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	84343
Gene name	HPS3 biogenesis of lysosomal organelles complex 2 subunit 1
Gene symbol	HPS3
Synonyms (NCBI Gene)	BLOC2S1SUTAL
Chromosome	3
Chromosome location	3q24
Summary	This gene encodes a protein containing a potential clathrin-binding motif, consensus dileucine signals, and tyrosine-based sorting signals for targeting to vesicles of lysosomal lineage. The encoded protein may play a role in organelle biogenesis associat

Show/Hide all (14)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908316	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs200079039	G>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs201227603	G>A	Pathogenic	Splice donor variant
rs281865093	T>G	Pathogenic	Splice donor variant
rs748883997	G>-	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs750685598	GA>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs753185316	C>G	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs755083879	C>G	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs778152054	GT>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs780183200	G>A	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1488175163	G>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553750083	GTGACGCGCTTTTCGTGGCGGCGGGC>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553750097	G>C,T	Uncertain-significance, likely-pathogenic	Stop gained, non coding transcript variant, missense variant, coding sequence variant
rs1576687466	C>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained

143

Show/Hide all (143)

miRTarBase ID	miRNA	Experiments	Reference
MIRT039577	hsa-miR-636	CLASH	23622248
MIRT609014	hsa-miR-410-3p	HITS-CLIP	24906430
MIRT609013	hsa-miR-5011-5p	HITS-CLIP	24906430
MIRT609012	hsa-miR-3689a-5p	HITS-CLIP	24906430
MIRT609011	hsa-miR-3689b-5p	HITS-CLIP	24906430
MIRT609010	hsa-miR-3689e	HITS-CLIP	24906430
MIRT609009	hsa-miR-3689f	HITS-CLIP	24906430
MIRT609008	hsa-miR-6867-5p	HITS-CLIP	24906430
MIRT609007	hsa-miR-6818-5p	HITS-CLIP	24906430
MIRT609006	hsa-miR-574-5p	HITS-CLIP	24906430
MIRT576701	hsa-miR-154-3p	HITS-CLIP	27418678
MIRT576701	hsa-miR-154-3p	HITS-CLIP	27418678
MIRT576701	hsa-miR-154-3p	HITS-CLIP	27418678
MIRT609012	hsa-miR-3689a-5p	HITS-CLIP	27418678
MIRT609012	hsa-miR-3689a-5p	HITS-CLIP	27418678
MIRT609012	hsa-miR-3689a-5p	HITS-CLIP	27418678
MIRT609012	hsa-miR-3689a-5p	HITS-CLIP	27418678
