This gene encodes a secreted protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta-like bone morphogenetic proteins and sequestering them in latent complexes. The encoded protein may also have roles in organogenesis and during adulthood. It has been suggested that this gene could be a candidate gene for Cornelia de Lange syndrome. Reduce... See more...

Aliases for CHRD Gene

Aliases for CHRD Gene

External Ids for CHRD Gene

Previous GeneCards Identifiers for CHRD Gene

  • GC03P180570
  • GC03P185091
  • GC03P185499
  • GC03P185419
  • GC03P185421
  • GC03P185580
  • GC03P184097
  • GC03P181483

Summaries for CHRD Gene

Entrez Gene Summary for CHRD Gene

  • This gene encodes a secreted protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta-like bone morphogenetic proteins and sequestering them in latent complexes. The encoded protein may also have roles in organogenesis and during adulthood. It has been suggested that this gene could be a candidate gene for Cornelia de Lange syndrome. Reduced expression of this gene results in enhanced bone regeneration. Alternative splicing results in multiple transcript variants. Other alternative splice variants have been described but their full length sequence has not been determined. [provided by RefSeq, Jan 2015]

GeneCards Summary for CHRD Gene

CHRD (Chordin) is a Protein Coding gene. Diseases associated with CHRD include Cornelia De Lange Syndrome and Holoprosencephaly. Among its related pathways are TGF-beta signaling pathway (KEGG) and Signaling by BMP. Gene Ontology (GO) annotations related to this gene include heparin binding and syndecan binding. An important paralog of this gene is MUC5B.

UniProtKB/Swiss-Prot Summary for CHRD Gene

  • Dorsalizing factor. Key developmental protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta family bone morphogenetic proteins (BMPs) and sequestering them in latent complexes (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CHRD Gene

Genomics for CHRD Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CHRD Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHRD on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CHRD

Top Transcription factor binding sites by QIAGEN in the CHRD gene promoter:
  • AP-1
  • STAT3

Genomic Locations for CHRD Gene

Latest Assembly
chr3:184,380,073-184,390,739
(GRCh38/hg38)
Size:
10,667 bases
Orientation:
Plus strand

Previous Assembly
chr3:184,097,861-184,108,527
(GRCh37/hg19 by Entrez Gene)
Size:
10,667 bases
Orientation:
Plus strand

chr3:184,097,861-184,108,524
(GRCh37/hg19 by Ensembl)
Size:
10,664 bases
Orientation:
Plus strand

Genomic View for CHRD Gene

Genes around CHRD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHRD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHRD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHRD Gene

Proteins for CHRD Gene

  • Protein details for CHRD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H2X0-CHRD_HUMAN
    Recommended name:
    Chordin
    Protein Accession:
    Q9H2X0
    Secondary Accessions:
    • O95254
    • Q2M1I8
    • Q6UW83
    • Q9H2D3
    • Q9H2W8
    • Q9H2W9
    • Q9P0Z2
    • Q9P0Z3
    • Q9P0Z4
    • Q9P0Z5

    Protein attributes for CHRD Gene

    Size:
    955 amino acids
    Molecular mass:
    102032 Da
    Quaternary structure:
    • Interacts with TWSG1 and/or BMP4.
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for CHRD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CHRD Gene

Post-translational modifications for CHRD Gene

  • Cleaved by tolloid proteases; cleavage participates in dorsoventral patterning during early development.
  • Glycosylation at Asn217, Asn351, Asn365, and Asn434
  • Modification sites at PhosphoSitePlus

Assay products for research

No data available for DME Specific Peptides for CHRD Gene

Domains & Families for CHRD Gene

Gene Families for CHRD Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for CHRD Gene

InterPro:
Blocks:
  • von Willebrand factor, type C
  • CHRD

Suggested Antigen Peptide Sequences for CHRD Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54880, moderately similar to Chordin (B7Z6F4_HUMAN)
  • Chordin (CHRD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H2X0

UniProtKB/Swiss-Prot:

CHRD_HUMAN :
  • Belongs to the chordin family.
Family:
  • Belongs to the chordin family.
genes like me logo Genes that share domains with CHRD: view

