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LOC111365204 CCNC and PRDM13 intergenic region DNase I hypersensitve site DHS6S1 [ Homo sapiens (human) ]

Gene ID: 111365204, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111365204
Gene description
CCNC and PRDM13 intergenic region DNase I hypersensitve site DHS6S1
Primary source
MIM:616842
Gene type
biological region
Feature type(s)
misc_feature: sequence_alteration
regulatory: DNase_I_hypersensitive_site
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MCDR1; PBCRA; DHS6S1
Summary
This genomic region represents a DNase I hypersensitive site (DHS) that is present in the intergenic region between the cyclin C (CCNC) and PR/SET domain 13 (PRDM13) genes on chromosome 6. Mutations in this region are associated with autosomal dominant retinal macular dystrophy of the North Carolina type (NCMD, also known as MCDR1). Multiple NCMD-associated single nucleotide variants, including V1, V2 and V3, have been identified within this DHS. This DHS is also known to be duplicated along with the PRDM13 and/or CCNC genes in forms of NCMD associated with genomic duplication events. It is thought that this DHS regulates the PRDM13 gene, whose expression is negatively correlated with retinal development, and dysregulation or overexpression of this gene results in the NCMD disease. [provided by RefSeq, Jan 2021]
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Genomic context

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Location:
6q16.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (99592885..99593339)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (100766332..100766786)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (100040761..100041215)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene thiosulfate sulfurtransferase like domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24862 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:100023517-100023714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:100051429-100052268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:100061850-100062398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17422 Neighboring gene cyclin C Neighboring gene ribosomal protein S3 pseudogene 5 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:100097329-100097949 Neighboring gene PR/SET domain 13 Neighboring gene Sharpr-MPRA regulatory region 7231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:100271711-100272281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:100379521-100380020 Neighboring gene melanin concentrating hormone receptor 2 Neighboring gene MCHR2 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. North Carolina macular dystrophy (MCDR1) locus: a fine resolution genetic map and haplotype analysis. Small KW, et al. Mol Vis, 1999 Dec 29. PMID 10617775
  2. Phenotype of a British North Carolina macular dystrophy family linked to chromosome 6q. Reichel MB, et al. Br J Ophthalmol, 1998 Oct. PMID 9924305, Free PMC Article
  3. North Carolina macular dystrophy (MCDR1) in Texas. Small KW, et al. Retina, 1998. PMID 9801042
  4. North Carolina macular dystrophy phenotype in France maps to the MCDR1 locus. Small KW, et al. Mol Vis, 1997 Jan 2. PMID 9238090
  5. Unique noncoding variants upstream of PRDM13 are associated with a spectrum of developmental retinal dystrophies including progressive bifocal chorioretinal atrophy. Silva RS, et al. Hum Mutat, 2019 May. PMID 30710461

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
North Carolina macular dystrophy
MedGen: C0730294 OMIM: 136550 GeneReviews: Not available
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Progressive bifocal chorioretinal atrophy
MedGen: C1833321 OMIM: 600790 GeneReviews: Not available
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Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • DNase1 hypersensitivity, chromosome 6, site 1

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_055818.1 

    Range
    101..555
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    99592885..99593339
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    100766332..100766786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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