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LOC108004532 3q13.2-q13.31 distal HERV-H recombination region [ Homo sapiens (human) ]

Gene ID: 108004532, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108004532
Gene description
3q13.2-q13.31 distal 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-proximal to this region, on the q arm of chromosome 3. Recombination with the 3q13.2-q13.31 proximal 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 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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Location:
3q13.31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (115795688..115798714)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (118515888..118518914)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (115514535..115517561)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115376638-115377510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115377511-115378382 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115417888-115418741 Neighboring gene growth associated protein 43 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115431872-115432372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115432373-115432873 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115502891-115503391 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:115503423-115504101 Neighboring gene uncharacterized LOC124909412 Neighboring gene uncharacterized LOC124906269 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115511955-115512480 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115512481-115513006 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:115513007-115513531 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115513693-115514194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115514334-115515272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115515273-115516210 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115517565-115518070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20285 Neighboring gene uncharacterized LOC124909413 Neighboring gene RNA, 7SL, cytoplasmic 815, pseudogene Neighboring gene limbic system associated membrane protein

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_050856.1 

    Range
    101..3127
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    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
    115795688..115798714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    118515888..118518914
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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