Function for CHRD Gene

Molecular function for CHRD Gene

UniProtKB/Swiss-Prot Function:
Dorsalizing factor. Key developmental protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta family bone morphogenetic proteins (BMPs) and sequestering them in latent complexes (By similarity).
GENATLAS Biochemistry:
chordin,developmental protein,highly conserved,inhibiting the ventralizing activity of bone morphogenetic proteins,active during gastrulation,expressed in fetal and adult liver and cerebellum

LifeMap Function Summary for CHRD Gene

During embryonic development, CHRD as signaling molecule is secreted from the following cells

Phenotypes From GWAS Catalog for CHRD Gene

Gene Ontology (GO) - Molecular Function for CHRD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19429706
GO:0019955 cytokine binding NAS 16449796
genes like me logo Genes that share ontologies with CHRD: view
genes like me logo Genes that share phenotypes with CHRD: view

Animal Models for CHRD Gene

MGI Knock Outs for CHRD:
  • Chrd Chrd<tm1Emdr>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHRD

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CHRD Gene

Localization for CHRD Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHRD Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHRD gene
Compartment Confidence
extracellular 5
plasma membrane 3
mitochondrion 3
cytoskeleton 2
nucleus 2
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CHRD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space NAS 16449796
genes like me logo Genes that share ontologies with CHRD: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CHRD Gene

Pathways & Interactions for CHRD Gene

genes like me logo Genes that share pathways with CHRD: view

Pathways by source for CHRD Gene

2 BioSystems pathways for CHRD Gene
1 KEGG pathway for CHRD Gene
1 GeneTex pathway for CHRD Gene

Gene Ontology (GO) - Biological Process for CHRD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9782094
GO:0002053 positive regulation of mesenchymal cell proliferation IMP 18533030
GO:0007275 multicellular organism development IEA --
GO:0021919 BMP signaling pathway involved in spinal cord dorsal/ventral patterning IMP 11472837
GO:0030336 negative regulation of cell migration IDA 16449796
genes like me logo Genes that share ontologies with CHRD: view

No data available for SIGNOR curated interactions for CHRD Gene

Drugs & Compounds for CHRD Gene

(2) Drugs for CHRD Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(5) Additional Compounds for CHRD Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CHRD: view

Transcripts for CHRD Gene

mRNA/cDNA for CHRD Gene

6 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
17 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHRD

Alternative Splicing Database (ASD) splice patterns (SP) for CHRD Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b ^ 12 ^ 13 ^
SP1: - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - - - - -
SP6: - - - - -
SP7: - - - - - -
SP8:
SP9: - - - - -
SP10: - -
SP11: - - - -
SP12: -
SP13:
SP14:

ExUns: 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24 ^ 25a · 25b
SP1: -
SP2: -
SP3: -
SP4: -
SP5: - -
SP6: - -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for CHRD Gene

GeneLoc Exon Structure for
CHRD

Expression for CHRD Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CHRD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CHRD Gene

This gene is overexpressed in Liver (x8.9), Brain - Cerebellum (x5.2), and Brain - Cerebellar Hemisphere (x4.7).

Protein differential expression in normal tissues from HIPED for CHRD Gene

This gene is overexpressed in Amniocyte (55.9) and Peripheral blood mononuclear cells (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CHRD Gene



Protein tissue co-expression partners for CHRD Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CHRD

SOURCE GeneReport for Unigene cluster for CHRD Gene:

Hs.166186

mRNA Expression by UniProt/SwissProt for CHRD Gene:

Q9H2X0-CHRD_HUMAN
Tissue specificity: Expressed at the highest level in liver.

Evidence on tissue expression from TISSUES for CHRD Gene

  • Nervous system(4.2)
  • Muscle(2.5)
  • Heart(2.4)
  • Kidney(2.3)
  • Liver(2.2)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with CHRD: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CHRD Gene

Orthologs for CHRD Gene

This gene was present in the common ancestor of animals.

