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LOC108281113 9q34.3 PNPLA7 recombination region [ Homo sapiens (human) ]

Gene ID: 108281113, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281113
Gene description
9q34.3 PNPLA7 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 overlaps the patatin like phospholipase domain containing 7 (PNPLA7) gene, and is known to undergo recombination, forming a terminal deletion on chromosome 9. Secondary structure prediction analysis indicates that this region could fold into a stem-loop structure. Clinical variability can be observed in individuals with 9q34.3 terminal 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 (137500382..137505297)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149750615..149758115)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140394834..140399749)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140330497-140330751 Neighboring gene NADPH oxidase activator 1 Neighboring gene Sharpr-MPRA regulatory region 12030 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 8 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140343721-140344920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140346657-140347540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140347541-140348422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140349307-140350188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140351970-140352667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20625 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20626 Neighboring gene microRNA 7114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140355491-140356424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140356425-140357357 Neighboring gene NMDA receptor synaptonuclear signaling and neuronal migration factor Neighboring gene patatin like phospholipase domain containing 7 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140377541-140378740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140389307-140389807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140438353-140438854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140443963-140444464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20628 Neighboring gene uncharacterized LOC124902317 Neighboring gene mitochondrial ribosomal protein L41 Neighboring gene diphthamide biosynthesis 7 Neighboring gene Sharpr-MPRA regulatory region 4489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20629

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 patatin like phospholipase domain containing 7 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_051054.1 

    Range
    101..5016
    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
    137500382..137505297
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149750615..149758115
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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