DSG3

desmoglein 3, the group of Desmosomal cadherins

Basic information

Region (hg38): 18:31447740-31478702

Links

ENSG00000134757 ∙ NCBI:1830 ∙ OMIM:169615 ∙ HGNC:3050 ∙ Uniprot:P32926 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• blistering, acantholytic, of oral and laryngeal mucosa (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Acantholytic blistering of the oral and laryngeal mucosa	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	30528827

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DSG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DSG3 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					5	5
missense			50	3	5	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					31	31
Total	0	0	51	3	41

Variants in DSG3

This is a list of pathogenic ClinVar variants found in the DSG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-31447782-C-T			Benign (Jun 19, 2021)
18-31447794-C-T			Benign (Jun 19, 2021)
18-31447808-C-T			Benign (Nov 11, 2018)
18-31447882-T-C		not specified	Likely benign (Jul 27, 2022)
18-31448221-C-G			Benign (Nov 11, 2018)
18-31456353-A-G			Benign (Jun 19, 2021)
18-31456879-C-G			Benign (Jun 19, 2021)
18-31457050-A-G		not specified	Uncertain significance (Mar 14, 2023)
18-31457168-T-C			Benign (Nov 11, 2018)
18-31457453-A-T			Benign (Jun 19, 2021)
18-31458160-A-C			Benign (Nov 11, 2018)
18-31458300-G-A			Benign (Jun 19, 2021)
18-31458353-T-C			Benign (Jun 19, 2021)
18-31458563-C-A		not specified	Uncertain significance (Dec 09, 2023)
18-31458568-A-G		not specified	Uncertain significance (May 31, 2023)
18-31458569-T-C		not specified	Uncertain significance (May 31, 2023)
18-31458573-C-T			Benign (Jun 09, 2021)
18-31458574-G-C		not specified	Uncertain significance (Dec 15, 2023)
18-31458578-G-A		not specified	Uncertain significance (Apr 25, 2023)
18-31458803-G-A			Benign (Nov 11, 2018)
18-31459042-C-T		not specified	Uncertain significance (May 13, 2024)
18-31459146-C-A		not specified	Uncertain significance (Feb 16, 2023)
18-31459172-C-A		not specified	Uncertain significance (Jun 02, 2023)
18-31459320-G-A			Benign (Nov 11, 2018)
18-31459798-T-C			Benign (Nov 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DSG3	protein_coding	protein_coding	ENST00000257189	16	30908

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-20	0.0369	125643	1	104	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.460	509	539	0.944	0.0000285	6468
Missense in Polyphen		162	191.8	0.84462		2406
Synonymous	-0.336	208	202	1.03	0.0000113	2056
Loss of Function	1.08	35	42.6	0.822	0.00000233	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00300	0.00219
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000544	0.000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000544	0.000544
South Asian	0.000409	0.000392
Other	0.000489	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.
• Pathway: Keratinization;Developmental Biology;Apoptotic cleavage of cell adhesion proteins;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.917
• rvis_EVS: -0.7
• rvis_percentile_EVS: 14.81

Haploinsufficiency Scores

• pHI: 0.327
• hipred: N
• hipred_score: 0.327
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dsg3
• Phenotype: digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; respiratory system phenotype; hematopoietic system phenotype; 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); 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;keratinization;cornification
• Cellular component: cornified envelope;cytosol;plasma membrane;integral component of membrane;desmosome;extracellular exosome
• Molecular function: calcium ion binding