BLOC1S6 biogenesis of lysosomal organelles complex 1 subunit 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: BLOC1S6provided by HGNC
Official Full Name: biogenesis of lysosomal organelles complex 1 subunit 6provided by HGNC
Primary source: HGNC:HGNC:8549
See related: Ensembl:ENSG00000104164 MIM:604310; AllianceGenome:HGNC:8549
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PA; HPS9; PLDN; BLOS6; PALLID
Summary: The protein encoded by this gene may play a role in intracellular vesicle trafficking. It interacts with Syntaxin 13 which mediates intracellular membrane fusion. Mutations in this gene cause symptoms associated with Hermansky-Pudlak syndrome-9. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on the X chromosome. [provided by RefSeq, Aug 2015]
Expression: Ubiquitous expression in thyroid (RPKM 21.0), prostate (RPKM 17.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q21.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (45587123..45609716)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (43395284..43417878)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (45879321..45901914)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results from a study on gene expression variability markers in early-stage human embryos shows that BLOC1S6 (PLDN) is a putative expression variability marker for the 3-day, 8-cell embryo stage.
Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
PLDN is a direct target of RUNX1 and its dysregulation is a mechanism for platelet dense granule deficiency associated with RUNX1 haplodeficiency
Title: Dysregulation of PLDN (pallidin) is a mechanism for platelet dense granule deficiency in RUNX1 haplodeficiency.
Mecp2 regulates the expression of components belonging to the dysbindin interactome
Title: MeCP2 regulates the synaptic expression of a Dysbindin-BLOC-1 network component in mouse brain and human induced pluripotent stem cell-derived neurons.
no defects in the known components of pallidin-muted complex (BLOC-1)have been identified in 142 patients with HPS, suggesting that BLOC-1 function may be critical in humans.
Title: Cappuccino, a mouse model of Hermansky-Pudlak syndrome, encodes a novel protein that is part of the pallidin-muted complex (BLOC-1).
role in biogenesis of lysosome-related organelles
Title: Pallidin is a component of a multi-protein complex involved in the biogenesis of lysosome-related organelles.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hermansky-Pudlak syndrome 9 MedGen: C3280026 OMIM: 614171 GeneReviews: Hermansky-Pudlak Syndrome	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

HUMHM01F10 (e-PCR)
- UniSTS:10512

RH11270 (e-PCR)
- UniSTS:64553

D8S2279 (e-PCR)
- UniSTS:473907

PLD3_2311 (e-PCR)
- UniSTS:280916

D1S1423 (e-PCR)
- UniSTS:149619

STS-N35229 (e-PCR)
- UniSTS:21719

D15S1094 (e-PCR)
- UniSTS:7156

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin filament binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables molecular adaptor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in ATP metabolic process	IEA Inferred from Electronic Annotation more info
involved_in actin filament bundle assembly	IEA Inferred from Electronic Annotation more info
involved_in adenosine metabolic process	IEA Inferred from Electronic Annotation more info
involved_in anterograde axonal transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in anterograde synaptic vesicle transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in blood coagulation	IEA Inferred from Electronic Annotation more info
involved_in bradykinin biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in cellular response to epidermal growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IEA Inferred from Electronic Annotation more info
involved_in circadian sleep/wake cycle	IEA Inferred from Electronic Annotation more info
involved_in dentate gyrus development	IEA Inferred from Electronic Annotation more info
involved_in endosome to melanosome transport	IDA Inferred from Direct Assay more info	PubMed
involved_in endothelium development	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in glutamate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in glutamine metabolic process	IEA Inferred from Electronic Annotation more info
involved_in homeostasis of number of cells	IEA Inferred from Electronic Annotation more info
involved_in hypothalamus development	IEA Inferred from Electronic Annotation more info
involved_in intracellular nitric oxide homeostasis	IEA Inferred from Electronic Annotation more info
involved_in intracellular transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in kidney development	IEA Inferred from Electronic Annotation more info
involved_in lipid homeostasis	IEA Inferred from Electronic Annotation more info
involved_in lung alveolus development	IEA Inferred from Electronic Annotation more info
involved_in melanocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in melanosome organization	NAS Non-traceable Author Statement more info	PubMed
involved_in melanosome transport	IDA Inferred from Direct Assay more info	PubMed
involved_in membrane fusion	IEA Inferred from Electronic Annotation more info
involved_in memory	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in phospholipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of natural killer cell activation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of pigment cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein targeting	IEA Inferred from Electronic Annotation more info
involved_in protein transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in respiratory system process	IEA Inferred from Electronic Annotation more info
involved_in response to acetylcholine	IEA Inferred from Electronic Annotation more info
involved_in response to activity	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in secretion of lysosomal enzymes	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle docking	NAS Non-traceable Author Statement more info	PubMed
involved_in vasodilation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of BLOC-1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of BLOC-1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of BLOC-1 complex	IPI Inferred from Physical Interaction more info	PubMed
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
located_in axon cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cell-cell contact zone	IEA Inferred from Electronic Annotation more info
located_in contractile ring	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endosome	IEA Inferred from Electronic Annotation more info
part_of filamentous actin	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
located_in membrane-bounded organelle	IDA Inferred from Direct Assay more info	PubMed
located_in microvesicle	IEA Inferred from Electronic Annotation more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
located_in ruffle	IEA Inferred from Electronic Annotation more info
located_in stress fiber	IEA Inferred from Electronic Annotation more info
is_active_in transport vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in transport vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: biogenesis of lysosome-related organelles complex 1 subunit 6

