CHRDL1 chordin like 1 [Homo sapiens (human)] - Gene

Summary

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

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Bioinformatics identify the role of chordin-like 1 in thyroid cancer.
Title: Bioinformatics identify the role of chordin-like 1 in thyroid cancer.
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.
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.
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.
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).
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.
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.
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.
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 EBI GWAS CatalogPubMed

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

DXS7756 (e-PCR)
- UniSTS:59924

AL031572 (e-PCR)
- UniSTS:80662

116YB8 (e-PCR)
- UniSTS:54051

DXS7506 (e-PCR)
- UniSTS:12843

AU048745 (e-PCR)
- UniSTS:145195

DXS94 (e-PCR)
- UniSTS:94763

AL032584 (e-PCR)
- UniSTS:93259

DXS87 (e-PCR)
- UniSTS:98892

STS-AA018704 (e-PCR)
- UniSTS:38499

AL022454 (e-PCR)
- UniSTS:59282

fl05f06.x1 (e-PCR)
- UniSTS:201902

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

NG_012816.1 RefSeqGene

Range

5242..127203

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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
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
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