MIRT609011	hsa-miR-3689b-5p	HITS-CLIP	27418678
MIRT609011	hsa-miR-3689b-5p	HITS-CLIP	27418678
MIRT609011	hsa-miR-3689b-5p	HITS-CLIP	27418678
MIRT609011	hsa-miR-3689b-5p	HITS-CLIP	27418678
MIRT609010	hsa-miR-3689e	HITS-CLIP	27418678
MIRT609010	hsa-miR-3689e	HITS-CLIP	27418678
MIRT609010	hsa-miR-3689e	HITS-CLIP	27418678
MIRT609010	hsa-miR-3689e	HITS-CLIP	27418678
MIRT609009	hsa-miR-3689f	HITS-CLIP	27418678
MIRT609009	hsa-miR-3689f	HITS-CLIP	27418678
MIRT609009	hsa-miR-3689f	HITS-CLIP	27418678
MIRT609009	hsa-miR-3689f	HITS-CLIP	27418678
MIRT609014	hsa-miR-410-3p	HITS-CLIP	27418678
MIRT576700	hsa-miR-487a-3p	HITS-CLIP	27418678
MIRT576700	hsa-miR-487a-3p	HITS-CLIP	27418678
MIRT576700	hsa-miR-487a-3p	HITS-CLIP	27418678
MIRT609013	hsa-miR-5011-5p	HITS-CLIP	27418678
MIRT576699	hsa-miR-511-3p	HITS-CLIP	27418678
MIRT576699	hsa-miR-511-3p	HITS-CLIP	27418678
MIRT576699	hsa-miR-511-3p	HITS-CLIP	27418678
MIRT576696	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT576696	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT576696	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT576696	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT576697	hsa-miR-6818-5p	HITS-CLIP	27418678
MIRT576697	hsa-miR-6818-5p	HITS-CLIP	27418678
MIRT576697	hsa-miR-6818-5p	HITS-CLIP	27418678
MIRT576697	hsa-miR-6818-5p	HITS-CLIP	27418678
MIRT576698	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT576698	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT576698	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT576698	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT1054216	hsa-miR-1913	CLIP-seq
MIRT1054217	hsa-miR-2113	CLIP-seq
MIRT1054218	hsa-miR-3117-5p	CLIP-seq
MIRT1054219	hsa-miR-3149	CLIP-seq
MIRT1054220	hsa-miR-324-3p	CLIP-seq
MIRT1054221	hsa-miR-340	CLIP-seq
MIRT1054222	hsa-miR-3611	CLIP-seq
MIRT1054223	hsa-miR-3646	CLIP-seq
MIRT1054224	hsa-miR-4293	CLIP-seq
MIRT1054225	hsa-miR-4422	CLIP-seq
MIRT1054226	hsa-miR-4704-5p	CLIP-seq
MIRT1054227	hsa-miR-4719	CLIP-seq
MIRT1054228	hsa-miR-4727-5p	CLIP-seq
MIRT1054229	hsa-miR-4766-5p	CLIP-seq
MIRT1054230	hsa-miR-487a	CLIP-seq
MIRT1054231	hsa-miR-544	CLIP-seq
MIRT1054232	hsa-miR-548a-3p	CLIP-seq
MIRT1054233	hsa-miR-548ag	CLIP-seq
MIRT1054234	hsa-miR-548ai	CLIP-seq
MIRT1054235	hsa-miR-548e	CLIP-seq
MIRT1054236	hsa-miR-548f	CLIP-seq
MIRT1054237	hsa-miR-602	CLIP-seq
MIRT1054238	hsa-miR-758	CLIP-seq
MIRT1054218	hsa-miR-3117-5p	CLIP-seq
