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LOC106736477 distal CHRNA7 low-copy repeat recombination region [ Homo sapiens (human) ]

Gene ID: 106736477, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106736477
Gene description
distal CHRNA7 low-copy repeat 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 proximal CHRNA7 low-copy repeat recombination region, located about 930 kb upstream of this region, in reverse orientation on the reference genome. Duplications and deletions of the intervening sequence as a result of NAHR between these recombination regions are thought to arise as a result of recombination events between chromosomes with the common chromosomal orientation observed on the reference genome with those containing the gamma inversion haplotype (an inverted BP4-BP5 region, see the 15q13.2-13.3 gamma inversion proximal and distal recombination regions, GeneID:106736468 and GeneID:106736469). Variability in the size of duplications and deletions amongst individuals has been observed, and it has been proposed that this variability may depend on the composition of the recombining haplotypes. A recurring 680 kb deletion has been associated with neurodevelopmental defects including seizures and mental deficiencies. Variability in penetrance, the presence of other structural variations in some individuals, and phenotypic differences have complicated interpretations of the pathological significance of the duplications and deletions. It has been suggested that copy number changes of the cholinergic receptor, nicotinic, alpha 7 (CHRNA7) gene may predispose some individuals to neuropsychiatric and neurodevelopmental disorders, but the pathogenic significance is uncertain at this time. This region is composed of multiple sub-regions, named sub-region 1'-6', where NAHR recombination events have been mapped. Meiotic recombination hotspots have also been mapped to this region. [provided by RefSeq, Nov 2015]
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Genomic context

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Location:
15q13.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (31669429..31708953)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (29463637..29503155)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (31961632..32001156)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31756624-31757124 Neighboring gene REX4 homolog, 3'-5' exonuclease pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31782018-31782667 Neighboring gene OTU deubiquitinase 7A Neighboring gene uncharacterized LOC105370753 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:31820681-31821180 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31830279-31830817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31846511-31847094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31897378-31898128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31901130-31901685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31901686-31902240 Neighboring gene uncharacterized LOC124903455 Neighboring gene DEP domain containing 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:32091007-32091506 Neighboring gene Sharpr-MPRA regulatory region 11410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:32197193-32197694 Neighboring gene small nucleolar RNA SNORA18

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 small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes. Shinawi M, et al. Nat Genet, 2009 Dec. PMID 19898479, Free PMC Article
  2. Common inversion polymorphisms and rare microdeletions at 15q13.3. Makoff A, et al. Eur J Hum Genet, 2009 Feb. PMID 18854863, Free PMC Article
  3. Structures and molecular mechanisms for common 15q13.3 microduplications involving CHRNA7: benign or pathological? Szafranski P, et al. Hum Mutat, 2010 Jul. PMID 20506139, Free PMC Article
  4. Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: precedent for disorders with complex inheritance. Dibbens LM, et al. Hum Mol Genet, 2009 Oct 1. PMID 19592580, Free PMC Article
  5. Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome. van Bon BW, et al. J Med Genet, 2009 Aug. PMID 19372089, Free PMC Article

See all (13) 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

  • distal CHRNA7 LCR recombination region
  • distal cholinergic receptor, nicotinic, alpha 7 low-copy repeat 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_044986.1 

    Range
    101..39625
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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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    31669429..31708953
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    3842125..3881643
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3954577..3994095
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    29463637..29503155
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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