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LOC109461478 ATXN8 opposite strand (non-protein coding) repeat instability region [ Homo sapiens (human) ]

Gene ID: 109461478, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109461478
Gene description
ATXN8 opposite strand (non-protein coding) repeat instability region
Gene type
biological region
Feature type(s)
misc_feature: 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 3' end of the ATXN8 opposite strand (non-protein coding) gene on the q arm of chromosome 13. This region contains a highly polymorphic (CTG)n trinucleotide repeat that is adjacent to a stably transmitted, but polymorphic, (CTA)n repeat. Expansions of the CTG repeat can be associated with spinocerebellar ataxia type 8, an autosomal dominant disorder. Most normal alleles contain about 15-50 triplet repeat units, but repeat lengths of greater than 1300 repeat units have been observed in some expanded alleles. Reduced penetrance is observed for some alleles, and is more commonly seen amongst alleles with less than 100 repeats. Paternal transmission of the allele is biased towards contractions of the repeat while maternal transmissions are biased towards expansion of the repeat. Both toxicity of transcripts with the expanded allele, and repeat-associated non-ATG translation (RAN translation) have been implicated in disease pathogenesis. [provided by RefSeq, Dec 2016]
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Genomic context

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Location:
13q21.33
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (70139352..70139429)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (69361215..69361271)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (70713484..70713561)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene kelch like family member 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:70544083-70545282 Neighboring gene 5',3'-nucleotidase, cytosolic pseudogene 3 Neighboring gene LUC7 like 3 pre-mRNA splicing factor pseudogene 1 Neighboring gene ATXN8 opposite strand lncRNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:70829090-70829790 Neighboring gene RNA, U6 small nuclear 54, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:71204047-71205022 Neighboring gene uncharacterized LOC105370255 Neighboring gene VISTA enhancer hs126 Neighboring gene VISTA enhancer hs540

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. Non-Ataxic Phenotypes of SCA8 Mimicking Amyotrophic Lateral Sclerosis and Parkinson Disease. Kim JS, et al. J Clin Neurol, 2013 Oct. PMID 24285970, Free PMC Article
  2. Novel neuronal cytoplasmic inclusions in a patient carrying SCA8 expansion mutation. Yokoyama T, et al. Neuropathology, 2014 Feb. PMID 23711133
  3. Coexisting huntingtin and SCA8 repeat expansion: case report of a severe complex neurodegenerative syndrome. Bereznai B, et al. J Neurol Sci, 2010 Jun 15. PMID 20403608
  4. Spinocerebellar ataxia 8: variable phenotype and unique pathogenesis. Gupta A, et al. Parkinsonism Relat Disord, 2009 Nov. PMID 19559641
  5. Clinicopathologic investigation of a family with expanded SCA8 CTA/CTG repeats. Ito H, et al. Neurology, 2006 Oct 24. PMID 17060579

See all (58) 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

  • ATXN8OS repeat instability region
  • SCA8 repeat instability region
  • spinocerebellar ataxia type 8 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_052616.1 

    Range
    101..178
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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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    70139352..70139429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    69361215..69361271
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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