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LOC109461479 huntingtin repeat instability region [ Homo sapiens (human) ]

Gene ID: 109461479, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109461479
Gene description
huntingtin 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 5' coding region of the huntingtin gene on the p arm of chromosome 4, and contains a CAG trinucleotide repeat. Expansions of this repeat result in an elongated polyglutamine tract in the encoded protein, and are known to be a cause of Huntington disease, an autosomal dominant disease. This is a highly polymorphic region, with 15-20 CAG repeats being most prevalent. Alleles with 27-35 repeats are more prone to expansion, while those with greater than 36 alleles can be pathogenic, with higher penetrance correlating to repeat size. There is a bias for expansions of the repeat from paternal transmissions. [provided by RefSeq, Dec 2016]
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Genomic context

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See LOC109461479 in Genome Data Viewer
Location:
4p16.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (3074877..3074940)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (3073631..3073694)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (3076604..3076667)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21213 Neighboring gene RNA, U6 small nuclear 204, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21214 Neighboring gene HTT antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21218 Neighboring gene RNA, U7 small nuclear 33 pseudogene Neighboring gene huntingtin Neighboring gene ReSE screen-validated silencer GRCh37_chr4:3137138-3137317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15201 Neighboring gene Sharpr-MPRA regulatory region 10599 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:3215178-3215678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:3215679-3216179 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:3239294-3239953 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:3239954-3240612 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:3248264-3248439 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:3252404-3253300 Neighboring gene Myb/SANT DNA binding domain containing 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. Enhanced Detection and Sizing of the HTT CAG Repeat Expansion in Huntington Disease Using an Improved Triplet-Primed PCR Assay. Zhao M, et al. Neurodegener Dis, 2016. PMID 27207688
  2. DNA Methylation Leads to DNA Repair Gene Down-Regulation and Trinucleotide Repeat Expansion in Patient-Derived Huntington Disease Cells. Mollica PA, et al. Am J Pathol, 2016 Jul. PMID 27182645
  3. Problems and solutions for the analysis of somatic CAG repeat expansion and their relationship to Huntington's disease toxicity. Budworth H, et al. Rare Dis, 2016. PMID 27141411, Free PMC Article
  4. Late onset Huntington's disease with 29 CAG repeat expansion. Garcia-Ruiz PJ, et al. J Neurol Sci, 2016 Apr 15. PMID 27000233
  5. The HTT CAG-Expansion Mutation Determines Age at Death but Not Disease Duration in Huntington Disease. Keum JW, et al. Am J Hum Genet, 2016 Feb 4. PMID 26849111, Free PMC Article

See all (74) 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

  • HTT repeat instability region
  • Huntington disease 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_052623.1 

    Range
    101..164
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    3074877..3074940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    3073631..3073694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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