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LOC108663993 ataxin 1 repeat instability region [ Homo sapiens (human) ]

Gene ID: 108663993, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108663993
Gene description
ataxin 1 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 within the coding region of the ataxin 1 (ATXN1) gene on the p arm of chromosome 6, and contains a CAG trinucleotide repeat. Expansions of this repeat result in an elongated polyglutamine tract in the encoded protein. Expansions are known to be a cause of spinocerebellar ataxia type 1 (SCA1) an autosomal dominant neurodegenerative disorder. There is allelic variation at this locus, with most non-disease alleles containing 6-44 CAG repeats, many with CAT trinucleotide interruptions. Alleles with 36-38 CAG repeats, but lacking CAT interruptions can expand upon transmission, resulting in a pathogenic allele. There is an inverse correlation between the length of uninterrupted CAG repeats and age of disease onset. [provided by RefSeq, Sep 2016]
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Genomic context

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Location:
6p23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (16327634..16327724)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (16200189..16200282)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (16327865..16327955)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24098 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16215087-16215263 Neighboring gene CRISPRi-validated cis-regulatory element chr6.847 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16217722-16217944 Neighboring gene RNA, U6 small nuclear 1114, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr6.848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16957 Neighboring gene NANOG hESC enhancer GRCh37_chr6:16259269-16259823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16262581-16263080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:16264120-16264690 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16264691-16265260 Neighboring gene Sharpr-MPRA regulatory region 9524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24099 Neighboring gene guanosine monophosphate reductase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16303323-16303902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24100 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16310151-16310359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16320601-16321434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16327606-16328166 Neighboring gene uncharacterized LOC127903862 Neighboring gene Sharpr-MPRA regulatory region 3581 Neighboring gene ataxin 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16387334-16387547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24111 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16603501-16603686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16672541-16673042 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16723974-16724586 Neighboring gene HNF1 motif-containing MPRA enhancer 207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16962 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16761792-16762007 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:16762145-16763344 Neighboring gene ATXN1 antisense RNA 1

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. Clinical characteristics of patients with spinocerebellar ataxias 1, 2, 3 and 6 in the US; a prospective observational study. Ashizawa T, et al. Orphanet J Rare Dis, 2013 Nov 13. PMID 24225362, Free PMC Article
  2. The role of interruptions in polyQ in the pathology of SCA1. Menon RP, et al. PLoS Genet, 2013. PMID 23935513, Free PMC Article
  3. Biological and clinical characteristics of individuals at risk for spinocerebellar ataxia types 1, 2, 3, and 6 in the longitudinal RISCA study: analysis of baseline data. Jacobi H, et al. Lancet Neurol, 2013 Jul. PMID 23707147
  4. Clinical features, neurogenetics and neuropathology of the polyglutamine spinocerebellar ataxias type 1, 2, 3, 6 and 7. Rüb U, et al. Prog Neurobiol, 2013 May. PMID 23438480
  5. Consensus and controversies in best practices for molecular genetic testing of spinocerebellar ataxias. Sequeiros J, et al. Eur J Hum Genet, 2010 Nov. PMID 20179748, Free PMC Article

See all (52) 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

  • ATXN1 repeat instability region
  • SCA1 repeat instability region
  • spinocerebellar ataxia type 1 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_051564.1 

    Range
    101..191
    Download
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    16327634..16327724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    16200189..16200282
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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