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LOC108281115 9q34.3 EHMT1 distal recombination region [ Homo sapiens (human) ]

Gene ID: 108281115, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281115
Gene description
9q34.3 EHMT1 distal recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
misc_recomb: meiotic, recombination_hotspot
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 found centromere-distal to the euchromatic histone lysine methyltransferase 1 (EHMT1) gene, and is known to undergo recombination, forming interstitial deletion on chromosome 9. Secondary structure prediction analysis indicates the possibility that this region could form a loop structure. Clinical variability can be observed in individuals with 9q34.3 deletions, but there is a characteristic phenotype for 9q34.3 microdeletions, including distinctive craniofacial features, hypotonia, obesity, microcephaly and speech delay (CHOMS). This region contains a meiotic recombination hotspot. [provided by RefSeq, Jul 2016]
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Genomic context

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Location:
9q34.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137839731..137842401)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (150097594..150099448)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140734183..140736853)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene euchromatic histone lysine methyltransferase 1 Neighboring gene forkhead box H1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140682311-140682830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140682831-140683350 Neighboring gene uncharacterized LOC651337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29371 Neighboring gene uncharacterized LOC100133077 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140767993-140769192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140772427-140773342 Neighboring gene microRNA 602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140775611-140776112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140780067-140780657 Neighboring gene uncharacterized LOC124902320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140786514-140787014 Neighboring gene calcium voltage-gated channel subunit alpha1 B Neighboring gene CACNA1B antisense RNA 1

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. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Yatsenko SA, et al. Hum Mol Genet, 2009 Jun 1. PMID 19293338, Free PMC Article
  2. Deletion 9q34.3 syndrome: genotype-phenotype correlations and an extended deletion in a patient with features of Opitz C trigonocephaly. Yatsenko SA, et al. J Med Genet, 2005 Apr. PMID 15805160, Free PMC Article
  3. A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome. Harada N, et al. J Hum Genet, 2004. PMID 15258833
  4. 9q34.3 deletion syndrome in three unrelated children. Iwakoshi M, et al. Am J Med Genet A, 2004 Apr 30. PMID 15054842
  5. Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. Kleefstra T, et al. Am J Hum Genet, 2006 Aug. PMID 16826528, Free PMC Article

See all (8) 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

  • 9q34.3 euchromatic histone lysine methyltransferase 1 distal 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_051058.1 

    Range
    101..2771
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137839731..137842401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    150097594..150099448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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