DCN
decorin, the group of Small leucine rich repeat proteoglycans
Basic information
Region (hg38): 12:91140484-91183217
Links
Phenotypes
GenCC
Source:
- congenital stromal corneal dystrophy (Strong), mode of inheritance: AD
- congenital stromal corneal dystrophy (Supportive), mode of inheritance: AD
- congenital stromal corneal dystrophy (Definitive), mode of inheritance: AD
- congenital stromal corneal dystrophy (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Corneal dystrophy, congenital stromal | AD | Ophthalmologic | In addition to other ophthalmologic care that may be effective (eg, penetrating keratoplasty), open-angle glaucoma has been described in several individuals, and awareness of this risk may allow surveillance and early treatment | Ophthalmologic | 5304426; 15671264; 16935612; 20301741; 21993463; 24413633 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (48 variants)
- Congenital_stromal_corneal_dystrophy (28 variants)
- not_provided (14 variants)
- DCN-related_disorder (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001920.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 11 | |||||
| missense | 49 | 58 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 4 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 4 | 0 | 50 | 10 | 9 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DCN | protein_coding | protein_coding | ENST00000052754 | 7 | 37876 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.312 | 0.687 | 125734 | 0 | 14 | 125748 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.801 | 164 | 196 | 0.839 | 0.0000101 | 2357 |
| Missense in Polyphen | 41 | 60.961 | 0.67256 | 748 | ||
| Synonymous | -0.149 | 77 | 75.4 | 1.02 | 0.00000395 | 708 |
| Loss of Function | 2.93 | 4 | 17.1 | 0.234 | 0.00000105 | 184 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000231 | 0.000231 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May affect the rate of fibrils formation.;
- Disease
- DISEASE: Corneal dystrophy, congenital stromal (CSCD) [MIM:610048]: A corneal dystrophy characterized by congenital corneal opacification consisting of a large number of flakes and spots throughout all layers of the stroma. It results in progressive, painless visual loss. Corneal erosions and photophobia are absent. {ECO:0000269|PubMed:15671264}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Human Complement System;BMP2-WNT4-FOXO1 Pathway in Human Primary Endometrial Stromal Cell Differentiation;Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate biosynthesis;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Extracellular matrix organization;Metabolism;Integrin;Degradation of the extracellular matrix;ECM proteoglycans;Validated transcriptional targets of AP1 family members Fra1 and Fra2
(Consensus)
Recessive Scores
- pRec
- 0.865
Intolerance Scores
- loftool
- 0.728
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.01
Haploinsufficiency Scores
- pHI
- 0.607
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.839
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dcn
- Phenotype
- respiratory system phenotype; neoplasm; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; digestive/alimentary phenotype; renal/urinary system phenotype; skeleton phenotype; cellular phenotype; immune system phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- dcn
- Affected structure
- ceratobranchial cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- kidney development;placenta development;skeletal muscle tissue development;aging;response to mechanical stimulus;animal organ morphogenesis;positive regulation of autophagy;negative regulation of endothelial cell migration;positive regulation of phosphatidylinositol 3-kinase signaling;positive regulation of macroautophagy;negative regulation of angiogenesis;peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan;extracellular matrix organization;chondroitin sulfate biosynthetic process;chondroitin sulfate catabolic process;dermatan sulfate biosynthetic process;response to lipopolysaccharide;wound healing;positive regulation of transcription by RNA polymerase II;positive regulation of mitochondrial depolarization;positive regulation of mitochondrial fission;negative regulation of vascular endothelial growth factor signaling pathway
- Cellular component
- extracellular region;collagen type VI trimer;extracellular space;Golgi lumen;lysosomal lumen;collagen-containing extracellular matrix
- Molecular function
- RNA binding;protein binding;collagen binding;glycosaminoglycan binding;extracellular matrix structural constituent conferring compression resistance;protein N-terminus binding;extracellular matrix binding