MIRT2012313	hsa-miR-3143	CLIP-seq
MIRT1054226	hsa-miR-4704-5p	CLIP-seq
MIRT2012314	hsa-miR-4709-5p	CLIP-seq
MIRT2012315	hsa-miR-485-3p	CLIP-seq
MIRT1054230	hsa-miR-487a	CLIP-seq
MIRT1054232	hsa-miR-548a-3p	CLIP-seq
MIRT1054235	hsa-miR-548e	CLIP-seq
MIRT1054236	hsa-miR-548f	CLIP-seq
MIRT2244656	hsa-miR-1343	CLIP-seq
MIRT2244657	hsa-miR-1976	CLIP-seq
MIRT1054218	hsa-miR-3117-5p	CLIP-seq
MIRT2244658	hsa-miR-3907	CLIP-seq
MIRT2244659	hsa-miR-4268	CLIP-seq
MIRT2244660	hsa-miR-4279	CLIP-seq
MIRT2244661	hsa-miR-4448	CLIP-seq
MIRT1054226	hsa-miR-4704-5p	CLIP-seq
MIRT2012315	hsa-miR-485-3p	CLIP-seq
MIRT1054232	hsa-miR-548a-3p	CLIP-seq
MIRT1054235	hsa-miR-548e	CLIP-seq
MIRT1054236	hsa-miR-548f	CLIP-seq
MIRT1054218	hsa-miR-3117-5p	CLIP-seq
MIRT1054226	hsa-miR-4704-5p	CLIP-seq
MIRT2012315	hsa-miR-485-3p	CLIP-seq
MIRT1054232	hsa-miR-548a-3p	CLIP-seq
MIRT1054235	hsa-miR-548e	CLIP-seq
MIRT1054236	hsa-miR-548f	CLIP-seq
MIRT2451370	hsa-miR-3121-3p	CLIP-seq
MIRT2451371	hsa-miR-3684	CLIP-seq
MIRT2451372	hsa-miR-4698	CLIP-seq
MIRT2547564	hsa-miR-2053	CLIP-seq
MIRT2547565	hsa-miR-30a	CLIP-seq
MIRT2547566	hsa-miR-30b	CLIP-seq
MIRT2547567	hsa-miR-30c	CLIP-seq
MIRT2547568	hsa-miR-30d	CLIP-seq
MIRT2547569	hsa-miR-30e	CLIP-seq
MIRT2547570	hsa-miR-3662	CLIP-seq
MIRT2547571	hsa-miR-3919	CLIP-seq
MIRT2547572	hsa-miR-4305	CLIP-seq
MIRT2547573	hsa-miR-4756-3p	CLIP-seq
MIRT2547574	hsa-miR-498	CLIP-seq
MIRT2547575	hsa-miR-548a-5p	CLIP-seq
MIRT2547576	hsa-miR-548ab	CLIP-seq
MIRT2547577	hsa-miR-548ak	CLIP-seq
MIRT2547578	hsa-miR-548b-5p	CLIP-seq
MIRT2547579	hsa-miR-548c-5p	CLIP-seq
MIRT2547580	hsa-miR-548d-5p	CLIP-seq
MIRT2547581	hsa-miR-548h	CLIP-seq
MIRT2547582	hsa-miR-548i	CLIP-seq
MIRT2547583	hsa-miR-548j	CLIP-seq
MIRT2547584	hsa-miR-548n	CLIP-seq
MIRT2547585	hsa-miR-548t	CLIP-seq
MIRT2547586	hsa-miR-548w	CLIP-seq
MIRT2547587	hsa-miR-548y	CLIP-seq
MIRT2547588	hsa-miR-559	CLIP-seq
MIRT2547589	hsa-miR-569	CLIP-seq
MIRT2547590	hsa-miR-579	CLIP-seq
MIRT2547591	hsa-miR-633	CLIP-seq
MIRT2547592	hsa-miR-802	CLIP-seq
MIRT2547564	hsa-miR-2053	CLIP-seq
MIRT2547565	hsa-miR-30a	CLIP-seq
MIRT2547566	hsa-miR-30b	CLIP-seq
MIRT2547567	hsa-miR-30c	CLIP-seq
MIRT2547568	hsa-miR-30d	CLIP-seq
MIRT2547569	hsa-miR-30e	CLIP-seq
MIRT2547571	hsa-miR-3919	CLIP-seq
MIRT2547572	hsa-miR-4305	CLIP-seq
MIRT2547573	hsa-miR-4756-3p	CLIP-seq
MIRT2547589	hsa-miR-569	CLIP-seq
MIRT2547590	hsa-miR-579	CLIP-seq
MIRT2547591	hsa-miR-633	CLIP-seq

