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    PCSK6 proprotein convertase subtilisin/kexin type 6 [ Homo sapiens (human) ]

    Gene ID: 5046, updated on 10-Dec-2024

    Summary

    Official Symbol
    PCSK6provided by HGNC
    Official Full Name
    proprotein convertase subtilisin/kexin type 6provided by HGNC
    Primary source
    HGNC:HGNC:8569
    See related
    Ensembl:ENSG00000140479 MIM:167405; AllianceGenome:HGNC:8569
    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
    SPC4; PACE4
    Summary
    This gene encodes a member of the subtilisin-like proprotein convertase family, which includes proteases that process protein and peptide precursors trafficking through regulated or constitutive branches of the secretory pathway. The encoded protein undergoes an initial autocatalytic processing event in the ER to generate a heterodimer which exits the ER and sorts to the trans-Golgi network where a second autocatalytic event takes place and the catalytic activity is acquired. The encoded protease is constitutively secreted into the extracellular matrix and expressed in many tissues, including neuroendocrine, liver, gut, and brain. This gene encodes one of the seven basic amino acid-specific members which cleave their substrates at single or paired basic residues. Some of its substrates include transforming growth factor beta related proteins, proalbumin, and von Willebrand factor. This gene is thought to play a role in tumor progression and left-right patterning. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Feb 2014]
    Expression
    Biased expression in spleen (RPKM 31.3), liver (RPKM 30.7) and 12 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PCSK6 in Genome Data Viewer
    Location:
    15q26.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (101303933..101489707, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (99058998..99244970, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (101844138..102029910, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6888 Neighboring gene selenoprotein S Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10192 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:101834407-101835038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10194 Neighboring gene small nuclear ribonucleoprotein polypeptide A' Neighboring gene SNRPA1 divergent transcript Neighboring gene uncharacterized LOC100507472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101866838-101867338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6890 Neighboring gene PCSK6 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:101897421-101898364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101899309-101900252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101900253-101901196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:101903043-101903860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101910467-101910968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101910969-101911468 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:101926563-101927064 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:101927065-101927564 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:101951801-101952617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101966524-101967114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:101991219-101991952 Neighboring gene Sharpr-MPRA regulatory region 2389 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:101996796-101996999 Neighboring gene uncharacterized LOC124903566 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:102009487-102010686 Neighboring gene uncharacterized LOC107987228 Neighboring gene uncharacterized LOC124903567

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Common variants in left/right asymmetry genes and pathways are associated with relative hand skill.
    EBI GWAS Catalog
    PCSK6 is associated with handedness in individuals with dyslexia.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of proprotein convertase subtilisin/kexin type 6 (PCSK6) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env Kexin/subtilisin-related convertases such as furin, PACE4, PC1, PC2, PC5 and its isoform PC5/6-B can process HIV-1 gp160 to gp120/gp41 PubMed
    Vpr vpr Vpr processing by soluble PCSK6 (PACE4) DOES NOT involve PAR1 PubMed
    vpr soluble PCSK6 (PACE4) cleaves Vpr PubMed
    vpr Proprotein convertase PC5 cleaves extracellular HIV-1 Vpr between amino-acids 88-89 located within the functionally important C-terminal arginine-rich domain RQRR(88)V/A/G(89)R in Vpr PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables endopeptidase activity TAS
    Traceable Author Statement
    more info
     
    enables heparin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nerve growth factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables serine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables serine-type endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in collagen-containing extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    proprotein convertase subtilisin/kexin type 6
    Names
    paired basic amino acid cleaving enzyme 4
    paired basic amino acid cleaving system 4
    subtilisin-like proprotein convertase 4
    subtilisin/kexin-like protease PACE4
    NP_001278238.1
    NP_002561.1
    NP_612192.1
    NP_612195.1
    NP_612196.1
    NP_612197.1
    NP_612198.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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

    1. NG_030047.4 RefSeqGene

      Range
      40496..226270
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_888

    mRNA and Protein(s)

