DEFA3

defensin alpha 3, the group of Defensins, alpha

Basic information

Region (hg38): 8:7015869-7018297

Previous symbols: [ "DEF3" ]

Links

ENSG00000239839 ∙ NCBI:1668 ∙ OMIM:604522 ∙ HGNC:2762 ∙ Uniprot:P59666 ∙ 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 DEFA3 gene.

• not_specified (17 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFA3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005217.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			17			17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	17	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFA3	protein_coding	protein_coding	ENST00000327857	2	2433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0905	0.583	110590	0	1	110591	0.00000452

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0932	34	32.5	1.05	0.00000180	584
Missense in Polyphen		16	14.801	1.081		296
Synonymous	-0.208	10	9.20	1.09	3.95e-7	178
Loss of Function	-0.0182	1	0.981	1.02	4.15e-8	19

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000496	0.0000496
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial activity against Gram- negative and Gram-positive bacteria. Defensins are thought to kill microbes by permeabilizing their plasma membrane. {ECO:0000269|PubMed:15616305, ECO:0000269|PubMed:15894545, ECO:0000269|PubMed:17452329, ECO:0000269|PubMed:2006422}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Antimicrobial peptides;Innate Immune System;Immune System;Alpha-defensins;Defensins (Consensus)

Recessive Scores

• pRec: 0.0489

Haploinsufficiency Scores

• pHI: 0.0191
• hipred: N
• hipred_score: 0.187
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000995

Gene Damage Prediction

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

Gene ontology

• Biological process: innate immune response in mucosa;antimicrobial humoral response;antibacterial humoral response;intracellular estrogen receptor signaling pathway;killing of cells of other organism;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;defense response to fungus;defense response to virus;membrane disruption in other organism;antimicrobial humoral immune response mediated by antimicrobial peptide;cellular response to lipopolysaccharide
• Cellular component: extracellular region;extracellular space;Golgi lumen;azurophil granule lumen;extracellular exosome
• Molecular function: molecular_function;protein homodimerization activity