Gene Gene information from NCBI Gene database.
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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606118 15597 ENSG00000163755
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
IHIDNITPVEVSFCVGYVAVMSDLEVLIVKLE
SGPKNGERVHHHPHKTNNRIRRTEEGIS
NEISQLESDDFVICQKPLELLGEKSEQSGLSVTLESTGLADEKRKYSHFQHLLYRRFAPD
ISSYVLSDDIKLHSLQLLPIYQTGSLTSDGKNLSQEKELLSLFCFFSLPHVGYLYMVVKS
VELMSVYQYPEKSQQAVLTPQFLHVITSNNLQCFTVRCSAAAAREEDPYMDTTLKACPPV
SMDVCALRIQLFIGLKAICHFKNHIILLTKAEPEAIPERRQSPKRLLSRKDTSVKIKIPP
VAEAGWNLYIVNTISPVQLYKEMVDYSNTYKTVKTQSCIHLLSEAHLLVRAALMDASQLE
PGEKAELLEAFKESCGHLGDCYSRLDSQHSHLTLPYYKMSGLSMAEVLARTDWTVEDGLQ
KYERGLIFYINHSLYENLDEELNEELAAKVVQMFYVAEPKQV
PHILCSPSMKNINPLTAM
SYLRKLDTSGFSSILVTLTKAAVALKMGDLDMHRNEMKSHSEMKLVCGFILEPRLLIQQR
KGQIVPTELALHLKETQPGLLVASVLGLQKNNKIGIEEADSFFKVLCAKDEDTIPQLLVD
FWEAQLVACLPDVVLQELFFKLTSQYIWRLSKRQPPDTTPLRTSEDLINACSHYGLIYPW
VHVVISSDSLADKNYTEDLSKLQSLICGPSFDIASIIPFLEPLSEDTIAGLSVHVLCRTR
LKEYEQCIDILLERCPEAVIPYANHELKEENRTLWWKKLLPELCQRIKCGGEKYQLYLSS
LKETLSIVAVELELKDFMNVLPEDGTATFFLPYLLYCSRKKP
LT
Sequence length 1004
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
20
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)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Hepatocellular carcinoma Pathogenic rs141023798 RCV005935076
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
View all (17 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hermansky-Pudlak syndrome 2 Likely pathogenic; Pathogenic rs200079039 RCV001003902
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
View all (144 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
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.
Phenotype Name Clinical Significance Source Evidence Score
Abnormal bleeding Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DEFICIENCY OF FERROXIDASE Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Gastric cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Albinism Albinism BEFREE 24766090
★☆☆☆☆
Found in Text Mining only
Albinism Albinism Pubtator 33808351, 35488210 Associate
★☆☆☆☆
Found in Text Mining only
Blood Platelet Disorders Platelet disorder Pubtator 38007062 Associate
★☆☆☆☆
Found in Text Mining only
Colorectal Carcinoma Colorectal Cancer UNIPROT_DG
★☆☆☆☆
Found in Text Mining only
Hermanski-Pudlak Syndrome Hermansky-Pudlak Syndrome LHGDN 11590544, 12125811
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Hermanski-Pudlak Syndrome Hermansky-Pudlak Syndrome CLINVAR_DG 11590544, 25525159
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Hermanski-Pudlak Syndrome Hermansky-Pudlak Syndrome BEFREE 15288994, 15632015, 30791930
★★☆☆☆
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 2 Hermansky-pudlak syndrome Pubtator 11590544 Associate
★☆☆☆☆
Found in Text Mining only