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LOC109396974 FRAXF repeat instability region [ Homo sapiens (human) ]

Gene ID: 109396974, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109396974
Gene description
FRAXF repeat instability region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif, repeat_instability_region
repeat_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This biological region is found near the 5' regulatory region of the transmembrane protein 185A (TMEM185A) gene on the q arm of the X chromosome. This region is a rare folate-sensitive fragile site and contains a highly polymorphic (GCCGTC)n(GCC)n motif, with most normal alleles containing less than 40 trinucleotide repeat units. Expansion of the GCC/CGG repeat to copy numbers greater than 300 has been observed and cause fragility at this site. Hypermethylation of a CpG island near the repeat expansion in large expansions can lead to transcriptional silencing of the TMEM185A gene. [provided by RefSeq, Dec 2016]
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Genomic context

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Location:
Xq28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (149631714..149631781)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (147897515..147897555)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X (PATCHES) NW_004070890.2 (5156112..5156179)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene MAGE family member A9B Neighboring gene transmembrane protein 185A Neighboring gene heat shock transcription factor family, X-linked 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21045 Neighboring gene MAGE family member A11 pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:148757169-148757709 Neighboring gene MAGE family member A11

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The identification of a third fragile site, FRAXF, in Xq27--q28 distal to both FRAXA and FRAXE. Hirst MC, et al. Hum Mol Genet, 1993 Feb. PMID 8499907
  2. The cloning of FRAXF: trinucleotide repeat expansion and methylation at a third fragile site in distal Xqter. Ritchie RJ, et al. Hum Mol Genet, 1994 Dec. PMID 7881407
  3. Isolation of a GCC repeat showing expansion in FRAXF, a fragile site distal to FRAXA and FRAXE. Parrish JE, et al. Nat Genet, 1994 Nov. PMID 7874164
  4. A novel gene, FAM11A, associated with the FRAXF CpG island is transcriptionally silent in FRAXF full mutation. Shaw MA, et al. Eur J Hum Genet, 2002 Nov. PMID 12404111
  5. Population genetics of the FRAXE and FRAXF GCC repeats, and a novel CGG repeat, in Xq28. Ritchie RJ, et al. Am J Med Genet, 1997 Dec 31. PMID 9415475

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • FAM11A repeat instability region
  • TMEM185A repeat instability region
  • fragile site, folic acid type, rare, fra(X)(q28) F repeat instability region

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_052601.1 

    Range
    101..168
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    GenBank, FASTA, Sequence Viewer (Graphics)

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
    149631714..149631781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    147897515..147897555
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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