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CHRDL1 chordin like 1 [ Homo sapiens (human) ]

Gene ID: 91851, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (110673856..110795817, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (109121756..109243896, complement)
105.20220307 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. Study on the expression and function of chordin-like 1 in oral squamous cell carcinoma. Han Y, et al. Oral Dis, 2023 Jul. PMID 35510812
  3. Hypermethylation of the CHRDL1 promoter induces proliferation and metastasis by activating Akt and Erk in gastric cancer. Pei YF, et al. Oncotarget, 2017 Apr 4. PMID 28423564, Free PMC Article
  4. Novel Mutation in the CHRDL1 Gene Detected in Patients With Megalocornea. Mangialavori D, et al. Cornea, 2015 Aug. PMID 26020825
  5. Molecular mechanism of CHRDL1-mediated X-linked megalocornea in humans and in Xenopus model. Pfirrmann T, et al. Hum Mol Genet, 2015 Jun 1. PMID 25712132

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Bioinformatics identify the role of chordin-like 1 in thyroid cancer.
    Title: Bioinformatics identify the role of chordin-like 1 in thyroid cancer.
  3. 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.
  4. 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.
  5. 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.
  6. 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).
  7. 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.
  8. 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.
  9. 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.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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)

Genotypes

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_2023_10

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

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