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LOC108004531 3q13.2-q13.31 proximal HERV-H recombination region [ Homo sapiens (human) ]

Gene ID: 108004531, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108004531
Gene description
3q13.2-q13.31 proximal HERV-H 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 3.4 Mb centromere-distal to this region, on the q arm of chromosome 3. Recombination with the 3q13.2-q13.31 distal HERV-H recombination region can result in deletions of the intervening sequence, and is a cause of 3q13.31 deletion syndrome. This syndrome can present with a range of phenotypes, but many individuals with this microdeletion have motor and language delays, hypotonia, variable cognitive impairment and dysmorphic features. While deletions of variable sizes have been described in this genomic region, this region represents the recombination region observed in the recurrent 3.4 Mb deletion in the 3q13.2-q13.31 region. Recombination breakpoints of individuals with the recurrent microdeletion are indicated as sub-regions on the record. [provided by RefSeq, Jun 2016]
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Genomic context

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See LOC108004531 in Genome Data Viewer
Location:
3q13.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (112419746..112422911)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (115140796..115143961)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (112138593..112141758)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374042 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112051670-112052627 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112052628-112053584 Neighboring gene NANOG hESC enhancer GRCh37_chr3:112054081-112054840 Neighboring gene CD200 molecule Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:112073606-112074235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20238 Neighboring gene uncharacterized LOC105374041 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112109833-112110448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20239 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112118629-112119141 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112119142-112119653 Neighboring gene uncharacterized LOC124909408 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112119654-112120166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112125128-112125650 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112132473-112132973 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112135621-112136474 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112136475-112137328 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112137329-112138182 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112141599-112142451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20240 Neighboring gene NANOG hESC enhancer GRCh37_chr3:112184939-112185454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:112192511-112193011 Neighboring gene B and T lymphocyte associated Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:112240775-112241275 Neighboring gene olfactory receptor family 7 subfamily E member 100 pseudogene

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. Female patient with autistic disorder, intellectual disability, and co-morbid anxiety disorder: Expanding the phenotype associated with the recurrent 3q13.2-q13.31 microdeletion. Quintela I, et al. Am J Med Genet A, 2015 Dec. PMID 26332054
  2. Microduplication 3q13.2q13.31 identified in a male with dysmorphic features and multiple congenital anomalies. Karavitakis E, et al. Am J Med Genet A, 2014 Mar. PMID 24375959
  3. Recurrent HERV-H-mediated 3q13.2-q13.31 deletions cause a syndrome of hypotonia and motor, language, and cognitive delays. Shuvarikov A, et al. Hum Mutat, 2013 Oct. PMID 23878096, Free PMC Article
  4. A novel microdeletion syndrome at 3q13.31 characterised by developmental delay, postnatal overgrowth, hypoplastic male genitals, and characteristic facial features. Molin AM, et al. J Med Genet, 2012 Feb. PMID 22180640, 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_050855.1 

    Range
    101..3266
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    112419746..112422911
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    115140796..115143961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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