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    FAM20B FAM20B glycosaminoglycan xylosylkinase [ Homo sapiens (human) ]

    Gene ID: 9917, updated on 3-Nov-2024

    Summary

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    Official Symbol
    FAM20Bprovided by HGNC
    Official Full Name
    FAM20B glycosaminoglycan xylosylkinaseprovided by HGNC
    Primary source
    HGNC:HGNC:23017
    See related
    Ensembl:ENSG00000116199 MIM:611063; AllianceGenome:HGNC:23017
    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
    gxk1
    Summary
    Enables phosphotransferase activity, alcohol group as acceptor. Predicted to be involved in proteoglycan biosynthetic process. Located in Golgi apparatus and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 13.7), brain (RPKM 12.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FAM20B in Genome Data Viewer
    Location:
    1q25.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (179017334..179076567)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (178372430..178431587)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (178994939..179045702)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Ral GEF with PH domain and SH3 binding motif 2 Neighboring gene angiopoietin like 1 Neighboring gene uncharacterized LOC102724754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:178908305-178908804 Neighboring gene MPRA-validated peak477 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:178915423-178916208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1582 Neighboring gene CRISPRi-validated cis-regulatory element chr1.10033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1584 Neighboring gene Sharpr-MPRA regulatory region 12139 Neighboring gene Sharpr-MPRA regulatory region 11809 Neighboring gene ribosomal protein S26 pseudogene 16 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:179055021-179055521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179056771-179057672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179057673-179058574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179060592-179061092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179061093-179061593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:179082493-179082994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:179082995-179083494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2149 Neighboring gene torsin family 3 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179107953-179108459 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:179111778-179112977 Neighboring gene ABL proto-oncogene 2, non-receptor tyrosine kinase Neighboring gene SET pseudogene 10

    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 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. Correlation of molecular characteristics, isotype, and in vitro functional activity of human antipneumococcal monoclonal antibodies. Baxendale HE, et al. Infect Immun, 2006 Feb. PMID 16428749, Free PMC Article
    2. Immunogenetic analysis of the immune response to pneumococcal polysaccharide. Baxendale HE, et al. Eur J Immunol, 2000 Apr. PMID 10760811
    3. FAM20B is a kinase that phosphorylates xylose in the glycosaminoglycan-protein linkage region. Koike T, et al. Biochem J, 2009 Jun 26. PMID 19473117
    4. Xylose phosphorylation functions as a molecular switch to regulate proteoglycan biosynthesis. Wen J, et al. Proc Natl Acad Sci U S A, 2014 Nov 4. PMID 25331875, Free PMC Article
    5. Comparative characteristics of mu chain and alpha chain transcripts expressed by individual tonsil plasma cells. Yavuz S, et al. Mol Immunol, 2001 Jan. PMID 11483207

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Altered Expression of Aggrecan, FAM20B, B3GALT6, and EXTL2 in Patients with Osteoarthritis and Kashin-Beck Disease.
      Title: Altered Expression of Aggrecan, FAM20B, B3GALT6, and EXTL2 in Patients with Osteoarthritis and Kashin-Beck Disease.
    2. The T allele of FAM20B (rs3766626) was associated with susceptibility to two mesiodens
      Title: Lack of association between PAX6/SOSTDC1/FAM20B gene polymorphisms and mesiodens.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphotransferase activity, alcohol group as acceptor IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphotransferase activity, alcohol group as acceptor IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in phosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteoglycan biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    glycosaminoglycan xylosylkinase
    Names
    family with sequence similarity 20, member B
    xylose kinase
    NP_001311239.1
    NP_001311240.1
    NP_055679.1
    XP_016858490.1
    XP_016858491.1
    XP_047292049.1
    XP_047292050.1
    XP_054195913.1
    XP_054195914.1
    XP_054195915.1
    XP_054195916.1

    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_001324310.2 → NP_001311239.1  glycosaminoglycan xylosylkinase

      Status: VALIDATED

      Source sequence(s)
      AL139132
      Consensus CDS
      CCDS1328.1
      UniProtKB/Swiss-Prot
      O75063, Q5W0C3, Q5W0C4
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    2. NM_001324311.2 → NP_001311240.1  glycosaminoglycan xylosylkinase

      Status: VALIDATED

      Source sequence(s)
      AL139132
      Consensus CDS
      CCDS1328.1
      UniProtKB/Swiss-Prot
      O75063, Q5W0C3, Q5W0C4
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    3. NM_014864.4 → NP_055679.1  glycosaminoglycan xylosylkinase

      See identical proteins and their annotated locations for NP_055679.1

      Status: VALIDATED

      Source sequence(s)
      AL139132, BC051794, CA844342
      Consensus CDS
      CCDS1328.1
      UniProtKB/Swiss-Prot
      O75063, Q5W0C3, Q5W0C4
      Related
      ENSP00000263733.4, ENST00000263733.5
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      179017334..179076567
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436093.1 → XP_047292049.1  glycosaminoglycan xylosylkinase isoform X1

    2. XM_047436094.1 → XP_047292050.1  glycosaminoglycan xylosylkinase isoform X1

    3. XM_017003001.3 → XP_016858490.1  glycosaminoglycan xylosylkinase isoform X1

    4. XM_017003002.2 → XP_016858491.1  glycosaminoglycan xylosylkinase isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      178372430..178431587
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339938.1 → XP_054195913.1  glycosaminoglycan xylosylkinase isoform X1

    2. XM_054339941.1 → XP_054195916.1  glycosaminoglycan xylosylkinase isoform X1

    3. XM_054339939.1 → XP_054195914.1  glycosaminoglycan xylosylkinase isoform X1

    4. XM_054339940.1 → XP_054195915.1  glycosaminoglycan xylosylkinase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75063.1 GenPept UniProtKB/Swiss-Prot:O75063

    Gene LinkOut

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