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LOC106020709 distal SMS-REP block C recombination region [ Homo sapiens (human) ]

Gene ID: 106020709, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106020709
Gene description
distal SMS-REP block C 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 (LCR) region, the proximal SMS-REP recombination block C region, which is located about 3.7 Mb centromere-proximal to this region. A third LCR, middle SMS-REP is located in reverse orientation, between the distal and proximal SMS-REPs. The majority of NAHR events occur between the proximal and distal SMS-REPs, and result in the 'common' 3.7 Mb deletion or duplication. Other NAHR events have also been described, resulting in genomic deletions and duplications ranging in size from 1.3 to 15.2 Mb. This recombination region is contained within a large LCR of about 176 kb in which there are 4 homology blocks, named A-D. This recombination region is contained within block C and is composed of multiple sub-regions that have been identified as NAHR exchange sites in different individuals, and also contains two overlapping meiotic recombination hotspots. The NAHR exchange sub-regions are named 1-4, and the majority of NAHR events have been observed in sub-region 2. These recombination events are the result of unequal crossing over (both inter- and intra-chromosomal) during meiotic recombination events, with no apparent bias for parental origin. NAHR between the proximal and distal SMS-REP recombination regions can result in either duplications or deletions of the intervening sequence, including the retinoic acid induced 1 (RAI1) gene. Deletion events are the cause of the autosomal dominant Smith-Magenis syndrome (SMS), while the reciprocal duplication is associated with Potocki-Lupski syndrome (PTLS), also an autosomal dominant disease. NAHR events involving another recombination region, the distal SMS-REP block A recombination region, about 30 kb centromere-distal to this region can also cause a similar sized duplication or deletion. A recurring, but less frequent duplication/deletion that is larger in size, but also causes PTLS/SMS has also been described (see the LCR17pA and LCR17pD recombination regions). [provided by RefSeq, Sep 2016]
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Genomic context

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Location:
17p11.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (16843044..16850881)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (16789131..16796965)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (16746358..16754195)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene keratin 16 pseudogene 6 Neighboring gene uncharacterized LOC105371552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16734092-16734602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16735814-16736326 Neighboring gene uncharacterized LOC105371551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16737352-16737864 Neighboring gene keratin 16 pseudogene 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16738378-16738890 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16738891-16739402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16743553-16744102 Neighboring gene keratin 17 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16748284-16749150 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16749151-16750015 Neighboring gene keratin 17 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16756688-16757188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16757189-16757689 Neighboring gene COTL1 pseudogene 1 Neighboring gene uncharacterized LOC124903939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16773690-16774683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16774796-16775646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16775647-16776497

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. Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Potocki L, et al. Am J Hum Genet, 2007 Apr. PMID 17357070, Free PMC Article
  2. Trisomy 17p10-p12 due to mosaic supernumerary marker chromosome: delineation of molecular breakpoints and clinical phenotype, and comparison to other proximal 17p segmental duplications. Yatsenko SA, et al. Am J Med Genet A, 2005 Oct 1. PMID 16152635
  3. Diagnostic FISH probes for del(17)(p11.2p11.2) associated with Smith-Magenis syndrome should contain the RAI1 gene. Vlangos CN, et al. Am J Med Genet A, 2005 Jan 30. PMID 15690371
  4. Variability in clinical phenotype despite common chromosomal deletion in Smith-Magenis syndrome [del(17)(p11.2p11.2)]. Potocki L, et al. Genet Med, 2003 Nov-Dec. PMID 14614393
  5. Genetic proof of unequal meiotic crossovers in reciprocal deletion and duplication of 17p11.2. Shaw CJ, et al. Am J Hum Genet, 2002 Nov. PMID 12375235, Free PMC Article

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)

General gene information

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Other Names

  • distal Potocki-Lupski syndrome block C repeat recombination region
  • distal Smith-Magenis syndrome block C repeat 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_042219.1 

    Range
    101..7938
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    16843044..16850881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    16789131..16796965
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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