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LOC108660405 protein phosphatase 2 regulatory subunit Bbeta repeat instability region [ Homo sapiens (human) ]

Gene ID: 108660405, updated on 17-Jun-2024

Summary

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Gene symbol
LOC108660405
Gene description
protein phosphatase 2 regulatory subunit Bbeta 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 protein phosphatase 2 regulatory subunit Bbeta (PPP2R2B) gene on the q arm of chromosome 5, and contains a CAG trinucleotide repeat. Expansions of this repeat are known to be a cause of spinocerebellar ataxia type 12 (SCA12), an autosomal dominant progressive disorder. There is allelic variation at this locus, with about 4-32 repeats for non-disease alleles and greater than 46 repeats for pathogenic alleles, with some variation in penetrance. [provided by RefSeq, Jan 2017]
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Genomic context

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See LOC108660405 in Genome Data Viewer
Location:
5q32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (146878728..146878759)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (147414749..147414780)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (146258291..146258322)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protein phosphatase 2 regulatory subunit Bbeta Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:146111026-146112225 Neighboring gene keratin 8 pseudogene 48 Neighboring gene uncharacterized LOC107986461 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:146168291-146168992 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:146176260-146177054 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:146196483-146197009 Neighboring gene MPRA-validated peak5525 silencer Neighboring gene uncharacterized LOC105378214 Neighboring gene PPP2R2B intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23362 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:146473503-146474702 Neighboring gene STK32A 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. Spinocerebellar ataxias in Brazil--frequencies and modulating effects of related genes. de Castilhos RM, et al. Cerebellum, 2014 Feb. PMID 23943520
  2. Analysis of spinocerebellar ataxias due to expanded triplet repeats in Greek patients with cerebellar ataxia. Koutsis G, et al. J Neurol Sci, 2012 Jul 15. PMID 22520093
  3. Spinocerebellar ataxias in mainland China: an updated genetic analysis among a large cohort of familial and sporadic cases. Wang J, et al. Zhong Nan Da Xue Xue Bao Yi Xue Ban, 2011 Jun. PMID 21743138
  4. Comparative genetics of functional trinucleotide tandem repeats in humans and apes. Andrés AM, et al. J Mol Evol, 2004 Sep. PMID 15553088
  5. Detection of large pathogenic expansions in FRDA1, SCA10, and SCA12 genes using a simple fluorescent repeat-primed PCR assay. Cagnoli C, et al. J Mol Diagn, 2004 May. PMID 15096564, Free PMC Article

See all (28) 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

  • PPP2R2B repeat instability region
  • SCA12 repeat instability region
  • spinocerebellar ataxia type 12 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_051539.1 

    Range
    101..132
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    146878728..146878759
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    147414749..147414780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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