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FAM20B FAM20B glycosaminoglycan xylosylkinase [ Homo sapiens (human) ]

Gene ID: 9917, updated on 5-Mar-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, Apr 2022]
Expression
Ubiquitous expression in adrenal (RPKM 13.7), brain (RPKM 12.6) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (179017334..179076567)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (178372430..178431587)
105.20220307 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
  • 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. 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
  4. FAM20B is a kinase that phosphorylates xylose in the glycosaminoglycan-protein linkage region. Koike T, et al. Biochem J, 2009 Jun 26. PMID 19473117
  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 (32) 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
  
NOT involved_in protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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

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