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LOC108004543 8q13.2-q13.3 proximal HERV-mediated recombination region [ Homo sapiens (human) ]

Gene ID: 108004543, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108004543
Gene description
8q13.2-q13.3 proximal HERV-mediated recombination region
Gene type
biological region
Feature type(s)
misc_recomb: non_allelic_homologous
mobile_element
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 another region, containing a similar human endogenous retrovirus (HERV) element about 2.7 Mb centromere-distal to this region, on the q arm of chromosome 8. Recombination with the 8q13.2-q13.3 distal HERV-mediated recombination region can result in deletions of the intervening sequence, and is a cause of branchio-oto-renal (BOR) syndrome. BOR is an autosomal dominant disorder characterized by branchial arch anomalies, hearing loss and renal dysmorphology. Anomalies within the EYA transcriptional coactivator and phosphatase 1 (EYA1) gene have been implicated as one cause of BOR, and this gene lies within the region that can be deleted due to NAHR between the 8q13.2-q13.3 proximal and distal HERV-mediated recombination regions. Individuals with the microdeletion as a result of NAHR have features consistent with EYA1-related BOR, but can also have additional features that could include short stature, structural anomalies and a mild learning disability. Recombination breakpoints of individuals with the recurrent microdeletion are indicated as NAHR sub-regions on the record. [provided by RefSeq, Jun 2016]
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Genomic context

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See LOC108004543 in Genome Data Viewer
Location:
8q13.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (68973432..68976574)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (69402002..69405144)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (69885667..69888809)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene chromosome 8 open reading frame 34 Neighboring gene RNA, 5S ribosomal pseudogene 269 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:69655931-69656489 Neighboring gene NANOG hESC enhancer GRCh37_chr8:69671922-69672423 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:69755751-69756502 Neighboring gene uncharacterized LOC107986951 Neighboring gene Sharpr-MPRA regulatory region 891 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:69837689-69838233 Neighboring gene long intergenic non-protein coding RNA 1592 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:69885119-69885678 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:69916922-69917442 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103601 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103615 Neighboring gene RNA, U7 small nuclear 102 pseudogene Neighboring gene TPM4 pseudogene 3

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. Phenotypes of 8q13.2-q13.3 microdeletion: Case report and literature review of an emerging recurrent microdeletion syndrome. Hamilton MJ, et al. Am J Med Genet A, 2016 Mar. PMID 26663483
  2. Recurrent 8q13.2-13.3 microdeletions associated with branchio-oto-renal syndrome are mediated by human endogenous retroviral (HERV) sequence blocks. Chen X, et al. BMC Med Genet, 2014 Aug 19. PMID 25135225, Free PMC Article
  3. Genome-wide copy number variation analysis of a Branchio-oto-renal syndrome cohort identifies a recombination hotspot and implicates new candidate genes. Brophy PD, et al. Hum Genet, 2013 Dec. PMID 23851940, Free PMC Article
  4. HERV-mediated genomic rearrangement of EYA1 in an individual with branchio-oto-renal syndrome. Sanchez-Valle A, et al. Am J Med Genet A, 2010 Nov. PMID 20979191, Free PMC Article
  5. Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination. Campbell IM, et al. BMC Biol, 2014 Sep 23. PMID 25246103, Free PMC Article

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)

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_050861.1 

    Range
    101..3243
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    68973432..68976574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    69402002..69405144
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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