REG3A
Basic information
Region (hg38): 2:79157003-79159753
Previous symbols: [ "PAP" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the REG3A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002580.3. 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 | 4 | |||||
| missense | 18 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 18 | 7 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| REG3A | protein_coding | protein_coding | ENST00000393878 | 5 | 2748 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000629 | 0.746 | 125724 | 0 | 12 | 125736 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.203 | 103 | 97.4 | 1.06 | 0.00000517 | 1122 |
| Missense in Polyphen | 18 | 28.863 | 0.62363 | 375 | ||
| Synonymous | -0.601 | 44 | 39.2 | 1.12 | 0.00000210 | 337 |
| Loss of Function | 0.947 | 6 | 9.08 | 0.661 | 3.86e-7 | 101 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000521 | 0.000521 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Bactericidal C-type lectin which acts exclusively against Gram-positive bacteria and mediates bacterial killing by binding to surface-exposed carbohydrate moieties of peptidoglycan. Regulates keratinocyte proliferation and differentiation after skin injury via activation of EXTL3-PI3K-AKT signaling pathway. {ECO:0000269|PubMed:16931762}.;
- Pathway
- Purine metabolism;Antimicrobial peptides;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- loftool
- 0.910
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.12
Haploinsufficiency Scores
- pHI
- 0.195
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.468
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.643
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Reg3b
- Phenotype
- homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- acute-phase response;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;multicellular organism development;cell population proliferation;positive regulation of cell population proliferation;positive regulation of keratinocyte proliferation;antimicrobial humoral response;response to peptide hormone;cell wall disruption in other organism;negative regulation of keratinocyte differentiation;antimicrobial humoral immune response mediated by antimicrobial peptide;positive regulation of wound healing
- Cellular component
- extracellular region;extracellular space;cytoplasm
- Molecular function
- transmembrane signaling receptor activity;protein binding;carbohydrate binding;identical protein binding;peptidoglycan binding;oligosaccharide binding