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LOC109029533 cystatin B upstream repeat instability region [ Homo sapiens (human) ]

Gene ID: 109029533, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109029533
Gene description
cystatin B upstream 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 just upstream of the cystatin B (CSTB) gene on the q arm of chromosome 22, and contains a CCCCGCCCCGCG dodecamer repeat. Allelic variation in this region has been observed, but the reference genome contains three copies of the repeat. Expansions of this repeat are known to be a cause of progressive myoclonus epilepsy of the Unverricht-Lundborg type (EPM1), an autosomal recessive disorder. Alleles with 12-17 repeats display reduced stability, while expanded alleles of about 45-75 repeats have been observed, and are disease-causing. Expansion of the repeat results in reduced expression of cystatin B in some cell types. In vitro studies indicate that the dodecamer repeat may adopt secondary structures. [provided by RefSeq, Nov 2016]
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Genomic context

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See LOC109029533 in Genome Data Viewer
Location:
21q22.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (43776443..43776479)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42132055..42132091)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45196324..45196360)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene pyridoxal kinase Neighboring gene uncharacterized LOC105372824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45157073-45157572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45159504-45160242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45160243-45160981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45183829-45184574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45184575-45185320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45186633-45187246 Neighboring gene PDXK-CSTB intergenic CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45189831-45190753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45190754-45191675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45198401-45199200 Neighboring gene uncharacterized LOC105372825 Neighboring gene cystatin B Neighboring gene transmembrane protein 97 pseudogene 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. Tandem repeat sequence variation as causative cis-eQTLs for protein-coding gene expression variation: the case of CSTB. Borel C, et al. Hum Mutat, 2012 Aug. PMID 22573514
  2. A patient with 2 different repeat expansion mutations. Nokelainen P, et al. Arch Neurol, 2000 Aug. PMID 10927802
  3. Instability of the EPM1 minisatellite. Larson GP, et al. Hum Mol Genet, 1999 Oct. PMID 10484766
  4. Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy. Lalioti MD, et al. Nature, 1997 Apr 24. PMID 9126745
  5. The contribution of cis-elements to disease-associated repeat instability: clinical and experimental evidence. Cleary JD, et al. Cytogenet Genome Res, 2003. PMID 14526163

See all (12) 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

  • CSTB upstream repeat instability region
  • EPM1 repeat instability region
  • progressive myoclonus epilepsy 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_052013.1 

    Range
    101..137
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    43776443..43776479
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    42132055..42132091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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