DEFB4A

defensin beta 4A, the group of Defensins, beta|Receptor ligands

Basic information

Region (hg38): 8:7894677-7896716

Previous symbols: [ "DEFB102", "DEFB2", "DEFB4" ]

Links

ENSG00000171711 ∙ NCBI:1673 ∙ OMIM:602215 ∙ HGNC:2767 ∙ Uniprot:O15263 ∙ 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 DEFB4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB4A 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			3		1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	1

Variants in DEFB4A

This is a list of pathogenic ClinVar variants found in the DEFB4A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-7894752-T-A		not specified	Uncertain significance (Aug 19, 2021)
8-7894760-G-A			Benign (Aug 03, 2017)
8-7894761-C-T		not specified	Uncertain significance (Jun 04, 2024)
8-7896510-T-G		not specified	Uncertain significance (Apr 13, 2022)
8-7896534-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFB4A	protein_coding	protein_coding	ENST00000302247	2	2083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00116	0.236	125482	0	6	125488	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.634	13	7.96	1.63	3.46e-7	397
Missense in Polyphen		0	0	NaN		42
Synonymous	0.492	2	3.10	0.645	2.32e-7	114
Loss of Function	-2.95	3	0.580	5.18	2.51e-8	11

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits antimicrobial activity against Gram-negative bacteria and Gram-positive bacteria. May act as a ligand for C-C chemokine receptor CCR6. Can bind to both human and mouse CCR6 and induce chemotactic activity of CCR6-expressing cells (PubMed:20068036). {ECO:0000269|PubMed:20068036}.
• Pathway: IL-17 signaling pathway - Homo sapiens (human);Vitamin D Receptor Pathway;Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins (Consensus)

Recessive Scores

• pRec: 0.0854

Haploinsufficiency Scores

• pHI: 0.0279
• hipred: N
• hipred_score: 0.229

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: chemotaxis;immune response;G protein-coupled receptor signaling pathway;antimicrobial humoral response;killing of cells of other organism;defense response to bacterium;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;positive chemotaxis;cell chemotaxis;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: extracellular region;extracellular space;Golgi lumen
• Molecular function: protein binding;CCR6 chemokine receptor binding;chemoattractant activity