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LOC106029240 S232-VCX3A recombination region [ Homo sapiens (human) ]

Gene ID: 106029240, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106029240
Gene description
S232-VCX3A recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
misc_recomb: meiotic, non_allelic_homologous
repeat_region
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 S232-VCX2 (S232 variable charge, X linked 2) recombination region, which is located about 1.6 Mb downstream of this region. NAHR between these regions can result in deletions of the intervening sequences, including the STS (steroid sulfatase, isozyme S) and VCX3A (variable charge, X-linked 3A) genes. This contiguous 1.6 Mb deletion can result in complex disorders including XLI (X-linked ichthyosis) together with cognitive impairment. Loss of STS is thought to be the cause of XLI. Some data argues that loss of VCX3A is responsible for cognitive impairment, while other data argues against this hypothesis. Duplications, triplications, and other complex rearrangements in this region have also been observed. This region contains two variable number of tandem repeat unit (VNTR) sub-regions named RU1 (repeating unit 1) and RU2 (repeating unit 2), an NAHR exchange sub-region contained within the RU2 VNTR, and an overlapping meiotic recombination hotspot. The majority of NAHR events occur within the RU2 VNTR sub-region, which is asymmetric in that it is composed of 90% purines with no C's on one strand, while the other strand is 90% pyrimidines, with no G's. The meiotic recombination hotspot motif, CCNCCNTNNCCNC, is found within many of the RU2 repeat units. [provided by RefSeq, Jul 2017]
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Genomic context

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Location:
Xp22.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (6531191..6535356)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (6083512..6088715)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (6449232..6453397)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene microRNA 4770 Neighboring gene RPS5 pseudogene 8 Neighboring gene variable charge X-linked 3A Neighboring gene uncharacterized LOC124905240 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:6582190-6583002 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:6610973-6611531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29381 Neighboring gene pseudouridine 5'-phosphatase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:6849955-6850621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:6850622-6851287 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:6876827-6877452 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:6877453-6878076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:6884751-6885264 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:6894281-6894451 Neighboring gene RPS27A pseudogene 17

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. The phenotype spectrum of X-linked ichthyosis identified by chromosomal microarray. Hand JL, et al. J Am Acad Dermatol, 2015 Apr. PMID 25659225
  2. Xp22.3 interstitial deletion: a recognizable chromosomal abnormality encompassing VCX3A and STS genes in a patient with X-linked ichthyosis and mental retardation. Ben Khelifa H, et al. Gene, 2013 Sep 25. PMID 23791652
  3. Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications. Liu P, et al. Hum Mol Genet, 2011 May 15. PMID 21355048, Free PMC Article
  4. The detection of steroid sulfatase gene deletion (STS) in Egyptian males with X-linked ichthyosis. Abdel-Hamed MF, et al. J Drugs Dermatol, 2010 Oct. PMID 20941942
  5. X-linked ichthyosis: an update. Hernández-Martín A, et al. Br J Dermatol, 1999 Oct. PMID 10583107

See all (12) 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)

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_042242.1 

    Range
    101..4266
    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
    6531191..6535356
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    6083512..6088715
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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