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

Gene ID: 9130, updated on 27-Nov-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
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Genomic context

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See FAM50A in Genome Data Viewer
Location:
Xq28
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154444141..154450654)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152680649..152687163)
RS_2024_09 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. Isolation and analysis of a novel gene, HXC-26, adjacent to the rab GDP dissociation inhibitor gene located at human chromosome Xq28 region. Toyoda A, et al. DNA Res, 1996 Oct 31. PMID 9039504
  3. 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
  4. Differential expression of XAP5, a candidate disease gene. Mazzarella R, et al. Genomics, 1997 Oct 1. PMID 9339379
  5. 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

See all (73) 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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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_2024_08

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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