DSC1

desmocollin 1, the group of Desmosomal cadherins

Basic information

Region (hg38): 18:31129236-31162856

Links

ENSG00000134765 ∙ NCBI:1823 ∙ OMIM:125643 ∙ HGNC:3035 ∙ Uniprot:Q08554 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DSC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DSC1 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					1	1
missense			44	1	2	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	44	1	4

Variants in DSC1

This is a list of pathogenic ClinVar variants found in the DSC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-31130528-A-T		not specified	Uncertain significance (Dec 30, 2023)
18-31130588-C-G		not specified	Uncertain significance (Jul 19, 2023)
18-31130596-C-A		not specified	Uncertain significance (Apr 07, 2023)
18-31130621-C-T		not specified	Uncertain significance (Aug 10, 2023)
18-31130624-C-T		not specified	Uncertain significance (Aug 10, 2021)
18-31130647-T-A		not specified	Uncertain significance (May 23, 2024)
18-31130648-T-C		not specified	Uncertain significance (Jul 27, 2022)
18-31131604-C-T		not specified	Uncertain significance (Jul 09, 2021)
18-31131685-G-A		not specified	Uncertain significance (Dec 14, 2023)
18-31131685-G-T		not specified	Uncertain significance (Aug 08, 2022)
18-31131763-C-G		not specified	Uncertain significance (Jan 31, 2023)
18-31131789-C-T		not specified	Uncertain significance (Mar 19, 2024)
18-31131812-A-C		not specified	Uncertain significance (Dec 08, 2023)
18-31132626-T-C		not specified	Uncertain significance (Oct 08, 2024)
18-31132633-G-A		not specified	Uncertain significance (Aug 30, 2022)
18-31132656-T-C		not specified	Uncertain significance (Mar 06, 2023)
18-31132676-T-C			Benign (Jun 27, 2018)
18-31133927-T-C		not specified	Uncertain significance (Nov 21, 2024)
18-31133929-G-A		not specified	Uncertain significance (Nov 18, 2022)
18-31133972-T-A		not specified	Uncertain significance (Jun 27, 2022)
18-31134019-C-G		not specified	Uncertain significance (Feb 16, 2023)
18-31134031-A-C			Benign (Jun 27, 2018)
18-31134082-T-A		not specified	Uncertain significance (Sep 20, 2023)
18-31134106-C-A		not specified	Uncertain significance (Oct 04, 2024)
18-31134106-C-T		not specified	Uncertain significance (Sep 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DSC1	protein_coding	protein_coding	ENST00000257198	16	33621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.50e-16	0.663	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0953	488	482	1.01	0.0000250	5859
Missense in Polyphen		164	197.04	0.83231		2404
Synonymous	-0.911	191	176	1.09	0.0000100	1692
Loss of Function	1.84	31	44.2	0.702	0.00000239	546

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000457	0.000456
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000383	0.000381
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000481	0.000475
Middle Eastern	0.000383	0.000381
South Asian	0.000462	0.000457
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of intercellular desmosome junctions. Involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion. May contribute to epidermal cell positioning (stratification) by mediating differential adhesiveness between cells that express different isoforms. Linked to the keratinization of epithelial tissues.
• Pathway: Keratinization;Developmental Biology;Neutrophil degranulation;Innate Immune System;Immune System;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.858
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.85

Haploinsufficiency Scores

• pHI: 0.351
• hipred: Y
• hipred_score: 0.510
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dsc1
• Phenotype: growth/size/body region 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); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; vision/eye phenotype; normal phenotype; immune system phenotype

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;keratinization;neutrophil degranulation;cornification
• Cellular component: cornified envelope;plasma membrane;gap junction;membrane;integral component of membrane;desmosome;extracellular exosome;ficolin-1-rich granule membrane
• Molecular function: calcium ion binding