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LOC107992388 chr4 t(4;18)(q35;q18) HERV-H recombination region [ Homo sapiens (human) ]

Gene ID: 107992388, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107992388
Gene description
chr4 t(4;18)(q35;q18) HERV-H recombination region
Gene type
biological region
Feature type(s)
misc_recomb: non_allelic_homologous
mobile_element
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 region is known to undergo non-allelic homologous recombination (NAHR) with another region, containing a similar human endogenous retrovirus (HERV) element on the q arm of chromosome 18, the chr18 t(4;18)(q35;q18) HERV-H recombination region. Recombination events between these two regions can result in a t(4;18)(q35;q18) translocation. While only a small number of individuals with this translocation have been identified, phenotypic characteristics of those individuals included developmental delays, auditory canal atresia, hypoplasia, microcephaly, and a broad nasal bridge. This recombination region is contained within an HERV element which contains a 61 nucleotide tandem repeat found in four copies on the reference genome. It has been noted that there is a polymorphic allele that contains only two copies of the tandem repeat, and such an allele more closely matches the sequence found within the HERV element on chromosome 18, with which the translocation occurs. [provided by RefSeq, Jun 2016]
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Genomic context

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See LOC107992388 in Genome Data Viewer
Location:
4q35.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (182814744..182818109)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (186157080..186159802)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (183735897..183739262)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene teneurin transmembrane protein 3 Neighboring gene RN7SK pseudogene 67 Neighboring gene uncharacterized LOC105377571 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:183705545-183706046 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183728786-183729724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183729853-183730354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15824 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:183735292-183735847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22177 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:183783101-183783676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183783677-183784250 Neighboring gene uncharacterized LOC105377576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:183816185-183816755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183818782-183819282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15825 Neighboring gene dCMP deaminase

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. A recurrent translocation is mediated by homologous recombination between HERV-H elements. Hermetz KE, et al. Mol Cytogenet, 2012 Jan 19. PMID 22260357, Free PMC Article
  2. Molecular and clinical characterization of a recurrent cryptic unbalanced t(4q;18q) resulting in an 18q deletion and 4q duplication. Horbinski C, et al. Am J Med Genet A, 2008 Nov 15. PMID 18932219, Free PMC Article
  3. Molecular characterization of a patient with central nervous system dysmyelination and cryptic unbalanced translocation between chromosomes 4q and 18q. Gunn SR, et al. Am J Med Genet A, 2003 Jul 1. PMID 12794705

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_050839.1 

    Range
    101..3466
    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
    182814744..182818109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    186157080..186159802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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