Show/Hide all (11)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25189619, 31611645, 33961781
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005769	Component	Early endosome	NAS	23247405
GO:0005829	Component	Cytosol	IEA
GO:0031084	Component	BLOC-2 complex	IBA
GO:0031084	Component	BLOC-2 complex	IPI	15030569
GO:0043473	Process	Pigmentation	IBA
GO:0043473	Process	Pigmentation	IEA
GO:0060155	Process	Platelet dense granule organization	NAS	23247405
GO:1903232	Process	Melanosome assembly	NAS	23247405

MIM	HGNC	e!Ensembl
606118	15597	ENSG00000163755

Q969F9

Protein name

BLOC-2 complex member HPS3 (Hermansky-Pudlak syndrome 3 protein)

Protein function

Involved in early stages of melanosome biogenesis and maturation.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF14761	HPS3_N	3 → 212	Hermansky-Pudlak syndrome 3	Domain
PF14762	HPS3_Mid	256 → 642	Hermansky-Pudlak syndrome 3, middle region	Domain
PF14763	HPS3_C	651 → 1002	Hermansky-Pudlak syndrome 3, C-terminal	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. Higher levels of expression are observed in kidney, liver and placenta.

Sequence

MVQLYNLHPFGSQQVVPCKLEPDRFCGGGRDALFVAAGCKVEAFAVAGQELCQPRCAFST
LGRVLRLAYSEAGDYLVAIEEKNKATFLRAYVNWRNKRTENSRVCIRMIGHNVEGPFSKA
FRDQMYIIEMPLSEAPLCISCCPVKGDLLVGCTNKLVLFSLKYQIINEEFSLLDFERSLI
IHIDNITPVEVSFCVGYVAVMSDLEVLIVKLESGPKNGERVHHHPHKTNNRIRRTEEGIS
NEISQLESDDFVICQKPLELLGEKSEQSGLSVTLESTGLADEKRKYSHFQHLLYRRFAPD
ISSYVLSDDIKLHSLQLLPIYQTGSLTSDGKNLSQEKELLSLFCFFSLPHVGYLYMVVKS
VELMSVYQYPEKSQQAVLTPQFLHVITSNNLQCFTVRCSAAAAREEDPYMDTTLKACPPV
SMDVCALRIQLFIGLKAICHFKNHIILLTKAEPEAIPERRQSPKRLLSRKDTSVKIKIPP
VAEAGWNLYIVNTISPVQLYKEMVDYSNTYKTVKTQSCIHLLSEAHLLVRAALMDASQLE
PGEKAELLEAFKESCGHLGDCYSRLDSQHSHLTLPYYKMSGLSMAEVLARTDWTVEDGLQ
KYERGLIFYINHSLYENLDEELNEELAAKVVQMFYVAEPKQVPHILCSPSMKNINPLTAM
SYLRKLDTSGFSSILVTLTKAAVALKMGDLDMHRNEMKSHSEMKLVCGFILEPRLLIQQR
KGQIVPTELALHLKETQPGLLVASVLGLQKNNKIGIEEADSFFKVLCAKDEDTIPQLLVD
FWEAQLVACLPDVVLQELFFKLTSQYIWRLSKRQPPDTTPLRTSEDLINACSHYGLIYPW
VHVVISSDSLADKNYTEDLSKLQSLICGPSFDIASIIPFLEPLSEDTIAGLSVHVLCRTR
LKEYEQCIDILLERCPEAVIPYANHELKEENRTLWWKKLLPELCQRIKCGGEKYQLYLSS
LKETLSIVAVELELKDFMNVLPEDGTATFFLPYLLYCSRKKPLT