    1. NM_001291309.2NP_001278238.1  proprotein convertase subtilisin/kexin type 6 isoform i preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) lacks two consecutive exons in the central coding region but maintains reading frame, compared to variant 1. The encoded isoform (i) is shorter, compared to isoform PACE4-AI.
      Source sequence(s)
      AB208955, AM491522, BU732171, DB143095, M80482
      UniProtKB/TrEMBL
      Q59H04
      Related
      ENSP00000381246.2, ENST00000398185.6
      Conserved Domains (7) summary
      cd04059
      Location:160436
      Peptidases_S8_Protein_convertases_Kexins_Furin-lik; Peptidase S8 family domain in Protein convertases
      smart00261
      Location:770812
      FU; Furin-like repeats
      cd00064
      Location:725771
      FU; Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
      pfam01483
      Location:465555
      P_proprotein; Proprotein convertase P-domain
      pfam08686
      Location:868891
      PLAC; PLAC (protease and lacunin) domain
      pfam14843
      Location:620730
      GF_recep_IV; Growth factor receptor domain IV
      pfam16470
      Location:73149
      S8_pro-domain; Peptidase S8 pro-domain
    2. NM_002570.5NP_002561.1  proprotein convertase subtilisin/kexin type 6 isoform PACE4-AI preproprotein

      See identical proteins and their annotated locations for NP_002561.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the predominant isoform (PACE4-AI, also known as PACE4 and PACE4-A).
      Source sequence(s)
      AL545278, AM491522, BU732171, BX428035, M80482
      Consensus CDS
      CCDS73790.1
      UniProtKB/Swiss-Prot
      P29122, Q15099, Q15100, Q9UEG7, Q9UEJ1, Q9UEJ2, Q9UEJ7, Q9UEJ8, Q9UEJ9, Q9Y4G9, Q9Y4H0, Q9Y4H1
      UniProtKB/TrEMBL
      A0A087WY68
      Related
      ENSP00000482760.1, ENST00000611716.5
      Conserved Domains (8) summary
      cd04059
      Location:160454
      Peptidases_S8_Protein_convertases_Kexins_Furin-like; Peptidase S8 family domain in Protein convertases
      smart00261
      Location:743789
      FU; Furin-like repeats
      cd00064
      Location:799845
      FU; Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
      pfam00082
      Location:196479
      Peptidase_S8; Subtilase family
      pfam01483
      Location:539629
      P_proprotein; Proprotein convertase P-domain
      pfam08686
      Location:942965
      PLAC; PLAC (protease and lacunin) domain
      pfam15913
      Location:751847
      Furin-like_2; Furin-like repeat, cysteine-rich
      pfam16470
      Location:73149
      S8_pro-domain; Peptidase S8 pro-domain
    3. NM_138319.4NP_612192.1  proprotein convertase subtilisin/kexin type 6 isoform PACE4-AII preproprotein

      See identical proteins and their annotated locations for NP_612192.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (PACE4-AII) is shorter but maintains the same reading frame, compared to isoform PACE4-AI.
      Source sequence(s)
      AL545278, AM491522, BU732171, BX428035, M80482
      Consensus CDS
      CCDS73789.1
      UniProtKB/TrEMBL
      A0A087WZR0
      Related
      ENSP00000479496.1, ENST00000618548.4
      Conserved Domains (8) summary
      cd04059
      Location:160454
      Peptidases_S8_Protein_convertases_Kexins_Furin-like; Peptidase S8 family domain in Protein convertases
      smart00261
      Location:730776
      FU; Furin-like repeats
      cd00064
      Location:786832
      FU; Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
      pfam00082
      Location:196479
      Peptidase_S8; Subtilase family
      pfam01483
      Location:539629
      P_proprotein; Proprotein convertase P-domain
      pfam08686
      Location:929952
      PLAC; PLAC (protease and lacunin) domain
      pfam15913
      Location:738834
      Furin-like_2; Furin-like repeat, cysteine-rich
      pfam16470
      Location:73149
      S8_pro-domain; Peptidase S8 pro-domain
    4. NM_138322.4NP_612195.1  proprotein convertase subtilisin/kexin type 6 isoform PACE4B preproprotein