Names: BLOC-1 subunit 6; BLOC-1 subunit pallidin; biogenesis of lysosomal organelles complex-1, subunit 5, pallidin; biogenesis of lysosomal organelles complex-1, subunit 6, pallidin; pallid protein homolog; syntaxin 13 binding protein 1; syntaxin 13-interacting protein pallid

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_028194.2 RefSeqGene

Range

4905..27498

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_883

mRNA and Protein(s)

NM_001311255.1 → NP_001298184.1 biogenesis of lysosome-related organelles complex 1 subunit 6 isoform 1

Status: REVIEWED

Source sequence(s)

AK128626, AL596952, BC026289, BP423071, DA230439

Consensus CDS

CCDS81878.1

UniProtKB/TrEMBL

B2RDK7, H3BST1

Related

ENSP00000456851.1, ENST00000565323.6

Conserved Domains (1) summary

pfam14712
Location:55 → 145

Snapin_Pallidin; Snapin/Pallidin
NM_001311256.1 → NP_001298185.1 biogenesis of lysosome-related organelles complex 1 subunit 6 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (12) lacks an alternate exon in the central coding region, which results in a frameshift and an early stop codon, compared to variant 1. It encodes isoform 3, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK128626, BC026289, BP423071, DA226593, DA230439, DA523523

UniProtKB/TrEMBL

B3KY40

Conserved Domains (1) summary

pfam14712
Location:56 → 80

Snapin_Pallidin; Snapin/Pallidin
NM_012388.4 → NP_036520.1 biogenesis of lysosome-related organelles complex 1 subunit 6 isoform 2

See identical proteins and their annotated locations for NP_036520.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 2, which has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AF080470, AK128626, BC026289

Consensus CDS

CCDS10126.1

UniProtKB/Swiss-Prot

Q9UL45

UniProtKB/TrEMBL

B2RDK7

Related

ENSP00000220531.4, ENST00000220531.9

Conserved Domains (1) summary

pfam14712
Location:51 → 140

Snapin_Pallidin; Snapin/Pallidin

RNA

NR_132350.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK128626, BC026289, BP423071, DA230439

Related

ENST00000568816.5
NR_132351.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate 5' terminal exon and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK057545, AK128626, BC026289
NR_132352.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) contains an alternate 5' terminal exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF080470, AK128626, BC026289, DA247079
NR_132353.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AK128626, BC026289, BP423071, DA468279, DB212570
NR_132354.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AF080470, AK128626, BC026289, BP423071, DA468279, DA798595
NR_132355.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) contains an alternate 5' exon and lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AK128626, BC026289, DB287075
NR_132356.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (9) contains an alternate 5' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK128626, BC026289, DA237963, DB289156
NR_132357.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (10) contains an alternate 5' exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AK128626, BC026289, DA237963, DA859617
NR_132358.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (11) lacks two alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK128626, BC026289, BP423071, DA226593, DA230439
NR_132359.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (13) contains an alternate 5' terminal exon and lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AK128626, BC026289, DA233328, DA237963