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LOC106780800 CYP21A2 recombination region [ Homo sapiens (human) ]

Gene ID: 106780800, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106780800
Gene description
CYP21A2 recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
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 CYP21A1P recombination region, located about 30 kb centromere-distal to this region, in direct orientation on the reference genome. Gene conversion events as well as duplications and deletions of the intervening sequence as a result of NAHR between these recombination regions have been observed. Deletions can result in a chimeric CYP21AP-CYP21A2 gene, and is a cause of congenital adrenal hyperplasia (CAH; also known as steroid 21-hydroxylase deficiency), while gene conversion events can result in deficiencies in the cytochrome P450 family 21 subfamily A member 2 gene and is also a cause of CAH. The severity of the disease can depend on the location of the recombination site, with the more severe phenotype resulting from recombination near the 3' end of the gene. This region is composed of multiple sub-regions, named CH-1' - CH-9', with each sub-region representing independent recombination events that result in a different chimeric CYP21AP-CYP21A2 gene. NAHR has been observed most frequently in the CH-1' and CH-5' sub-regions. Regions of increased meiotic recombination as shown by meiotic double-strand break mapping and using HapMap data have also been found in this region. This biological region is found within the MHC region, and multiple haplotypes of this region are represented on the GRCh38 reference genome assembly. [provided by RefSeq, Oct 2016]
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Genomic context

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See LOC106780800 in Genome Data Viewer
Location:
6p21.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32037872..32041144)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31891079..31894348)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32005649..32008921)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene serine/threonine kinase 19B (pseudogene) Neighboring gene complement C4B (Chido/Rodgers blood group) Neighboring gene CYP21A2 5' regulatory region Neighboring gene tenascin XB recombination region Neighboring gene ReSE screen-validated silencer GRCh37_chr6:32013699-32013950 Neighboring gene cytochrome P450 family 21 subfamily A member 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:32014364-32015563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32015753-32016386 Neighboring gene tenascin XB Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32038327-32039327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32040222-32041078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32041114-32041614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32049385-32049900 Neighboring gene RNA, 5S ribosomal pseudogene 206 Neighboring gene Sharpr-MPRA regulatory region 2290 Neighboring gene activating transcription factor 6 beta

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. Genotype-phenotype correlation in 1,507 families with congenital adrenal hyperplasia owing to 21-hydroxylase deficiency. New MI, et al. Proc Natl Acad Sci U S A, 2013 Feb 12. PMID 23359698, Free PMC Article
  2. Erroneous prenatal diagnosis of congenital adrenal hyperplasia owing to a duplication of the CYP21A2 gene. Lekarev O, et al. J Perinatol, 2013 Jan. PMID 23269230
  3. Junction site analysis of chimeric CYP21A1P/CYP21A2 genes in 21-hydroxylase deficiency. Chen W, et al. Clin Chem, 2012 Feb. PMID 22156666, Free PMC Article
  4. Sequence analysis of CYP21A1P in a German population to aid in the molecular biological diagnosis of congenital adrenal hyperplasia. Cantürk C, et al. Clin Chem, 2011 Mar. PMID 21148302
  5. Molecular diagnosis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency: an update of new CYP21A2 mutations. Concolino P, et al. Clin Chem Lab Med, 2010 Aug. PMID 20482300

See all (46) 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

  • cytochrome P450, family 21, subfamily A, polypeptide 2 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_045215.1 

    Range
    101..3373
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    32037872..32041144
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    3379909..3383177
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31891079..31894348
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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