DEFA3
Basic information
Region (hg38): 8:7015869-7018297
Previous symbols: [ "DEF3" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 0 |
Variants in DEFA3
This is a list of pathogenic ClinVar variants found in the DEFA3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-7016013-T-C | not specified | Uncertain significance (Sep 26, 2024) | ||
| 8-7016039-C-T | not specified | Uncertain significance (Feb 27, 2023) | ||
| 8-7016043-G-A | not specified | Uncertain significance (Nov 09, 2024) | ||
| 8-7016051-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 8-7016687-G-T | not specified | Uncertain significance (Jul 14, 2021) | ||
| 8-7016700-C-G | not specified | Uncertain significance (Apr 20, 2023) | ||
| 8-7016700-C-T | not specified | Uncertain significance (Mar 29, 2024) | ||
| 8-7016717-A-G | not specified | Uncertain significance (Jan 31, 2024) | ||
| 8-7016733-T-G | not specified | Uncertain significance (Oct 26, 2024) | ||
| 8-7016737-C-T | Likely benign (Feb 01, 2023) | |||
| 8-7016823-T-G | not specified | Uncertain significance (Jul 14, 2021) | ||
| 8-7016847-T-C | not specified | Uncertain significance (Jan 23, 2024) |
GnomAD
Source:
| 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:
- 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_CRISPR2
- 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