Orthologs for CHRD Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CHRD 29 30
  • 99.33 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CHRD 29 30
  • 90.46 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CHRD 29 30
  • 89.23 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Chrd 29 16 30
  • 85.64 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Chrd 29
  • 84.81 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CHRD 30
  • 69 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CHRD 30
  • 33 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CHRD 29 30
  • 64.32 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CHRD 30
  • 51 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia chrd 29
  • 59.02 (n)
Str.2204 29
African clawed frog
(Xenopus laevis)
Amphibia LOC398045 29
Zebrafish
(Danio rerio)
Actinopterygii chd 29 30
  • 56.38 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta sog 29 30 31
  • 44.92 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000472 29
  • 38.9 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 29 (a)
OneToOne
Species where no ortholog for CHRD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CHRD Gene

ENSEMBL:
Gene Tree for CHRD (if available)
TreeFam:
Gene Tree for CHRD (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CHRD: view image
Alliance of Genome Resources:
Additional Orthologs for CHRD

Paralogs for CHRD Gene

(1) SIMAP similar genes for CHRD Gene using alignment to 3 proteins:

  • CHRD_HUMAN
  • B7Z6F4_HUMAN
  • E7ESX1_HUMAN
genes like me logo Genes that share paralogs with CHRD: view

Variants for CHRD Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CHRD Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs145052186 Benign: not provided 184,387,076(+) A/G
NM_003741.3(CHRD):c.2316A>G (p.Pro772=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs145871696 Likely Benign: Anophthalmia-microphthalmia syndrome 184,383,572(+) C/G
NM_003741.3(CHRD):c.1370C>G (p.Thr457Ser)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs1560294370 Uncertain Significance: not provided 184,380,464(+) CA/C
NM_003741.3(CHRD):c.147del (p.Gly50fs)
FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR
rs34052076 Benign: not provided 184,386,051(+) G/A
NM_003741.3(CHRD):c.1824G>A (p.Gln608=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs34147749 Benign: not provided 184,383,109(+) G/A
NM_003741.3(CHRD):c.1159G>A (p.Gly387Ser)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CHRD Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CHRD Gene

Variant ID Type Subtype PubMed ID
dgv2651n106 CNV deletion 24896259
esv2422400 CNV duplication 17116639
esv25970 CNV loss 19812545
nsv511206 CNV gain 21212237
nsv518580 CNV loss 19592680
nsv592667 CNV loss 21841781
nsv829813 CNV loss 17160897

Variation tolerance for CHRD Gene

Residual Variation Intolerance Score: 71.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.74; 86.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHRD Gene

Human Gene Mutation Database (HGMD)
CHRD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHRD
Leiden Open Variation Database (LOVD)
CHRD

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHRD Gene

Disorders for CHRD Gene

MalaCards: The human disease database

(12) MalaCards diseases for CHRD Gene - From: COP and GCD

Disorder Aliases PubMed IDs
cornelia de lange syndrome
  • brachmann de lange syndrome
holoprosencephaly
  • holoprosencephaly sequence
holoprosencephaly 4
  • hpe4
tarsal-carpal coalition syndrome
  • tcc
brachydactyly, type b2
  • bdb2
- elite association - COSMIC cancer census association via MalaCards
Search CHRD in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CHRD

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CHRD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CHRD Gene

Publications for CHRD Gene

  1. The human chordin gene encodes several differentially expressed spliced variants with distinct BMP opposing activities. (PMID: 11472837) Millet C … François V (Mechanisms of development 2001) 2 3 4 22
  2. Coding sequence and expression patterns of mouse chordin and mapping of the cognate mouse chrd and human CHRD genes. (PMID: 9782094) Pappano WN … Greenspan DS (Genomics 1998) 2 3 4 22
  3. BMP-binding modules in chordin: a model for signalling regulation in the extracellular space. (PMID: 10648240) Larraín J … De Robertis EM (Development (Cambridge, England) 2000) 3 4 22
  4. Structural and functional evidence for a substrate exclusion mechanism in mammalian tolloid like-1 (TLL-1) proteinase. (PMID: 20043912) Berry R … Baldock C (FEBS letters 2010) 3 22
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40

Products for CHRD Gene

Sources for CHRD Gene