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LOC106050103 IDSP1 recombination region [ Homo sapiens (human) ]

Gene ID: 106050103, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106050103
Gene description
IDSP1 recombination region
Gene type
biological region
Feature type(s)
misc_recomb: meiotic, non_allelic_homologous
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region is known to undergo non-allelic homologous recombination (NAHR) with a similar low-copy repeat region, the IDS (iduronate 2-sulfatase) recombination region, which is located about 39 kb upstream of this region, in reverse orientation. NAHR between these regions can result in genomic rearrangements, including inversions and deletions. Rearrangements that disrupt the IDS (iduronate 2-sulfatase) gene can be a cause of Hunter syndrome (also known as mucopolysaccharidosis type II, MPS-II). Genomic structural rearrangements have been observed in about 20% of individuals with Hunter syndrome. This region is composed of multiple sub-regions that have been identified as NAHR exchange sites in different individuals, and also contains an overlapping meiotic recombination hotspot. The NAHR exchange sub-regions are named a' and b'. NAHR involving the a' sub-region has been observed in individuals with inversions, while exchanges in the b' sub-region have been observed in deletion rearrangements. Hunter syndrome is an X-linked lysosomal storage disorder caused by deficiencies of the iduronate sulfatase enzyme, leading to the build-up of mucopolysaccharides in bodily tissues. The accumulation of partially degraded dermatan and heparin sulfates can result in skeletal deformities, cognitive deficits, and connective tissue abnormalities. [provided by RefSeq, Sep 2015]
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Genomic context

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Location:
Xq27.3-q28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (149526165..149528854)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (147791911..147794598)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (148607704..148610391)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 6851 Neighboring gene uncharacterized LOC107985667 Neighboring gene IDS recombination region Neighboring gene iduronate 2-sulfatase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:148585415-148585963 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:148586087-148586588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30015 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:148591963-148593162 Neighboring gene Sharpr-MPRA regulatory region 15241 Neighboring gene EOLA1 divergent transcript Neighboring gene iduronate 2-sulfatase pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21043 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:148621960-148622150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30016 Neighboring gene endothelium and lymphocyte associated ASCH domain 1 Neighboring gene heat shock transcription factor family, X-linked member 3 Neighboring gene MAGE family member A9B

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. Identification of 11 novel mutations in 49 Korean patients with mucopolysaccharidosis type II. Sohn YB, et al. Clin Genet, 2012 Feb. PMID 21291454
  2. Characterization of iduronate-2-sulfatase gene-pseudogene recombinations in eight patients with Mucopolysaccharidosis type II revealed by a rapid PCR-based method. Lualdi S, et al. Hum Mutat, 2005 May. PMID 15832315
  3. Novel type of genetic rearrangement in the iduronate-2-sulfatase (IDS) gene involving deletion, duplications, and inversions. Karsten S, et al. Hum Mutat, 1999. PMID 10571944
  4. Homologous nonallelic recombinations between the iduronate-sulfatase gene and pseudogene cause various intragenic deletions and inversions in patients with mucopolysaccharidosis type II. Bunge S, et al. Eur J Hum Genet, 1998 Sep-Oct. PMID 9801874
  5. DNA deletion confined to the iduronate-2-sulfatase promoter abolishes IDS gene expression. Timms KM, et al. Hum Mutat, 1998. PMID 9482575

See all (17) 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

  • IDS2 recombination region
  • iduronate 2-sulfatase pseudogene 1 recombination 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_042270.1 

    Range
    101..2790
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    149526165..149528854
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    147791911..147794598
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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