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    FRA10AC1 FRA10A associated CGG repeat 1 [ Homo sapiens (human) ]

    Gene ID: 118924, updated on 3-May-2024

    Summary

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    Official Symbol
    FRA10AC1provided by HGNC
    Official Full Name
    FRA10A associated CGG repeat 1provided by HGNC
    Primary source
    HGNC:HGNC:1162
    See related
    Ensembl:ENSG00000148690 MIM:608866; AllianceGenome:HGNC:1162
    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
    FRA10A; NEDGFC; C10orf4; F26C11.1-like
    Summary
    The protein encoded by this gene is a nuclear phosphoprotein of unknown function. This gene contains a tandem CGG repeat region within a CpG island that normally consists of 8-14 repeats but can expand to over 200 repeats. The repeat region is within the 5' UTR of some transcript variants, but is intronic to another variant. The expanded repeat allele is a fragile site and becomes hypermethylated, causing a reduction in gene expression. A disease phenotype has not been associated with expanded alleles. This gene is found within the rare FRA10A folate-sensitive fragile site. [provided by RefSeq, Dec 2016]
    Expression
    Ubiquitous expression in brain (RPKM 6.1), testis (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FRA10AC1 in Genome Data Viewer
    Location:
    10q23.33
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (93667883..93702959, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (94547814..94582886, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (95427640..95462716, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene retinol binding protein 4 Neighboring gene phosphodiesterase 6C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3786 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:95474242-95474394 Neighboring gene fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) Neighboring gene uncharacterized LOC101927013 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:95505761-95506512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:95508859-95509841 Neighboring gene uncharacterized LOC105378437 Neighboring gene leucine rich glioma inactivated 1

    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. Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation. von Elsner L, et al. Brain, 2022 May 24. PMID 34694367, Free PMC Article
    2. Variations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aβ1-42 Level. Li QS, et al. PLoS One, 2015. PMID 26252872, Free PMC Article
    3. Folate-sensitive fragile site FRA10A is due to an expansion of a CGG repeat in a novel gene, FRA10AC1, encoding a nuclear protein. Sarafidou T, et al. Genomics, 2004 Jul. PMID 15203205
    4. Gene expression profiling in human fetal liver and identification of tissue- and developmental-stage-specific genes through compiled expression profiles and efficient cloning of full-length cDNAs. Yu Y, et al. Genome Res, 2001 Aug. PMID 11483580, Free PMC Article
    5. Dynamic protein-protein interaction wiring of the human spliceosome. Hegele A, et al. Mol Cell, 2012 Feb 24. PMID 22365833

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation.
      Title: Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation.
    2. variants in FRA10AC1 associated with CSF Abeta1-42 level passing the genome-wide significance threshold, were identified.
      Title: Variations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aβ1-42 Level.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities
    MedGen: C5774251 OMIM: 620113 GeneReviews: Not available
    		not available

    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 phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein FRA10AC1
    Names
    fragile site 10q23.3
    fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1
    rare folic acid-type fragile site, FRA(10)(q23.3), candidate gene 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.

    Genomic

    1. NG_016832.1 RefSeqGene

      Range
      4981..39690
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001347712.2 → NP_001334641.1  protein FRA10AC1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-5 all encode the same protein.
      Source sequence(s)
      AA505135, AK090955, AL157396, CN298116, DB452961
      Consensus CDS
      CCDS7430.1
      UniProtKB/Swiss-Prot
      C9JCR4, C9JCR5, C9JMY4, Q70Z49, Q70Z50, Q70Z51, Q70Z52, Q70Z53, Q8N293, Q8WVH5, Q96JQ8
      Conserved Domains (1) summary
      pfam09725
      Location:104 → 215
      Fra10Ac1; Folate-sensitive fragile site protein Fra10Ac1

    2. NM_001347713.2 → NP_001334642.1  protein FRA10AC1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-5 all encode the same protein.
      Source sequence(s)
      AA505135, AK090955, AL157396, CN298116
      Consensus CDS
      CCDS7430.1
      UniProtKB/Swiss-Prot
      C9JCR4, C9JCR5, C9JMY4, Q70Z49, Q70Z50, Q70Z51, Q70Z52, Q70Z53, Q8N293, Q8WVH5, Q96JQ8
      Conserved Domains (1) summary
      pfam09725
      Location:104 → 215
      Fra10Ac1; Folate-sensitive fragile site protein Fra10Ac1

    3. NM_001347714.2 → NP_001334643.1  protein FRA10AC1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1-5 all encode the same protein.
      Source sequence(s)
      AA505135, AK090955, AK309016, AL157396, CN298116
      Consensus CDS
      CCDS7430.1
      UniProtKB/Swiss-Prot
      C9JCR4, C9JCR5, C9JMY4, Q70Z49, Q70Z50, Q70Z51, Q70Z52, Q70Z53, Q8N293, Q8WVH5, Q96JQ8
      Conserved Domains (1) summary
      pfam09725
      Location:104 → 215
      Fra10Ac1; Folate-sensitive fragile site protein Fra10Ac1

    4. NM_001347715.2 → NP_001334644.1  protein FRA10AC1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1-5 all encode the same protein.
      Source sequence(s)
      AA505135, AJ431721, AK090955, AL157396, CN298116
      Consensus CDS
      CCDS7430.1
      UniProtKB/Swiss-Prot
      C9JCR4, C9JCR5, C9JMY4, Q70Z49, Q70Z50, Q70Z51, Q70Z52, Q70Z53, Q8N293, Q8WVH5, Q96JQ8
      Conserved Domains (1) summary
      pfam09725
      Location:104 → 215
      Fra10Ac1; Folate-sensitive fragile site protein Fra10Ac1

    5. NM_145246.5 → NP_660289.2  protein FRA10AC1

      See identical proteins and their annotated locations for NP_660289.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the most abundant transcript. Variants 1-5 all encode the same protein.
      Source sequence(s)
      AK090955, AL157396, CN298116
      Consensus CDS
      CCDS7430.1
      UniProtKB/Swiss-Prot
      C9JCR4, C9JCR5, C9JMY4, Q70Z49, Q70Z50, Q70Z51, Q70Z52, Q70Z53, Q8N293, Q8WVH5, Q96JQ8
      Related
      ENSP00000360488.3, ENST00000359204.5
      Conserved Domains (1) summary
      pfam09725
      Location:104 → 215
      Fra10Ac1; Folate-sensitive fragile site protein Fra10Ac1

    RNA

    1. NR_144635.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA505135, AK090955, AL157396, CN298116

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      93667883..93702959 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      94547814..94582886 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_203438.2: Suppressed sequence

      Description
      NM_203438.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_203439.2: Suppressed sequence

      Description
      NM_203439.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    3. NM_203440.2: Suppressed sequence

      Description
      NM_203440.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    4. NM_203441.2: Suppressed sequence

      Description
      NM_203441.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q70Z53.3 GenPept UniProtKB/Swiss-Prot:Q70Z53

    Gene LinkOut

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