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LOC109029536 junctophilin 3 repeat instability region [ Homo sapiens (human) ]

Gene ID: 109029536, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109029536
Gene description
junctophilin 3 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 alternatively spliced exon of the junctophilin 3 (JPH3) gene on the q arm of chromosome 16, and contains a CTG/CAG trinucleotide repeat. Expansions of this repeat are associated with Huntington disease-like 2 (HDL2), an autosomal dominant disease. Allelic variation occurs in this region, with repeat sizes of 6-28 observed in normal alleles. Expansions to 40-59 repeats are associated with pathogenicity, with earlier disease onset with highly expanded alleles. Depending on the transcript to which it is being compared, the repeat region could lie within an intronic region, coding region, or 3' untranslated region. While the repeat region is not found within the coding region of the canonical junctophilin-3 gene product, both the canonical transcript and JPH3 protein product levels are reduced in the presence of expanded alleles, and it is thought that this loss of expression largely contributes to pathogenicity. Protein products with expanded polyalanine, polyleucine or polyglutamine tracts have not been detected in individuals with Huntington disease-like 2. Experiments using untranslatable constructs with expanded repeats suggest that RNA toxicity may contribute to pathogenicity. [provided by RefSeq, Nov 2016]
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Genomic context

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Location:
16q24.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (87604283..87604329)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (93675724..93675776)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (87637889..87637935)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903749 Neighboring gene uncharacterized LOC124903750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87634653-87635215 Neighboring gene MPRA-validated peak2658 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87648002-87648502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87653056-87653900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87653901-87654745 Neighboring gene junctophilin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11324 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:87691195-87691930 and GRCh37_chr16:87691931-87692664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87692665-87693398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87695971-87696921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87709103-87709651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87713011-87713917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87718372-87718956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87718957-87719539 Neighboring gene uncharacterized LOC100129215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11327 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:87736382-87737581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87738231-87738840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87738841-87739448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87742491-87743098 Neighboring gene kelch domain containing 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:87750381-87750569 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:87758101-87759300 Neighboring gene uncharacterized LOC124903752

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 and genetic analysis of 29 Brazilian patients with Huntington's disease-like phenotype. Rodrigues GR, et al. Arq Neuropsiquiatr, 2011 Jun. PMID 21755114
  2. Huntington's disease phenocopy syndromes. Wild EJ, et al. Curr Opin Neurol, 2007 Dec. PMID 17992089
  3. Huntington's disease--like 2 is associated with CUG repeat-containing RNA foci. Rudnicki DD, et al. Ann Neurol, 2007 Mar. PMID 17387722
  4. Patients with features similar to Huntington's disease, without CAG expansion in huntingtin. Rosenblatt A, et al. Neurology, 1998 Jul. PMID 9674805
  5. Junctophilin 3 (JPH3) expansion mutations causing Huntington disease like 2 (HDL2) are common in South African patients with African ancestry and a Huntington disease phenotype. Krause A, et al. Am J Med Genet B Neuropsychiatr Genet, 2015 Oct. PMID 26079385, Free PMC Article

See all (13) 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

  • HDL2 repeat instability region
  • Huntington disease-like 2 repeat instability region
  • JPH3 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_052016.1 

    Range
    101..147
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    87604283..87604329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    93675724..93675776
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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