DEFA4

defensin alpha 4, the group of Defensins, alpha

Basic information

Region (hg38): 8:6935820-6938306

Previous symbols: [ "DEF4" ]

Links

ENSG00000164821 ∙ NCBI:1669 ∙ OMIM:601157 ∙ HGNC:2763 ∙ Uniprot:P12838 ∙ 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 DEFA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFA4 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						0
missense			8	2		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	0

Variants in DEFA4

This is a list of pathogenic ClinVar variants found in the DEFA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-6936030-C-T		not specified	Uncertain significance (Jun 22, 2021)
8-6936733-A-G		not specified	Uncertain significance (Aug 02, 2021)
8-6936739-A-G		not specified	Uncertain significance (Jul 14, 2021)
8-6936769-A-G		not specified	Uncertain significance (Feb 28, 2023)
8-6936796-C-T		not specified	Uncertain significance (Dec 19, 2022)
8-6936812-G-A		not specified	Uncertain significance (Mar 29, 2023)
8-6936821-C-T		not specified	Uncertain significance (May 03, 2023)
8-6936847-C-T		not specified	Likely benign (Dec 27, 2023)
8-6936850-A-G		not specified	Likely benign (Feb 28, 2023)
8-6936887-C-T		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFA4	protein_coding	protein_coding	ENST00000297435	2	2517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.498	0.434	118727	42	1817	120586	0.00774

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.34	112	60.8	1.84	0.00000379	608
Missense in Polyphen		31	14.836	2.0895		186
Synonymous	-1.76	32	21.6	1.48	0.00000119	206
Loss of Function	1.28	0	1.92	0.00	8.18e-8	21

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0187	0.0187
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.0635	0.0634
Finnish	0.0000469	0.0000469
European (Non-Finnish)	0.000146	0.000146
Middle Eastern	0.0635	0.0634
South Asian	0.00384	0.00385
Other	0.00430	0.00431

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has antimicrobial activity against Gram-negative bacteria, and to a lesser extent also against Gram-positive bacteria and fungi. Protects blood cells against infection with HIV-1 (in vitro). Inhibits corticotropin (ACTH)-stimulated corticosterone production. {ECO:0000269|PubMed:15616305, ECO:0000269|PubMed:15620707}.
• Pathway: Neutrophil degranulation;Antimicrobial peptides;Innate Immune System;Immune System;Alpha-defensins;Defensins (Consensus)

Intolerance Scores

• loftool: 0.418
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.04

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.127

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;antifungal humoral response;killing of cells of other organism;neutrophil degranulation;innate immune response;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;defense response to fungus;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;specific granule lumen;azurophil granule
• Molecular function: protein homodimerization activity