U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC107988024 IKBKGP1 recombination region [ Homo sapiens (human) ]

Gene ID: 107988024, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC107988024
Gene description
IKBKGP1 recombination region
Gene type
biological region
Feature type(s)
misc_recomb: meiotic, 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 either the IKBKGP1 upstream recombination region, found in direct orientation about 11 kb upstream of this region relative to the reference genome, as well as with the IKBKG recombination region, found in reverse orientation, about 80 kb upstream of this region relative to the reference genome, on the q arm of the X chromosome. This recombination region is located within inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma pseudogene 1 (IKBKGP1) and is part of a larger 35 kb low-copy repeat known as LCR2, while the IKBKG recombination region is found within LCR1. Copy number variation (CNV) due to NAHR events between misaligned Medium Reiterated 67B (MER67B) repeat units involving the repeat about 11 kb upstream of this region, in direct orientation, have been observed and result in duplications (known as MER6Bdup) and deletions (known as IKBKGPdel) of the intervening sequence. While these CNVs are benign, it has been suggested the presence of these alleles could promote other recombination events that result in the pathological IKBKGdel deletion, which removes a portion of the inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma (IKBKG) gene. Recombination between this region and the IKBKG recombination region, found in reverse orientation within LCR1, has also been observed. Gene conversion events that result in the unidirectional transfer of genetic information from the IKBKGP1 pseudogene to the IKBKG locus can introduce pathological mutations to the IKBKG gene. It has been suggested that inversion events between these recombination regions can also occur. Alterations that result in a non-functional IKBKG gene are a cause of incontinentia pigmenti (IP), and X-linked neuroectodermal disorder that causes lethality in males. This region contains an overlapping meiotic recombination hotspot. [provided by RefSeq, Jun 2016]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC107988024 in Genome Data Viewer
Location:
Xq28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154646128..154647897)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152882569..152884338)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153874402..153876171)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene activating transcription factor 4 pseudogene 1 Neighboring gene family with sequence similarity 223 member B Neighboring gene IKBKGP1 upstream recombination region Neighboring gene inhibitor of nuclear factor kappa B kinase subunit gamma pseudogene 1 Neighboring gene uncharacterized LOC105373387 Neighboring gene cancer/testis antigen 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. The LCR at the IKBKG locus is prone to recombine. Fusco F, et al. Am J Hum Genet, 2010 Apr 9. PMID 20380930, Free PMC Article
  2. Two cases of misinterpretation of molecular results in incontinentia pigmenti, and a PCR-based method to discriminate NEMO/IKKgamma dene deletion. Bardaro T, et al. Hum Mutat, 2003 Jan. PMID 12497627
  3. Microdeletion/duplication at the Xq28 IP locus causes a de novo IKBKG/NEMO/IKKgamma exon4_10 deletion in families with Incontinentia Pigmenti. Fusco F, et al. Hum Mutat, 2009 Sep. PMID 19603533
  4. Multiple pathogenic and benign genomic rearrangements occur at a 35 kb duplication involving the NEMO and LAGE2 genes. Aradhya S, et al. Hum Mol Genet, 2001 Oct 15. PMID 11709543
  5. DNA recombination. Recombination initiation maps of individual human genomes. Pratto F, et al. Science, 2014 Nov 14. PMID 25395542, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • delta NEMO recombination region
  • inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma pseudogene 1 recombination region

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_050773.1 

    Range
    101..1870
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154646128..154647897
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152882569..152884338
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases