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LOC106736468 15q13.2-13.3 gamma inversion proximal recombination region [ Homo sapiens (human) ]

Gene ID: 106736468, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106736468
Gene description
15q13.2-13.3 gamma inversion proximal recombination region
Gene type
biological region
Feature type(s)
misc_recomb: 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 15q13.2-13.3 gamma inversion distal recombination region, which is located about 1.8 Mb centromere-distal to this region, in reverse orientation. Genomic instability has been observed in the 15q13 region, with many structural variants reported due to the presence of regions sharing high sequence identity as a result of segmental duplications. The recombination region represented here is located within a region on chromosome 15 referred to as BP4 (breakpoint 4), while its recombination partner, the 15q13 gamma inversion distal recombination region, is located in BP5. In many individuals, BP4 and BP5 are composed of two regions known as CNP alpha and CNP beta (copy number polymorphism alpha and beta). NAHR between this region and the 15q13.2-13.3 gamma inversion distal recombination region can give rise to inversions of the intervening sequence, and haplotypes with this inversion have been observed in the population. This inversion is referred to as the gamma inversion (also known as the BP4-BP5 inversion). Individuals with the gamma inversion were shown to have a BP4 region lacking the CNP beta region, and a BP5 region lacking the CNP alpha region, thus making the intervening sequence between BP4 and BP5 shorter than that observed in some other haplotypes. The structure of the gamma inversion haplotype suggests that it may have arisen from inversion of a simpler haplotype, the H alpha 1 haplotype, which contains only a single copy of the CNP alpha region. The presence of the gamma inversion is thought to predispose individuals to NAHR events resulting in deletions and duplications of the 15q13.2-15q13.3 region. [provided by RefSeq, Oct 2016]
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Genomic context

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Location:
15q13.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (30565815..30597289)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (28359061..28390485)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (30858018..30889492)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene MPHOSPH10 pseudogene 3 Neighboring gene golgin subfamily A member 6-like protein 1 Neighboring gene 15q13.2 beta inversion distal recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:30852659-30853158 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:30859663-30859840 Neighboring gene golgin A8 family member Q Neighboring gene RNA, 7SL, cytoplasmic 796, pseudogene Neighboring gene U8 small nucleolar RNA Neighboring gene dynamin 1 pseudogene 50 Neighboring gene ARHGAP11B divergent transcript Neighboring gene ULK4 pseudogene 2 Neighboring gene 15q13 proximal microdeletion recombination region Neighboring gene golgin A8 family member H Neighboring gene RNA, 7SL, cytoplasmic 628, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:30917238-30918231 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:30918882-30919057 Neighboring gene Rho GTPase activating protein 11B Neighboring gene OTU deubiquitinase 7A 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. Delineating the 15q13.3 microdeletion phenotype: a case series and comprehensive review of the literature. Lowther C, et al. Genet Med, 2015 Feb. PMID 25077648, Free PMC Article
  2. High frequency of known copy number abnormalities and maternal duplication 15q11-q13 in patients with combined schizophrenia and epilepsy. Stewart LR, et al. BMC Med Genet, 2011 Nov 25. PMID 22118685, Free PMC Article
  3. 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
  4. 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
  5. Microdeletion 15q13.3: a locus with incomplete penetrance for autism, mental retardation, and psychiatric disorders. Ben-Shachar S, et al. J Med Genet, 2009 Jun. PMID 19289393, Free PMC Article

See all (12) 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

  • BP4-BP5 inversion proximal recombination region
  • breakpoint 4 to breakpoint 5 inversion proximal 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_044981.1 

    Range
    101..31575
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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
    30565815..30597289
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    2738331..2769777
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_012132920.1 Reference GRCh38.p14 PATCHES

    Range
    1928784..1960288 complement
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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
    2850783..2882229
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    28359061..28390485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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