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LOC106780804 tenascin XA (pseudogene) recombination region [ Homo sapiens (human) ]

Gene ID: 106780804, updated on 17-Sep-2024

Summary

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Gene symbol
LOC106780804
Gene description
tenascin XA (pseudogene) 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 tenascin XB recombination region, located about 28 kb centromere-proximal to this region, in direct orientation on the reference genome. NAHR events between these two regions, including gene conversions and deletions, have been observed. Such deletions remove several genes, including the cytochrome P450, family 21, subfamily A, polypeptide 2 (CYP21A2) gene and also creates a chimeric tenascin XA (pseudogene)-tenascin XB (TNXA-TNXB) gene. Loss of CYP21A2 together with mutations within TNXB cause congenital adrenal hyperplasia (CAH) with tenascin-X deficiency (CAH-X) syndrome. Individuals with CAH-X syndrome have both the endocrine imbalances associated with CAH as well as Ehlers-Danlos syndrome, a connective tissue disorder that results from the tenascin-X deficiency. Gene conversion events between these regions that result in mutations within the tenascin XB gene can be a cause of Ehlers-Danlos syndrome, in the absence of CAH. This region is composed of multiple sub-regions, named TNXA/TNXB-1, TNXA/TNXB-2, and TNXA/TNXB-3, with each sub-region representing independent recombination events that result in different chimeric genes. A meiotic recombination hotspot has also been mapped to this region. This biological region is found within the MHC region, and multiple haplotypes of this region are represented in the GRCh38 reference genome assembly. This biological region is found within the MHC region, and multiple haplotypes of this region are represented in the GRCh38 reference genome assembly. [provided by RefSeq, Oct 2016]
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Genomic context

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See LOC106780804 in Genome Data Viewer
Location:
6p21.3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32008873..32013268)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31862079..31866474)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31976650..31981045)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31939702-31940412 Neighboring gene serine/threonine kinase 19 Neighboring gene decapping exoribonuclease Neighboring gene complement C4A (Chido/Rodgers blood group) Neighboring gene CYP21A1P recombination region Neighboring gene cytochrome P450 family 21 subfamily A member 1, pseudogene Neighboring gene tenascin XA (pseudogene) Neighboring gene serine/threonine kinase 19B (pseudogene) Neighboring gene complement C4B (Chido/Rodgers blood group) Neighboring gene CYP21A2 5' regulatory region

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. Broadening the Spectrum of Ehlers Danlos Syndrome in Patients With Congenital Adrenal Hyperplasia. Morissette R, et al. J Clin Endocrinol Metab, 2015 Aug. PMID 26075496, Free PMC Article
  2. The phenotypic spectrum of contiguous deletion of CYP21A2 and tenascin XB: quadricuspid aortic valve and other midline defects. Chen W, et al. Am J Med Genet A, 2009 Dec. PMID 19921645, Free PMC Article
  3. Chimeric CYP21P/CYP21 and TNXA/TNXB genes in the RCCX module. Lee HH. Mol Genet Metab, 2005 Jan. PMID 15639189
  4. PCR-based detection of the CYP21 deletion and TNXA/TNXB hybrid in the RCCX module. Lee HH, et al. Genomics, 2004 May. PMID 15081125
  5. Haploinsufficiency of TNXB is associated with hypermobility type of Ehlers-Danlos syndrome. Zweers MC, et al. Am J Hum Genet, 2003 Jul. PMID 12865992, Free PMC Article

See all (16) 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

  • TNXA 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_045228.1 

    Range
    101..4496
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    32008873..32013268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31862079..31866474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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