PRG2
Basic information
Region (hg38): 11:57386780-57390650
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRG2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002728.6. 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 | 1 | |||||
missense | 31 | 34 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 31 | 3 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PRG2 | protein_coding | protein_coding | ENST00000311862 | 5 | 3864 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000191 | 0.730 | 125519 | 0 | 63 | 125582 | 0.000251 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.315 | 115 | 125 | 0.921 | 0.00000717 | 1422 |
Missense in Polyphen | 28 | 32.321 | 0.8663 | 422 | ||
Synonymous | 0.0194 | 45 | 45.2 | 0.996 | 0.00000253 | 426 |
Loss of Function | 0.966 | 7 | 10.4 | 0.676 | 5.09e-7 | 117 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00348 | 0.00348 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000884 | 0.00000880 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000983 | 0.0000980 |
Other | 0.000329 | 0.000327 |
dbNSFP
Source:
- Function
- FUNCTION: Cytotoxin and helminthotoxin. Also induces non-cytolytic histamine release from human basophils. Involved in antiparasitic defense mechanisms and immune hypersensitivity reactions. The proform acts as a proteinase inhibitor, reducing the activity of PAPPA. {ECO:0000269|PubMed:10913121}.;
- Pathway
- Asthma - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- 0.846
- rvis_EVS
- -0.11
- rvis_percentile_EVS
- 45.26
Haploinsufficiency Scores
- pHI
- 0.251
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.413
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.580
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prg2
- Phenotype
- immune system phenotype; respiratory system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- defense response to bacterium;neutrophil degranulation
- Cellular component
- extracellular region;transport vesicle;collagen-containing extracellular matrix;extracellular exosome;ficolin-1-rich granule lumen
- Molecular function
- heparin binding;extracellular matrix structural constituent conferring compression resistance;carbohydrate binding