      See identical proteins and their annotated locations for NP_612195.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the coding region, one of which is a frameshift, compared to variant 1. The encoded isoform PACE4B (also known as PACE4.1) has a distinct C-terminus compared to isoform PACE4-AI. This isoform is thought to be catalytically inactive.
      Source sequence(s)
      AC087528, AM491522, HY122769, M80482
      UniProtKB/Swiss-Prot
      P29122
      UniProtKB/TrEMBL
      A2RQD9
      Conserved Domains (3) summary
      cd04059
      Location:160454
      Peptidases_S8_Protein_convertases_Kexins_Furin-like; Peptidase S8 family domain in Protein convertases
      pfam00082
      Location:196455
      Peptidase_S8; Subtilase family
      pfam16470
      Location:73149
      S8_pro-domain; Peptidase S8 pro-domain
    5. NM_138323.3NP_612196.1  proprotein convertase subtilisin/kexin type 6 isoform PACE4CS preproprotein

      See identical proteins and their annotated locations for NP_612196.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate exon in the 3' coding region and lacks several downstream exons when compared to variant 1. These differences cause a frameshift and thus isoform PACE4CS has a distinct C-terminus compared to isoform PACE4-AI.
      Source sequence(s)
      AC023024, AL545278, AM491522, BX428035, D28513, M80482
      Consensus CDS
      CCDS73791.1
      UniProtKB/TrEMBL
      H0YKZ4
      Related
      ENSP00000478081.1, ENST00000615296.4
      Conserved Domains (4) summary
      cd04059
      Location:160454
      Peptidases_S8_Protein_convertases_Kexins_Furin-like; Peptidase S8 family domain in Protein convertases
      pfam00082
      Location:196455
      Peptidase_S8; Subtilase family
      pfam01483
      Location:539623
      P_proprotein; Proprotein convertase P-domain
      pfam16470
      Location:73149
      S8_pro-domain; Peptidase S8 pro-domain
    6. NM_138324.3NP_612197.1  proprotein convertase subtilisin/kexin type 6 isoform PACE4C preproprotein

      See identical proteins and their annotated locations for NP_612197.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses two alternate exons in the 3' coding region and lacks several downstream exons when compared to variant 1. These differences cause a frameshift and thus isoform PACE4C has a distinct C-terminus compared to isoform PACE4-AI.
      Source sequence(s)
      AC023024, AL545278, AM491522, BX428035, D28513, M80482
      Consensus CDS
      CCDS73793.1
      UniProtKB/TrEMBL
      H0YKZ4
      Related
      ENSP00000477768.1, ENST00000611967.4
      Conserved Domains (4) summary
      cd04059
      Location:160454
      Peptidases_S8_Protein_convertases_Kexins_Furin-like; Peptidase S8 family domain in Protein convertases
      pfam00082
      Location:196479
      Peptidase_S8; Subtilase family
      pfam01483
      Location:539623
      P_proprotein; Proprotein convertase P-domain
      pfam16470
      Location:73149
      S8_pro-domain; Peptidase S8 pro-domain
    7. NM_138325.4NP_612198.2  proprotein convertase subtilisin/kexin type 6 isoform f preproprotein

      See identical proteins and their annotated locations for NP_612198.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks multiple 3' exons and uses an alternate 3' terminal exon, compared to variant 1. This results in a shorter isoform (f) that has a distinct C-terminus, compared to isoform PACE4-AI.
      Source sequence(s)
      AC023024, AL545278, AM491522, BX428035, D28514, HY205376, M80482
      Consensus CDS
      CCDS73792.1
      UniProtKB/TrEMBL
      H0YKZ4, H7BXT3
      Related
      ENSP00000332052.8, ENST00000331826.12
      Conserved Domains (4) summary
      cd04059
      Location:160454
      Peptidases_S8_Protein_convertases_Kexins_Furin-like; Peptidase S8 family domain in Protein convertases
      pfam00082
      Location:196479
      Peptidase_S8; Subtilase family
      pfam01483
      Location:539623
      P_proprotein; Proprotein convertase P-domain
      pfam16470
      Location:73149
      S8_pro-domain; Peptidase S8 pro-domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      101303933..101489707 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      99058998..99244970 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_138320.1: Suppressed sequence

      Description
      NM_138320.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    2. NM_138321.1: Suppressed sequence

      Description
      NM_138321.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.