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    FAM50A family with sequence similarity 50 member A [ Homo sapiens (human) ]

    Gene ID: 9130, updated on 5-Mar-2024

    Summary

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    Official Symbol
    FAM50Aprovided by HGNC
    Official Full Name
    family with sequence similarity 50 member Aprovided by HGNC
    Primary source
    HGNC:HGNC:18786
    See related
    Ensembl:ENSG00000071859 MIM:300453; AllianceGenome:HGNC:18786
    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
    9F; XAP5; HXC26; MRXSA; HXC-26; DXS9928E
    Summary
    This gene belongs to the FAM50 family. The encoded protein is highly conserved in length and sequence across different species. It is a basic protein containing a nuclear localization signal, and may function as a DNA-binding protein or a transcriptional factor. [provided by RefSeq, Sep 2009]
    Expression
    Ubiquitous expression in fat (RPKM 32.0), placenta (RPKM 25.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    Xq28
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154444141..154450654)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152680649..152687163)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153672488..153679002)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153656739-153657240 Neighboring gene ATPase H+ transporting accessory protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153665032-153665532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153666887-153667386 Neighboring gene GDP dissociation inhibitor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153672115-153672682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153673251-153673818 Neighboring gene microRNA 6858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153687524-153688076 Neighboring gene plexin A3 Neighboring gene Sharpr-MPRA regulatory region 3405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21109 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153707495-153707994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30063 Neighboring gene L antigen family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153713643-153714401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153714402-153715160 Neighboring gene ubiquitin like 4A

    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. Upregulation of FAM50A promotes cancer development. Hu MZ, et al. Med Oncol, 2023 Jul 1. PMID 37393403
    2. Proto-Oncogene FAM50A Can Regulate the Immune Microenvironment and Development of Hepatocellular Carcinoma In Vitro and In Vivo. Xie X, et al. Int J Mol Sci, 2023 Feb 6. PMID 36834630, Free PMC Article
    3. Detection of a DNA Methylation Signature for the Intellectual Developmental Disorder, X-Linked, Syndromic, Armfield Type. Haghshenas S, et al. Int J Mol Sci, 2021 Jan 23. PMID 33498634, Free PMC Article
    4. X-linked mental retardation syndrome with short stature, small hands and feet, seizures, cleft palate, and glaucoma is linked to Xq28. Armfield K, et al. Am J Med Genet, 1999 Jul 30. PMID 10398235
    5. Differential expression of XAP5, a candidate disease gene. Mazzarella R, et al. Genomics, 1997 Oct 1. PMID 9339379

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Upregulation of FAM50A promotes cancer development.
      Title: Upregulation of FAM50A promotes cancer development.
    2. Proto-Oncogene FAM50A Can Regulate the Immune Microenvironment and Development of Hepatocellular Carcinoma In Vitro and In Vivo.
      Title: Proto-Oncogene FAM50A Can Regulate the Immune Microenvironment and Development of Hepatocellular Carcinoma In Vitro and In Vivo.
    3. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.
      Title: Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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
    Armfield syndrome
    MedGen: C1846057 OMIM: 300261 GeneReviews: Not available
    		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)

    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 RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spermatogenesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein FAM50A
    Names
    Armfield X-linked mental retardation syndrome
    protein XAP-5

    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

    1. NG_013233.2 RefSeqGene

      Range
      5002..11515
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004699.4 → NP_004690.1  protein FAM50A

      See identical proteins and their annotated locations for NP_004690.1

      Status: REVIEWED

      Source sequence(s)
      BQ018378, CR992165, D83260
      Consensus CDS
      CCDS14751.1
      UniProtKB/Swiss-Prot
      A8KAQ4, B2R997, Q14320, Q5HY37, Q6PJH5
      Related
      ENSP00000377225.3, ENST00000393600.8
      Conserved Domains (1) summary
      pfam04921
      Location:152 → 338
      XAP5; circadian clock regulator

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      154444141..154450654
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152680649..152687163
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14320.2 GenPept UniProtKB/Swiss-Prot:Q14320

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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