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    DCHS2 dachsous cadherin-related 2 [ Homo sapiens (human) ]

    Gene ID: 54798, updated on 11-Apr-2024

    Summary

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    Official Symbol
    DCHS2provided by HGNC
    Official Full Name
    dachsous cadherin-related 2provided by HGNC
    Primary source
    HGNC:HGNC:23111
    See related
    Ensembl:ENSG00000197410 MIM:612486; AllianceGenome:HGNC:23111
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDHJ; CDH27; CDHR7; PCDHJ; PCDH23
    Summary
    This gene encodes a large protein that contains many cadherin domains and likely functions in cell adhesion. Genome-wide association studies suggest that this gene may be important in Alzheimer's disease, compressive strength index, and appendicular lean mass. [provided by RefSeq, May 2017]
    Expression
    Broad expression in stomach (RPKM 1.1), testis (RPKM 0.9) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4q31.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (154231742..154491799, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (157563483..157823579, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (155152894..155412951, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377499 Neighboring gene Sharpr-MPRA regulatory region 15425 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74848 Neighboring gene ring finger protein 175 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154710463-154711164 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154711165-154711866 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74856/74857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154713271-154713972 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74859 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74875 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74882 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74898 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74905 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74906 Neighboring gene uncharacterized LOC101927947 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74908 Neighboring gene secreted frizzled related protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:154802179-154802342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22072 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:154855107-154855606 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:154871827-154872023 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:154908563-154909762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154944484-154945005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154945006-154945526 Neighboring gene Sharpr-MPRA regulatory region 8445 Neighboring gene MPRA-validated peak5134 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22073 Neighboring gene kelch domain containing 4 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:155337853-155338354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:155410779-155411735 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:155411736-155412691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22077 Neighboring gene RNA, U6 small nuclear 1285, pseudogene Neighboring gene WDR77 pseudogene 1 Neighboring gene pleiotropic regulator 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Association between DCHS2 gene and mild cognitive impairment and Alzheimer's disease in an elderly Brazilian sample. Vieira RN, et al. Int J Geriatr Psychiatry, 2016 Dec. PMID 26876984
    2. Genes associated with the progression of neurofibrillary tangles in Alzheimer's disease. Miyashita A, et al. Transl Psychiatry, 2014 Jun 10. PMID 26126179, Free PMC Article
    3. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation. Adhikari K, et al. Nat Commun, 2016 May 19. PMID 27193062, Free PMC Article
    4. Identification of new human cadherin genes using a combination of protein motif search and gene finding methods. Hoeng JC, et al. J Mol Biol, 2004 Mar 19. PMID 15003449
    5. Frameshift mutations of cadherin genes DCHS2, CDH10 and CDH24 genes in gastric and colorectal cancers with high microsatellite instability. An CH, et al. Pathol Oncol Res, 2015 Jan. PMID 24898286

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Requirement of FAT and DCHS protocadherins during hypothalamic-pituitary development.
      Title: Requirement of FAT and DCHS protocadherins during hypothalamic-pituitary development.
    2. We found significant differences between the genotype frequency of DCHS2 between controls and amnestic mild cognitive impairment but not between controls and Alzheimers disease.
      Title: Association between DCHS2 gene and mild cognitive impairment and Alzheimer's disease in an elderly Brazilian sample.
    3. DCHS2 gene is expressed in the cerebral cortex and thus is a potential candidate for affecting Age of onset in AD.
      Title: Genome-wide association analysis of age-at-onset in Alzheimer's disease.
    4. Findings suggest that the 3 genes, FADS1, FADS2, and DCHS2, containing these SNPs might play dual roles influencing both CSI and ALM in males.
      Title: Bivariate genome-wide association study suggests fatty acid desaturase genes and cadherin DCHS2 for variation of both compressive strength index and appendicular lean mass in males.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Assessment of genetic determinants of the association of γ' fibrinogen in relation to cardiovascular disease.
    EBI GWAS Catalog
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog
    Genome-wide association analysis of age-at-onset in Alzheimer's disease.
    EBI GWAS Catalog
    Genome-wide association of serum bilirubin levels in Korean population.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20047

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in condensed mesenchymal cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nephron development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin-23
    Names
    cadherin J
    cadherin-like 27
    cadherin-like protein CDHJ
    cadherin-like protein VR8
    cadherin-related family member 7
    protein dachsous homolog 2
    protocadherin 23
    protocadherin J
    protocadherin PCDHJ

    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_054879.2 RefSeqGene

      Range
      5000..265057
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001142552.2 → NP_001136024.1  protocadherin-23 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: Transcript Variant: This variant (2) represents the allele encoded by the GRCh38 reference genome and encodes isoform 2.
      Source sequence(s)
      AC110775, AK127704, AY354497, AY354498, BC140919, DB288709
      Consensus CDS
      CCDS47150.1
      UniProtKB/TrEMBL
      A0A0A0MRC0
      Related
      ENSP00000345062.1, ENST00000339452.2
      Conserved Domains (1) summary
      cd11304
      Location:300 → 409
      Cadherin_repeat; Cadherin tandem repeat domain

    2. NM_001358235.2 → NP_001345164.1  protocadherin-23 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC079298, AC110775, AK127704, AY354497, AY354498, BC140919, BX647835
      Consensus CDS
      CCDS87275.1
      UniProtKB/Swiss-Prot
      A0A096LNH0, B2RU14, E9PC11, Q4W5P9, Q6V1P9, Q6ZS61, Q9NXU8
      Related
      ENSP00000349768.5, ENST00000357232.10
      Conserved Domains (2) summary
      cd11304
      Location:2246 → 2343
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:2162 → 2240
      CA; Cadherin repeats

    3. NM_001412223.1 → NP_001399152.1  protocadherin-23 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses the same exon combination as variant 3 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. The encoded isoform (4) has a frameshifted C-terminus compared to isoform 2.
      Source sequence(s)
      CP068274

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      154231742..154491799 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_017363814.1 Reference GRCh38.p14 PATCHES

      Range
      159371..419428 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      157563483..157823579 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001142553.1: Suppressed sequence

      Description
      NM_001142553.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_017639.3: Suppressed sequence

      Description
      NM_017639.3: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.

    3. NM_199348.1: Suppressed sequence

      Description
      NM_199348.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6V1P9.2 GenPept UniProtKB/Swiss-Prot:Q6V1P9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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