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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	84343
Gene name Gene Name - the full gene name approved by the HGNC.	HPS3 biogenesis of lysosomal organelles complex 2 subunit 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	HPS3
Synonyms (NCBI Gene) Gene synonyms aliases	BLOC2S1, SUTAL
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3q24
Summary Summary of gene provided in NCBI Entrez Gene.	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

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

Protein

UniProt ID

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

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 3, hermansky-pudlak syndrome 2	rs1576695913, rs200079039, rs121908316, rs748883997, rs1330496818, rs1277509410, rs750685598, rs1553750083, rs778152054, rs201227603, rs753185316, rs755083879, rs281865093, rs1488175163, rs397507168 View all (3 more)	N/A
hermansky-pudlak syndrome	Hermansky-Pudlak syndrome	rs1576708708, rs200079039, rs121908316, rs750685598, rs753185316, rs755083879, rs201227603, rs1553750097, rs780183200, rs397507168, rs1576695913	N/A

Show/Hide Unknown Diseases (1)

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 Without Pulmonary Fibrosis	Hermansky-Pudlak syndrome without pulmonary fibrosis	N/A	N/A	GenCC

Show/Hide Text Mining Associations (7)

Disease Name	Relationship Type	References
Associations from Text Mining Disease 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)