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    XKR6 XK related 6 [ Homo sapiens (human) ]

    Gene ID: 286046, updated on 5-Mar-2024

    Summary

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    Official Symbol
    XKR6provided by HGNC
    Official Full Name
    XK related 6provided by HGNC
    Primary source
    HGNC:HGNC:27806
    See related
    Ensembl:ENSG00000171044 AllianceGenome:HGNC:27806
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    XRG6; C8orf5; C8orf7; C8orf21
    Summary
    Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in thyroid (RPKM 1.5), lymph node (RPKM 1.4) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    8p23.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (10896045..11201833, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (8537206..8882964)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (10753555..11059342, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:10697101-10697601 Neighboring gene uncharacterized LOC101929248 Neighboring gene uncharacterized LOC112268022 Neighboring gene PINX1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10785877-10786571 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:10795001-10795652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10818763-10819262 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:10828786-10829181 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10833945-10834446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10865365-10866070 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10917857-10918374 Neighboring gene uncharacterized LOC101929269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10926551-10927368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:10930301-10930846 Neighboring gene microRNA 598 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:10938390-10939589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26999 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:10996613-10997114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18924 Neighboring gene ribosomal protein L17 pseudogene 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27002 Neighboring gene Sharpr-MPRA regulatory region 9232 Neighboring gene long intergenic non-protein coding RNA 529 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18926 Neighboring gene ribosomal protein L19 pseudogene 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11141809-11142310 Neighboring gene myotubularin related protein 9 Neighboring gene solute carrier family 35 member G5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. XKR6 rs7014968 SNP Increases Serum Total Cholesterol Levels and the Risk of Coronary Heart Disease and Ischemic Stroke. Li KG, et al. Clin Appl Thromb Hemost, 2020 Jan-Dec. PMID 32024373, Free PMC Article
    2. Association between the XKR6 rs7819412 SNP and serum lipid levels and the risk of coronary artery disease and ischemic stroke. Zheng PF, et al. BMC Cardiovasc Disord, 2019 Aug 20. PMID 31429711, Free PMC Article
    3. Genetic variants in systemic lupus erythematosus susceptibility loci, XKR6 and GLT1D1 are associated with childhood-onset SLE in a Korean cohort. Joo YB, et al. Sci Rep, 2018 Jul 2. PMID 29967481, Free PMC Article
    4. Physical and transcriptional map of the critical region for keratolytic winter erythema (KWE) on chromosome 8p22-p23 between D8S550 and D8S1759. Appel S, et al. Eur J Hum Genet, 2002 Jan. PMID 11896452
    5. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. Weissglas-Volkov D, et al. Circ Cardiovasc Genet, 2010 Feb. PMID 20160193, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. XKR6 rs7014968 SNP Increases Serum Total Cholesterol Levels and the Risk of Coronary Heart Disease and Ischemic Stroke.
      Title: XKR6 rs7014968 SNP Increases Serum Total Cholesterol Levels and the Risk of Coronary Heart Disease and Ischemic Stroke.
    2. XKR6 rs7819412 A allele was related to increased serum triglyceride levels in coronary artery disease, total cholesterol levels in ischemic stroke patients and high risk of CAD and ischemic stroke.
      Title: Association between the XKR6 rs7819412 SNP and serum lipid levels and the risk of coronary artery disease and ischemic stroke.
    3. XKR6 single nucleotide polymorphism rs7460469 is associated with childhood-onset systemic lupus erythematosus.
      Title: Genetic variants in systemic lupus erythematosus susceptibility loci, XKR6 and GLT1D1 are associated with childhood-onset SLE in a Korean cohort.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic loci associated with lipid concentrations and cardiovascular risk factors in the Korean population.
    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

    EBI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    EBI GWAS Catalog
    Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype.
    EBI GWAS Catalog
    Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ31557

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in apoptotic process involved in development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in engulfment of apoptotic cell IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylserine exposure on apoptotic cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    XK-related protein 6
    Names
    Transmembrane protein C8orf5
    X Kell blood group precursor-related family, member 6
    X-linked Kx blood group related 6
    XK, Kell blood group complex subunit-related family, member 6

    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.

    mRNA and Protein(s)

    1. NM_173683.4 → NP_775954.2  XK-related protein 6

      See identical proteins and their annotated locations for NP_775954.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the protein-coding variant.
      Source sequence(s)
      AC011008, AF131215, AY534244, BC024146
      Consensus CDS
      CCDS5978.2
      UniProtKB/Swiss-Prot
      Q5GH73, Q8TBA0
      Related
      ENSP00000416707.2, ENST00000416569.3
      Conserved Domains (1) summary
      pfam09815
      Location:131 → 501
      XK-related; XK-related protein

    RNA

    1. NR_138152.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AF131215

    2. NR_138153.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AF131215

    3. NR_138154.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AF131215, CX755744

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      10896045..11201833 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447129.2 → XP_024302897.1  XK-related protein 6 isoform X1

      Conserved Domains (2) summary
      pfam09815
      Location:131 → 534
      XK-related; XK-related protein
      cl27167
      Location:82 → 138
      HemX; putative uroporphyrinogen-III C-methyltransferase

    2. XM_011543821.3 → XP_011542123.1  XK-related protein 6 isoform X2

      See identical proteins and their annotated locations for XP_011542123.1

      UniProtKB/TrEMBL
      Q96KT3
      Related
      ENSP00000297303.4, ENST00000297303.4
      Conserved Domains (2) summary
      pfam09815
      Location:131 → 254
      XK-related; XK-related protein
      cl27167
      Location:82 → 138
      HemX; HemX, putative uroporphyrinogen-III C-methyltransferase

    RNA

    1. XR_948899.4 RNA Sequence

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_018654717.1 Reference GRCh38.p14 PATCHES

      Range
      2145097..2451195
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      8537206..8882964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360303.1 → XP_054216278.1  XK-related protein 6 isoform X1

    2. XM_054360304.1 → XP_054216279.1  XK-related protein 6 isoform X2

      UniProtKB/TrEMBL
      Q96KT3

    RNA

    1. XR_008487836.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5GH73.1 GenPept UniProtKB/Swiss-Prot:Q5GH73

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