DEFB126
Basic information
Region (hg38): 20:142590-145751
Previous symbols: [ "C20orf8" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (11 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFB126 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030931.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DEFB126 | protein_coding | protein_coding | ENST00000382398 | 2 | 3383 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.408 | 0.478 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.262 | 68 | 62.2 | 1.09 | 0.00000321 | 711 |
| Missense in Polyphen | 9 | 6.9787 | 1.2896 | 70 | ||
| Synonymous | -0.740 | 27 | 22.5 | 1.20 | 0.00000138 | 221 |
| Loss of Function | 0.986 | 0 | 1.13 | 0.00 | 4.80e-8 | 13 |
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 | 0.00 | 0.00 |
| 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: Highly glycosylated atypical beta-defensin involved in several aspects of sperm function. Facilitates sperm transport in the female reproductive tract and contributes to sperm protection against immunodetection; both functions are probably implicating the negative surface charge provided by its O-linked oligosaccharides in the sperm glycocalyx. Involved in binding of sperm to oviductal epithelial cells to form a sperm reservoir until ovulation. Release from the sperm surface during capacitation and ovaluation by an elevation of oviductal fluid pH is unmasking other surface components and allows sperm to penetrate the cumulus matrix and bind to the zona pellucida of the oocyte (By similarity). In vitro has antimicrobial activity and may inhibit LPS-mediated inflammation (PubMed:19373462, PubMed:23229569). {ECO:0000250|UniProtKB:Q9BEE3, ECO:0000269|PubMed:19373462, ECO:0000269|PubMed:23229569}.;
- Disease
- DISEASE: Note=May be involved in infertility. Homozygosity for frameshift truncating mutations are associated with reduced sperm O-linked glycan content, impaired sperm mobility and a reduced live birth rate (PubMed:21775668, PubMed:25721098). However, for one common mutation the change in sperm sialic acid levels has been challenged (PubMed:26832966). {ECO:0000269|PubMed:21775668, ECO:0000269|PubMed:25721098, ECO:0000305|PubMed:26832966}.;
- Pathway
- Antimicrobial peptides;Innate Immune System;Immune System;Beta defensins;Defensins
(Consensus)
Intolerance Scores
- loftool
- 0.828
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.06
Haploinsufficiency Scores
- pHI
- 0.0127
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0718
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Defb22
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- single fertilization;innate immune response;defense response to Gram-negative bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide
- Cellular component
- extracellular region
- Molecular function