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LOC106501713 CLCNKB recombination region [ Homo sapiens (human) ]

Gene ID: 106501713, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106501713
Gene description
CLCNKB 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 region, the CLCNKA recombination region, which is located centromere-distal to this region. This recombination region partially overlaps the chloride channel, voltage-sensitive Kb gene (CLCNKB), and is composed of three sub-regions, named a', b', and c'. NAHR involving sub-regions a' or b', and the corresponding sub-regions on the CLCNKA recombination region (sub-region a or b) can result in deletions of the intervening sequences, leading to chimeric chloride channel ClC-Ka and ClC-Kb proteins. NAHR involving sub-region c' and the corresponding sub-region on the CLCNKA recombination region (sub-region c) can result in deletions of the intervening sequences, leading to full deletions of the CLCNKB gene. These rearrangements can be a cause of Bartter's syndrome type III, an autosomal recessive kidney disorder that causes an imbalance of ions in the body. Numerous mutations within multiple genes, including CLCNKA and CLCNKB have also been described in individuals with Bartter's syndrome. A meiotic recombination hotspot has been identified within this region using HapMap data. [provided by RefSeq, Oct 2016]
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Genomic context

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See LOC106501713 in Genome Data Viewer
Location:
1p36
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (16044593..16059459)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (15485905..15500843)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (16371088..16385954)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CLCNKA recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16352537-16353445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16356923-16357422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16358660-16359467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16359468-16360274 Neighboring gene chloride voltage-gated channel Ka Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16365121-16365621 Neighboring gene family with sequence similarity 131 member C pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16374236-16375139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16375140-16376042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16376043-16376946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16376947-16377848 Neighboring gene chloride voltage-gated channel Kb Neighboring gene ReSE screen-validated silencer GRCh37_chr1:16387001-16387191 Neighboring gene family with sequence similarity 131 member C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16400409-16400908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16408357-16408856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16408906-16409838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16440794-16441636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16442478-16443319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16444655-16445328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16446600-16447156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16449091-16449770 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:16457212-16457413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16467866-16468833 Neighboring gene EPH receptor A2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16470345-16470872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16470873-16471401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16472987-16473515 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16476741-16477376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16477377-16478012 Neighboring gene hESC enhancers GRCh37_chr1:16488540-16489068 and GRCh37_chr1:16489069-16489596 Neighboring gene EPHA2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16489597-16490124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16490125-16490652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16491605-16492545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16494833-16495478 Neighboring gene Sharpr-MPRA regulatory region 6356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16508387-16509367 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16510195-16510694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16510785-16511286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16511287-16511786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16533787-16534760 Neighboring gene Rho guanine nucleotide exchange factor 19 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16534761-16535733 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16538951-16539649

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. Genetics of type III Bartter syndrome in Spain, proposed diagnostic algorithm. García Castaño A, et al. PLoS One, 2013. PMID 24058621, Free PMC Article
  2. Molecular analysis of digenic inheritance in Bartter syndrome with sensorineural deafness. Nozu K, et al. J Med Genet, 2008 Mar. PMID 18310267
  3. Genetic basis of Bartter syndrome in Korea. Lee BH, et al. Nephrol Dial Transplant, 2012 Apr. PMID 21865213
  4. Molecular analysis of patients with type III Bartter syndrome: picking up large heterozygous deletions with semiquantitative PCR. Nozu K, et al. Pediatr Res, 2007 Sep. PMID 17622951
  5. Molecular analysis of the CLCNKB gene in Japanese patients with classic Bartter syndrome. Tajima T, et al. Endocr J, 2006 Oct. PMID 16902263

See all (10) 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

  • chloride channel, voltage-sensitive Kb 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_042865.1 

    Range
    101..14967
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    16044593..16059459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    15485905..15500843
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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