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

Gene ID: 54798, updated on 27-Nov-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
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Genomic context

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See DCHS2 in Genome Data Viewer
Location:
4q31.3
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (154231742..154491799, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (157563483..157823579, complement)
RS_2024_09 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 (20) 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)

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
  
Process Evidence Code Pubs
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
located_in plasma membrane IEA
Inferred from Electronic Annotation
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_2024_08

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

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