DCN

decorin, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 12:91140483-91183217

Links

ENSG00000011465 ∙ NCBI:1634 ∙ OMIM:125255 ∙ HGNC:2705 ∙ Uniprot:P07585 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the DCN gene.

• Congenital stromal corneal dystrophy (42 variants)
• Inborn genetic diseases (15 variants)
• not provided (10 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	4	8
missense			19	2	4	25
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding			12	3	4	19
Total	0	0	32	9	12

Variants in DCN

This is a list of pathogenic ClinVar variants found in the DCN region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-91145492-A-T		Congenital stromal corneal dystrophy	Uncertain significance (Jan 12, 2018)
12-91145615-A-C		Congenital stromal corneal dystrophy	Uncertain significance (Jan 12, 2018)
12-91145681-A-G		Congenital stromal corneal dystrophy	Benign (Jan 12, 2018)
12-91145704-T-C		Congenital stromal corneal dystrophy	Uncertain significance (Jan 12, 2018)
12-91145707-A-G		Congenital stromal corneal dystrophy	Uncertain significance (Jan 13, 2018)
12-91145717-T-C		Congenital stromal corneal dystrophy	Uncertain significance (Jan 12, 2018)
12-91145769-T-A		Congenital stromal corneal dystrophy	Uncertain significance (Jan 13, 2018)
12-91145838-C-G		Congenital stromal corneal dystrophy	Uncertain significance (Jan 13, 2018)
12-91145898-G-A		Congenital stromal corneal dystrophy	Benign (Jan 13, 2018)
12-91145910-A-C		Congenital stromal corneal dystrophy	Uncertain significance (Jan 13, 2018)
12-91145953-C-T		Congenital stromal corneal dystrophy	Benign (Jan 13, 2018)
12-91145978-G-A		Congenital stromal corneal dystrophy	Uncertain significance (Jan 12, 2018)
12-91146007-T-C		Congenital stromal corneal dystrophy	Benign (Jan 13, 2018)
12-91146072-C-T		Congenital stromal corneal dystrophy • Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 01, 2024)
12-91146076-T-A		Congenital stromal corneal dystrophy	Uncertain significance (Jan 13, 2018)
12-91146088-G-T		DCN-related disorder	Likely benign (Aug 19, 2019)
12-91146090-G-A		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
12-91146093-C-T		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
12-91146102-A-C		Congenital stromal corneal dystrophy	not provided (-)
12-91146105-T-C		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
12-91146124-C-G		Inborn genetic diseases	Uncertain significance (Jul 05, 2023)
12-91146163-C-T		Congenital stromal corneal dystrophy	Benign (Jan 12, 2018)
12-91146170-GA-G		Congenital stromal corneal dystrophy	Pathogenic (Sep 01, 2006)
12-91146175-CT-C		Congenital stromal corneal dystrophy	Pathogenic (Mar 01, 2014)
12-91146179-T-C		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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