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LOC108745275 distal SMS-REP block A recombination region [ Homo sapiens (human) ]

Gene ID: 108745275, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108745275
Gene description
distal SMS-REP block A recombination region
Gene type
biological region
Feature type(s)
misc_recomb: 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 A region, which is located about 3.6 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 distal SMS-REP LCR is about 176 kb and is composed of four homology blocks named A-D, and this recombination region is located within block A. 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 C recombination region, about 30 kb centromere-proximal to this region can result in a 3.7 Mb deletion or duplication. 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 (16808919..16810023)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (16711631..16712735)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (16712233..16713337)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 32 pseudogene 1 Neighboring gene signal recognition particle 68 pseudogene 1 Neighboring gene family with sequence similarity 106 member C Neighboring gene nitric oxide synthase 2 pseudogene 4 Neighboring gene MPRA-validated peak2752 silencer Neighboring gene keratin 16 pseudogene 6 Neighboring gene uncharacterized LOC105371552

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 (11) 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 A repeat recombination region
  • distal Smith-Magenis syndrome repeat block A 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_051623.1 

    Range
    101..1205
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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
    16808919..16810023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    16711631..16712735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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