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LOC108228197 LCR2q21.1 proximal recombination region [ Homo sapiens (human) ]

Gene ID: 108228197, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108228197
Gene description
LCR2q21.1 proximal recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
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, the LCR2q21.1 distal recombination region, found about 606 kb centromere-distal to this region, in direct orientation relative to this region. Both this region and the LCR2q21.1 distal recombination region are found within 109 kb low-copy repeat regions that share high DNA sequence identity. NAHR between the two regions can result in deletions and duplications of the intervening sequence. Multiple genes are found in the intervening sequence, including the Rho guanine nucleotide exchange factor 4 (ARHGEF4) and G protein-coupled receptor 148 (GPR148) genes. Phenotypic consequences of the deletion may include developmental delays, attention-deficit hyperactivity disorder (ADHD), epilepsy or electroencephalogram (EEG) abnormalities and behavioral problems. A recombination breakpoint of an individual with the genomic rearrangement is indicated as an NAHR sub-region on the record. [provided by RefSeq, Jun 2016]
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Genomic context

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Location:
2q21.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (130687741..130688006)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (131121897..131122162)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (131445314..131445579)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene POTE ankyrin domain family member J Neighboring gene RNA, U6 small nuclear 848, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:131422411-131422912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:131422913-131423412 Neighboring gene cytochrome P450 family 4 subfamily F member 30, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:131451031-131451531 Neighboring gene fatty acyl-CoA reductase 2 pseudogene 3 Neighboring gene Kruppel like factor 2 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:131484365-131484892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:131485214-131485793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:131485794-131486372 Neighboring gene G protein-coupled receptor 148

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. Recurrent microdeletion 2q21.1: report on a new patient with neurological disorders. Gimelli S, et al. Am J Med Genet A, 2014 Mar. PMID 24591035
  2. Small rare recurrent deletions and reciprocal duplications in 2q21.1, including brain-specific ARHGEF4 and GPR148. Dharmadhikari AV, et al. Hum Mol Genet, 2012 Aug 1. PMID 22543972, Free PMC Article
  3. Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. Startek M, et al. Nucleic Acids Res, 2015 Feb 27. PMID 25613453, Free PMC Article
  4. A common sequence motif associated with recombination hot spots and genome instability in humans. Myers S, et al. Nat Genet, 2008 Sep. PMID 19165926

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_050970.1 

    Range
    101..366
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    130687741..130688006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    131121897..131122162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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