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LOC108663985 calcium voltage-gated channel subunit alpha1 A repeat instability region [ Homo sapiens (human) ]

Gene ID: 108663985, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108663985
Gene description
calcium voltage-gated channel subunit alpha1 A 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 an exon of the calcium voltage-gated channel subunit alpha1 A (CACNA1A) gene on the p arm of chromosome 19, and contains a CAG trinucleotide repeat. This trinucleotide repeat is found in the 3' coding region of some transcript variants of the CACNA1A gene, while it is in the 3' untranslated region of other variants. For those variants containing the trinucleotide repeat in the coding region, 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 6 (SCA6), an autosomal dominant progressive disorder. There is allelic variation at this locus, with up to 19 CAG repeats for most non-pathogenic alleles. Individuals with expanded alleles of 20-33 CAG repeats typically develop symptoms at some point during their lifetime. [provided by RefSeq, Jan 2017]
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Genomic context

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Location:
19p13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13207859..13207898)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13333137..13333176)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13318673..13318712)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14114 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13263956-13264839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10201 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13276087-13276664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13278116-13278743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13280436-13280936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13280937-13281437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14124 Neighboring gene OCT4 hESC enhancer GRCh37_chr19:13295659-13296160 Neighboring gene Sharpr-MPRA regulatory region 13602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13297985-13298895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13297074-13297984 Neighboring gene ribosomal protein L12 pseudogene 42 Neighboring gene CRISPRi-FlowFISH-validated PRDX2 regulatory element 7 Neighboring gene MPRA-validated peak3367 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10203 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13319630-13320530 Neighboring gene immediate early response 2 Neighboring gene MPRA-validated peak3368 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13335615-13336116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13336117-13336616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13337139-13337640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13341838-13342338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13342339-13342839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10204 Neighboring gene calcium voltage-gated channel subunit alpha1 A Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:13371552-13372751 Neighboring gene Sharpr-MPRA regulatory region 13658 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:13385818-13387017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14132 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:13445719-13446918 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:13509521-13510720 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13511134-13511634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13511635-13512135 Neighboring gene Sharpr-MPRA regulatory region 1233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13618335-13618861 Neighboring gene uncharacterized LOC107985287 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:13700158-13700387 Neighboring gene Sharpr-MPRA regulatory region 13460 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:13732208-13732929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13776728-13777228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13777229-13777729 Neighboring gene uncharacterized LOC105372284 Neighboring gene MPRA-validated peak3373 silencer Neighboring gene MPRA-validated peak3374 silencer

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. An miRNA-mediated therapy for SCA6 blocks IRES-driven translation of the CACNA1A second cistron. Miyazaki Y, et al. Sci Transl Med, 2016 Jul 13. PMID 27412786, Free PMC Article
  2. Molecular mechanism of Spinocerebellar Ataxia type 6: glutamine repeat disorder, channelopathy and transcriptional dysregulation. The multifaceted aspects of a single mutation. Giunti P, et al. Front Cell Neurosci, 2015. PMID 25762895, Free PMC Article
  3. Modulation of the age at onset in spinocerebellar ataxia by CAG tracts in various genes. Tezenas du Montcel S, et al. Brain, 2014 Sep. PMID 24972706, Free PMC Article
  4. Mini-review: spinocerebellar ataxias: an update of SCA genes. Trott A, et al. Recent Pat DNA Gene Seq, 2012 Aug. PMID 22670601
  5. Case control analysis of repeat expansion size in ataxia. Majounie E, et al. Neurosci Lett, 2007 Dec 11. PMID 17961920

See all (44) 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

  • CACNA1A repeat instability region
  • SCA6 repeat instability region
  • spinocerebellar ataxia type 6 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_051543.1 

    Range
    101..140
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    13207859..13207898
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    13333137..13333176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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