DEFA5
Basic information
Region (hg38): 8:7055304-7056739
Previous symbols: [ "DEF5" ]
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 DEFA5 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 | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 1 |
Variants in DEFA5
This is a list of pathogenic ClinVar variants found in the DEFA5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-7055435-C-T | not specified | Uncertain significance (Dec 09, 2024) | ||
| 8-7055456-C-T | not specified | Uncertain significance (Dec 26, 2023) | ||
| 8-7055478-C-T | not specified | Uncertain significance (Dec 10, 2024) | ||
| 8-7055493-G-A | not specified | Uncertain significance (Jun 21, 2022) | ||
| 8-7055504-C-T | Benign (Aug 05, 2018) | |||
| 8-7055508-C-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| 8-7055513-C-T | not specified | Uncertain significance (May 31, 2023) | ||
| 8-7055540-G-C | not specified | Uncertain significance (Feb 06, 2024) | ||
| 8-7056573-A-C | not specified | Uncertain significance (Jun 29, 2023) | ||
| 8-7056580-G-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 8-7056586-C-G | not specified | Uncertain significance (Sep 25, 2024) | ||
| 8-7056592-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 8-7056612-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 8-7056628-C-G | not specified | Uncertain significance (Sep 25, 2024) | ||
| 8-7056638-C-G | not specified | Uncertain significance (Apr 24, 2024) | ||
| 8-7056649-C-A | not specified | Uncertain significance (Aug 27, 2024) | ||
| 8-7056658-C-T | not specified | Uncertain significance (May 04, 2022) | ||
| 8-7056673-C-T | not specified | Uncertain significance (Jun 14, 2022) | ||
| 8-7056687-A-G | not specified | Uncertain significance (Jun 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DEFA5 | protein_coding | protein_coding | ENST00000330590 | 2 | 1426 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000519 | 0.0751 | 125728 | 0 | 17 | 125745 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.91 | 97 | 56.5 | 1.72 | 0.00000328 | 583 |
| Missense in Polyphen | 31 | 20.021 | 1.5484 | 230 | ||
| Synonymous | -1.63 | 29 | 19.8 | 1.47 | 9.13e-7 | 202 |
| Loss of Function | -2.16 | 6 | 2.39 | 2.51 | 1.02e-7 | 25 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000541 | 0.000521 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000440 | 0.0000440 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has antimicrobial activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by permeabilizing their plasma membrane. All DEFA5 peptides exert antimicrobial activities, but their potency is affected by peptide processing. {ECO:0000269|PubMed:12021776, ECO:0000269|PubMed:15616305, ECO:0000269|PubMed:17088326}.;
- Pathway
- Antimicrobial peptides;Innate Immune System;Immune System;Alpha-defensins;Defensins
(Consensus)
Recessive Scores
- pRec
- 0.0341
Intolerance Scores
- loftool
- 0.717
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.107
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0102
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;killing of cells of other organism;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;positive regulation of membrane permeability
- Cellular component
- extracellular region;extracellular space;Golgi lumen;transport vesicle;secretory granule lumen
- Molecular function
- protein homodimerization activity