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LOC105980006 PLCR-B recombination region [ Homo sapiens (human) ]

Gene ID: 105980006, updated on 10-Oct-2023

Summary

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Gene symbol
LOC105980006
Gene description
PLCR-B 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 region, the DLCR-2B (distal low-copy repeat 2B) recombination region, which is located a little over 1.9 Mb downstream of this region. NAHR between these regions can result in deletions of the intervening sequence, including the NSD1 (nuclear receptor binding SET domain protein 1) gene. This region is contained within a larger 390 kb low-copy repeat region, PLCR (proximal low-copy repeat, also known as Sos-PREP, for Sotos proximal repeat), that shares over 98% sequence identity to the downstream DLCR (also known as Sos-DREP) region. While the DLCR and PLCR large repeat regions are in reverse orientation, the small sub-regions, PLCR-B and DLCR-2B, of the repeats in which recombination is observed are found in direct orientation. The 1.9 Mb deletion that can occur as a result of NAHR between the PLCR-B and DLCR-2B recombination regions has been observed in some individuals with Sotos syndrome (Sos, also known as cerebral gigantism). Sotos syndrome is an autosomal dominant syndrome characterized by excessive growth, distinct craniofacial features, including macrocephaly a prominent forehead, pointed chin, large hands and feet, as well as variable degrees of intellectual disability. Gene dosage differences of NSD1 (nuclear receptor binding SET domain protein 1), a gene that resides between the PLCR-B and DLCR-2B recombination hotspots, is thought to be the major cause of Sos in those individuals bearing the 1.9 Mb deletion. Point mutations within NSD1 have also been identified as a cause of Sos. Those Sos individuals with the 1.9 Mb microdeletion display a more severe phenotype relative to those with point mutations in NSD1, including anomalies of the central nervous system, cardiovascular, and urinary systems. The 1.9 Mb microdeletion has been observed in about 50% of individuals with Sos amongst Japanese populations, but in only about 9% of Sos individuals of European ancestry. Studies have shown that the microdeletion between repeat units occurs more frequently on the paternally-derived chromosome, and can be the result of either inter- or intra-chromosomal rearrangements. [provided by RefSeq, Jul 2017]
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Genomic context

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Location:
5q35
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (176072563..176075552)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (176616236..176619225)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (175499566..175502555)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protein FAM83G-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175471779-175472279 Neighboring gene uncharacterized LOC100996385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175478652-175479152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175479153-175479653 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:175491282-175491899 Neighboring gene protein FAM153B Neighboring gene uncharacterized LOC107986487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175559705-175560206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175560207-175560706 Neighboring gene Sharpr-MPRA regulatory region 12759 Neighboring gene selenophosphate synthetase 1 pseudogene 3 Neighboring gene CEP192 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:175579338-175580322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:175580323-175581305 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:175588089-175588329 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:175610533-175611123 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:175621561-175622251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175624383-175624884

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. NSD1 mutations in Sotos syndrome. Faravelli F. Am J Med Genet C Semin Med Genet, 2005 Aug 15. PMID 16010675
  2. Fifty microdeletions among 112 cases of Sotos syndrome: low copy repeats possibly mediate the common deletion. Kurotaki N, et al. Hum Mutat, 2003 Nov. PMID 14517949
  3. Phenotypic consequences of genetic variation at hemizygous alleles: Sotos syndrome is a contiguous gene syndrome incorporating coagulation factor twelve (FXII) deficiency. Kurotaki N, et al. Genet Med, 2005 Sep. PMID 16170239
  4. Sotos syndrome common deletion is mediated by directly oriented subunits within inverted Sos-REP low-copy repeats. Kurotaki N, et al. Hum Mol Genet, 2005 Feb 15. PMID 15640245
  5. Identification of a 3.0-kb major recombination hotspot in patients with Sotos syndrome who carry a common 1.9-Mb microdeletion. Visser R, et al. Am J Hum Genet, 2005 Jan. PMID 15580547, Free PMC Article

See all (7) 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

  • Sos-PREP subunit C recombination region
  • Sotos syndrome proximal repeat subunit C recombination region
  • proximal low copy repeat B 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_042200.1 

    Range
    101..3090
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    176072563..176075552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    176616236..176619225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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