Sequence length

1004

Interactions

View interactions

447

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hepatocellular carcinoma	Pathogenic	rs141023798	RCV005935076
Hermansky-Pudlak syndrome	Likely pathogenic; Pathogenic	rs1411572278, rs1476066527, rs760577035, rs2108184819, rs34388030, rs201227603, rs397507168, rs121908316, rs2472689274, rs2473069453, rs753185316, rs1553750097, rs780183200, rs1576695913, rs1576708708 View all (7 more)	RCV001826144 RCV001826149 RCV005057830 RCV005614688 RCV005616391 RCV000826142 RCV001831513 RCV001272473 RCV003226866 RCV005616643 RCV000852039 RCV000851675 RCV000851268 RCV000852087 RCV000851759 RCV001830815 RCV001272477 RCV001827166 RCV001828612 RCV005236707 RCV001828839 RCV001834054
Hermansky-Pudlak syndrome 2	Likely pathogenic; Pathogenic	rs200079039	RCV001003902
Hermansky-Pudlak syndrome 3	Likely pathogenic; Pathogenic	rs746906314, rs1411572278, rs1476066527, rs1309602954, rs1292407171, rs1363245838, rs1032570128, rs2108173648, rs763305108, rs1723609962, rs1286892626, rs1466073004, rs770108122, rs760577035, rs868868714 View all (132 more)	RCV003145647 RCV001780288 RCV003462958 RCV001780368 RCV003469685 RCV003469708 RCV003473954 RCV003469665 RCV001783429 RCV001782263 RCV003475301 RCV003448433 RCV003471135 RCV003475220 RCV003471106 RCV002482749 RCV003471160 RCV003475178 RCV003475180 RCV003475119 RCV005025520 RCV003471286 RCV005023313 RCV002051961 RCV002306469 RCV002306536 RCV002306549 RCV002306630 RCV002306673 RCV002306818 RCV002309647 RCV002309680 RCV002309722 RCV002309773 RCV002309812 RCV002309851 RCV002309863 RCV002309897 RCV002309906 RCV002309946 RCV002307887 RCV002307895 RCV002307950 RCV002307966 RCV002307988 RCV002308090 RCV002308205 RCV002308257 RCV002308297 RCV002308378 RCV002309097 RCV002309265 RCV002309436 RCV002309444 RCV002307040 RCV002307067 RCV002310115 RCV002308472 RCV004572781 RCV005870021 RCV000004872 RCV000004873 RCV000004874 RCV000004875 RCV000004876 RCV003465793 RCV004571185 RCV005032361 RCV003465809 RCV003465820 RCV004571253 RCV003465846 RCV004798973 RCV004571380 RCV004571790 RCV003476450 RCV003469792 RCV003469793 RCV003469794 RCV003469795 RCV003476451 RCV003476452 RCV003469796 RCV003469797 RCV003476453 RCV003469798 RCV003476454 RCV003469799 RCV003469801 RCV003469802 RCV003469804 RCV003469805 RCV003469806 RCV003469807 RCV003469808 RCV003461725 RCV003469809 RCV003469810 RCV003469811 RCV003469812 RCV003469813 RCV003469814 RCV003461726 RCV003469815 RCV003469816 RCV003469817 RCV003469818 RCV003469819 RCV003461727 RCV003469820 RCV003469821 RCV003469823 RCV003469824 RCV003461728 RCV003469825 RCV003469826 RCV003461729 RCV005030070 RCV005030086 RCV004576725 RCV004576726 RCV004576727 RCV004576728 RCV004576730 RCV004576731 RCV004576732 RCV004576733 RCV004576734 RCV004576735 RCV004576736 RCV000672579 RCV003465685 RCV003465684 RCV003465686 RCV003467433 RCV003473517 RCV001095689 RCV002495161 RCV003472386 RCV000824870 RCV003467565 RCV003467820 RCV001196934 RCV002504284 RCV003469414 RCV002504306 RCV003473834 RCV003469443 RCV003469437
HPS3-related disorder	Likely pathogenic; Pathogenic	rs752837159, rs201227603, rs2473120616, rs750685598	RCV003892970 RCV004745146 RCV003911369 RCV003392626

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Abnormal bleeding	Uncertain significance	rs979740599	RCV001270521
Cervical cancer	Uncertain significance	rs199722122	RCV005913912
Gastric cancer	Benign	rs73166808	RCV005918764
Lung cancer	Benign	rs73166808	RCV005918767
Nonpapillary renal cell carcinoma	Uncertain significance	rs147557809	RCV005913897
Ovarian serous cystadenocarcinoma	Uncertain significance	rs188661079	RCV005913911
Prostate cancer	Uncertain significance	rs193920800	RCV000149318
Squamous cell carcinoma of the head and neck	Uncertain significance	rs2473119899	RCV005926754
Thrombocytopenia	Uncertain significance	rs979740599	RCV001270521
Thymoma	Benign	rs73166808	RCV005918766
Uterine carcinosarcoma	Benign	rs73166808	RCV005918765

Show/Hide Text Mining Associations (7)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Albinism	Associate	33808351, 35488210
Blood Platelet Disorders	Associate	38007062
Hermanski Pudlak Syndrome	Associate	11590544, 16159387, 16417222, 24766090, 30990103, 31880485, 34608437, 36672886, 38007062
Hermansky Pudlak syndrome 2	Associate	11590544
Inflammatory Bowel Diseases	Associate	33423334
Menorrhagia	Stimulate	30659653
Vision Disorders	Associate	11590544

HPS3 (HPS3 biogenesis of lysosomal organelles complex 2 subunit 1)