DCD

dermcidin

Basic information

Region (hg38): 12:54644589-54648493

Links

ENSG00000161634 ∙ NCBI:117159 ∙ OMIM:606634 ∙ HGNC:14669 ∙ Uniprot:P81605 ∙ 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 DCD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCD 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			8	1	1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	1

Variants in DCD

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

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

Position	Type	Phenotype	Significance	ClinVar
12-54644720-A-G		not specified	Uncertain significance (Jun 11, 2021)
12-54644743-G-T		not specified	Uncertain significance (Oct 25, 2024)
12-54644751-C-T		not specified	Likely benign (Jan 10, 2022)
12-54645182-C-T		not specified	Uncertain significance (Jun 02, 2023)
12-54645187-T-C		not specified	Uncertain significance (Dec 05, 2024)
12-54645221-C-T		not specified	Uncertain significance (Dec 20, 2023)
12-54645251-C-T			Benign (Sep 03, 2018)
12-54645612-G-A		not specified	Uncertain significance (May 21, 2024)
12-54647122-G-T		not specified	Uncertain significance (Dec 10, 2024)
12-54647129-G-A		not specified	Uncertain significance (Apr 25, 2022)
12-54647135-G-C		not specified	Uncertain significance (Dec 22, 2024)
12-54647146-G-A			Likely benign (Jun 25, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCD	protein_coding	protein_coding	ENST00000293371	5	3903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000158	0.453	125680	0	8	125688	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.488	71	60.3	1.18	0.00000325	683
Missense in Polyphen		16	8.7777	1.8228		68
Synonymous	-0.406	30	27.3	1.10	0.00000193	230
Loss of Function	0.257	6	6.72	0.893	3.71e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DCD-1 displays antimicrobial activity thereby limiting skin infection by potential pathogens in the first few hours after bacterial colonization. Highly effective against E.coli, E.faecalis, S.aureus and C.albicans. Optimal pH and salt concentration resemble the conditions in sweat. Also exhibits proteolytic activity, cleaving on the C-terminal side of Arg and, to a lesser extent, Lys residues (PubMed:17448443). {ECO:0000269|PubMed:17448443}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.425
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.16

Haploinsufficiency Scores

• pHI: 0.0580
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

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

Gene ontology

• Biological process: proteolysis;antimicrobial humoral response;killing of cells of other organism;defense response to bacterium;defense response to fungus
• Cellular component: extracellular region;extracellular exosome
• Molecular function: RNA binding;protein binding;peptidase activity