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    CHRDL1 chordin like 1 [ Homo sapiens (human) ]

    Gene ID: 91851, updated on 27-Nov-2024

    Summary

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    Official Symbol
    CHRDL1provided by HGNC
    Official Full Name
    chordin like 1provided by HGNC
    Primary source
    HGNC:HGNC:29861
    See related
    Ensembl:ENSG00000101938 MIM:300350; AllianceGenome:HGNC:29861
    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
    CHL; MGC1; MGCN; VOPT; NRLN1; dA141H5.1
    Summary
    This gene encodes an antagonist of bone morphogenetic protein 4. The encoded protein may play a role in topographic retinotectal projection and in the regulation of retinal angiogenesis in response to hypoxia. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]
    Expression
    Broad expression in fat (RPKM 100.2), prostate (RPKM 57.9) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CHRDL1 in Genome Data Viewer
    Location:
    Xq23
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (110673856..110795817, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (109121756..109243896, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (109917084..110039045, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:109763200-109764196 Neighboring gene cripto, EGF-CFC family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:109844205-109844705 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:109911493-109912258 Neighboring gene M6PR pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29856 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:110065211-110065764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:110187999-110188834 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:110207796-110208396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:110254037-110254537 Neighboring gene p21 (RAC1) activated kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29857 Neighboring gene NANOG hESC enhancer GRCh37_chrX:110438658-110439159 Neighboring gene FCF1 pseudogene 4 Neighboring gene glutamate dehydrogenase 1 pseudogene 9

    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. Bioinformatics identify the role of chordin-like 1 in thyroid cancer. Yu JW, et al. Medicine (Baltimore), 2023 Feb 3. PMID 36749222, Free PMC Article
    2. X-linked megalocornea: close linkage to DXS87 and DXS94. Chen JD, et al. Hum Genet, 1989 Oct. PMID 2571565
    3. Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors. Kosinski C, et al. Proc Natl Acad Sci U S A, 2007 Sep 25. PMID 17881565, Free PMC Article
    4. Effect of chordin-like 1 on MC3T3-E1 and human mesenchymal stem cells. Fernandes H, et al. Cells Tissues Organs, 2010. PMID 20130390
    5. X-linked Megalocornea Associated with the Novel CHRDL1 Gene Mutation p.(Pro56Leu*8). Han J, et al. Ophthalmic Genet, 2015 Jun. PMID 24073597, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CHRDL1 inhibits OSCC metastasis via MAPK signaling-mediated inhibition of MED29.
      Title: CHRDL1 inhibits OSCC metastasis via MAPK signaling-mediated inhibition of MED29.
    2. Study on the expression and function of chordin-like 1 in oral squamous cell carcinoma.
      Title: Study on the expression and function of chordin-like 1 in oral squamous cell carcinoma.
    3. Bioinformatics identify the role of chordin-like 1 in thyroid cancer.
      Title: Bioinformatics identify the role of chordin-like 1 in thyroid cancer.
    4. Finally, in vivo experiments confirmed that CHRDL1 acted as a tumor suppressor gene in suppressing tumor growth and metastasis
      Title: Hypermethylation of the CHRDL1 promoter induces proliferation and metastasis by activating Akt and Erk in gastric cancer.
    5. Results show that Chrdl1 expression is upregulated in numerous breast cancer cells following TGF-beta stimulation and demonstrated that Chrdl1 acts as an inhibitor of BMP4-induced migration and invasion.
      Title: Chordin-Like 1 Suppresses Bone Morphogenetic Protein 4-Induced Breast Cancer Cell Migration and Invasion.
    6. These studies have identified and validated new factors enriched in juvenile chondrocytes as compared to adult chondrocytes including secreted extracellular matrix factors chordin-like 1 (CHRDL1) and microfibrillar-associated protein 4 (MFAP4).
      Title: Identification of Human Juvenile Chondrocyte-Specific Factors that Stimulate Stem Cell Growth.
    7. We provide the initial confirmation that X-linked megalocornea is associated with mutations in the CHRDL1 gene.
      Title: X-linked Megalocornea Associated with the Novel CHRDL1 Gene Mutation p.(Pro56Leu*8).
    8. CHRDL1 plays a key role in cornea homeostasis as evidenced by disease causing mutations in X-linked megalocornea.
      Title: Molecular mechanism of CHRDL1-mediated X-linked megalocornea in humans and in Xenopus model.
    9. The detection of mutations in the CHRDL1 gene is useful for differential diagnosis with different forms of megalocornea.
      Title: Novel Mutation in the CHRDL1 Gene Detected in Patients With Megalocornea.
    10. Novel CHRDL1 mutations in ten families with X-linked megalocornea, are reported.
      Title: Association of CHRDL1 mutations and variants with X-linked megalocornea, Neuhäuser syndrome and central corneal thickness.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    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
    Isolated congenital megalocornea
    MedGen: C4518341 OMIM: 309300 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2016-12-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2016-12-08)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables BMP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transforming growth factor beta binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in AMPA glutamate receptor clustering IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic axis specification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in excitatory chemical synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in eye development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of BMP signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ossification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of synaptic plasticity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synapse maturation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    chordin-like protein 1
    Names
    neuralin-1
    neurogenesin-1
    ventroptin

