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 4. Among its related pathways are Mesodermal Commitment Pathway 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 SSPO.

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).

Additional gene information for CHRD Gene

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 for CHRD Gene

Promoters and enhancers for CHRD Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J184377 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 505.4 -0.6 -572 4.6 HNRNPK POLR2G NCOR1 ZIC2 ZBTB10 ZNF263 TGIF2 CTBP1 SKI MYC CHRD 5EW4_A-039 THPO lnc-CHRD-1 lnc-CLCN2-8 ABCF3
GH03J184772 Promoter/Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.4 +393.1 393101 1.5 FOXP2 ZNF366 ZNF512 MTA2 PRDM1 LINC02069 LOC105374253 RF00017-4194 lnc-VPS8-1 LINC01840 EPHB3 MAGEF1 CHRD THPO LOC107986163
GH03J184417 Enhancer 1 Ensembl ENCODE 11.5 +38.0 37953 0.5 CTCF USF1 ZBTB10 ZNF423 REST RFX1 MYC RAD21 TRIM22 U2AF2 CHRD THPO LINC01840 EPHB3 FAM131A CLCN2 POLR2H EIF4G1 PSMD2 LINC02054
GH03J184777 Enhancer 1 Ensembl ENCODE CraniofacialAtlas 10.9 +398.3 398328 2 CTCF REST CUX1 RAD21 TRIM22 SMC3 MXI1 CEBPB PBX2 USF1 EPHB3 LINC01840 MAGEF1 CHRD THPO VPS8 LOC107986163 LOC105374253 lnc-VPS8-1
GH03J184541 Enhancer 0.9 Ensembl ENCODE 11.9 +161.2 161216 0.6 CTCF TEAD4 GABPA REST RAD21 CTBP1 SMC3 DEK ZNF263 YY1 THPO CHRD CLCN2 POLR2H MAGEF1 EIF4G1 FAM131A LINC01840 HSALNG0031250 LINC01839
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for CHRD Gene
chr3:184,380,073-184,390,736
(GRCh38/hg38)
Size:
10,664 bases
Orientation:
Plus strand
chr3:184,097,861-184,108,524
(GRCh37/hg19)
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

  • Signalway ELISA kits for CHRD

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

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

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 IEA,IPI 19429706
GO:0008201 heparin binding IEA --
GO:0019955 cytokine binding NAS 16449796
GO:0045545 syndecan binding IEA --
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>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • 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:0001649 osteoblast differentiation IEA --
GO:0001702 gastrulation with mouth forming second IEA --
GO:0001707 mesoderm formation IEA --
GO:0002053 positive regulation of mesenchymal cell proliferation IMP 18533030
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 :

CRISPR Products

Inhibitory RNA Products

  • 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(4.1)
genes like me logo Genes that share expression patterns with CHRD: view

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 31 30
  • 99.33 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CHRD 31 30
  • 90.46 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CHRD 31 30
  • 89.23 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Chrd 17 31 30
  • 85.64 (n)
rat
(Rattus norvegicus)
Mammalia Chrd 30
  • 84.81 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CHRD 31
  • 69 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CHRD 31
  • 33 (a)
OneToOne
chicken
(Gallus gallus)
Aves CHRD 31 30
  • 64.32 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CHRD 31
  • 51 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chrd 30
  • 59.02 (n)
Str.2204 30
African clawed frog
(Xenopus laevis)
Amphibia LOC398045 30
zebrafish
(Danio rerio)
Actinopterygii chd 31 30 30
  • 56.38 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta sog 31 32 30
  • 44.92 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000472 30
  • 38.9 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 29 (a)
OneToOne
Species where no ortholog for CHRD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

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
709673 Benign: not provided 184,382,695(+) C/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
709674 Benign: not provided 184,386,051(+) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
771358 Benign: not provided 184,387,076(+) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
780902 Benign: not provided 184,383,109(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs145871696 Likely Benign: Anophthalmia - microphthalmia 184,383,572(+) C/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for CHRD Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CHRD Gene

MalaCards: The human disease database

(10) MalaCards diseases for CHRD Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cornelia de lange syndrome
  • cdls
holoprosencephaly 4
  • hpe4
holoprosencephaly
  • holoprosencephaly sequence
tarsal-carpal coalition syndrome
  • tcc
sclerosteosis 1
  • sost1
- 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

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 23 54
  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 23 54
  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 23 54
  4. 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 41 54
  5. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 41 54

Products for CHRD Gene

  • Signalway ELISA kits for CHRD
  • Signalway Proteins for CHRD

Sources for CHRD Gene