281865114, rs281865110, rs281865107, rs281865112, rs727502866, rs786205464, rs869312835, rs869312836, rs869312837, rs869312838, rs369053765, rs879255646, rs886041723, rs1591055649, rs753928208, rs113304476, rs1131692151, rs1131692149, rs1131692146, rs1131692148, rs1131692147, rs764296457, rs1131692150, rs1131692332, rs1131692333, rs766602179, rs281865115, rs1554903728, rs1220869113, rs773323079, rs1554948134, rs1486224265, rs1277509410, rs1553750083, rs372020804, rs1564899012, rs1590262288, rs753185316, rs1553750097, rs780183200, rs1576695913, rs1576708708, rs1590262450, rs756471925, rs1478574193, rs1590263807, rs1590263820, rs779921624, rs755827664, rs374689398, rs886077189, rs1591120765, rs1260083432, rs748883997, rs750685598, rs778152054, rs755083879, rs1488175163, rs1591092841, rs1576687466, rs756325364, rs1591002808, rs1591045080, rs1602079277, rs1591109881, rs1591031929, rs200079039, rs1595560288, rs772475341, rs1330496818, rs1745947620, rs552340796, rs1453977337, rs754841982, rs1568469902, rs1763106978	31064749, 12548288, 19843503, 17041891
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Ocular albinism	Albinism, Ocular	rs137852296, rs137852297, rs62635018, rs62645741, rs281865178, rs281865183, rs281865184, rs672601353, rs1057518841, rs1057518763, rs1057518787

Unknown
Disease name	Disease term	dbSNP ID	References
Hermansky-pudlak syndrome without pulmonary fibrosis	Hermansky-Pudlak syndrome without pulmonary fibrosis
Strabismus	Strabismus