    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_012816.1 RefSeqGene

      Range
      5242..127203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001143981.2 → NP_001137453.1  chordin-like protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001137453.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 5 both encode the same isoform (1).
      Source sequence(s)
      AK293106, AL049176, AL591489
      Consensus CDS
      CCDS48149.1
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000361112.1, ENST00000372042.6
      Conserved Domains (1) summary
      cl17735
      Location:116 → 179
      VWC; von Willebrand factor type C domain

    2. NM_001143982.2 → NP_001137454.1  chordin-like protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001137454.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the identical N- and C-termini compared to isoform 1.
      Source sequence(s)
      AK312270, AL049176, BC002909
      Consensus CDS
      CCDS48150.1
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000399739.2, ENST00000444321.2
      Conserved Domains (1) summary
      cl17735
      Location:115 → 178
      VWC; von Willebrand factor type C domain

    3. NM_001143983.3 → NP_001137455.2  chordin-like protein 1 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001137455.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons, resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The resulting protein (isoform 4) is shorter but has the identical N- and C-termini compared to isoform 1.
      Source sequence(s)
      AA057564, AK297563, AL049176
      Consensus CDS
      CCDS48148.2
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000418443.1, ENST00000482160.5
      Conserved Domains (1) summary
      cl17735
      Location:181 → 243
      VWC; von Willebrand factor type C domain

    4. NM_001367204.1 → NP_001354133.1  chordin-like protein 1 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), as well as variant 1, encodes isoform 1.
      Source sequence(s)
      AL049176, AL591489
      Consensus CDS
      CCDS48149.1
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116 → 179
      VWC; von Willebrand factor type C domain

    5. NM_001367205.1 → NP_001354134.1  chordin-like protein 1 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variant 7, encodes isoform 5.
      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116 → 179
      VWC; von Willebrand factor type C domain

    6. NM_001367206.1 → NP_001354135.1  chordin-like protein 1 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), as well as variant 6, encodes isoform 5.
      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116 → 179
      VWC; von Willebrand factor type C domain

    7. NM_001367207.1 → NP_001354136.1  chordin-like protein 1 isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:115 → 178
      VWC; von Willebrand factor type C domain

    8. NM_001367208.1 → NP_001354137.1  chordin-like protein 1 isoform 7 precursor

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116 → 179
      VWC; von Willebrand factor type C domain

    9. NM_001367209.1 → NP_001354138.1  chordin-like protein 1 isoform 8 precursor

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116 → 179
      VWC; von Willebrand factor type C domain

    10. NM_145234.4 → NP_660277.2  chordin-like protein 1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_660277.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses alternate in-frame splice sites in the coding region compared to variant 1. The resulting protein (isoform 3) is shorter but has the identical N- and C-termini compared to isoform 1.
      Source sequence(s)
      AL049176, BC002909, BP377491
      Consensus CDS
      CCDS14553.1
      UniProtKB/Swiss-Prot
      B1AKD0, B4DMP3, D3DUY6, E9PGS5, Q539E4, Q9BU40, Q9Y3H7
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000361115.1, ENST00000372045.5
      Conserved Domains (1) summary
      cl17735
      Location:115 → 178
      VWC; von Willebrand factor type C domain

    RNA

    1. NR_159734.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      110673856..110795817 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005262222.3 → XP_005262279.1  chordin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005262279.1

      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:115 → 178
      VWC; von Willebrand factor type C domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      109121756..109243896 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328104.1 → XP_054184079.1  chordin-like protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BU40.2 GenPept UniProtKB/Swiss-Prot:Q9BU40

    Gene LinkOut

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

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