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

Gene ID: 118924, updated on 5-Mar-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
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Genomic context

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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

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