PRG2

proteoglycan 2, pro eosinophil major basic protein, the group of C-type lectin domain containing

Basic information

Region (hg38): 11:57386780-57390650

Links

ENSG00000186652NCBI:5553OMIM:605601HGNC:9362Uniprot:P13727AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRG2 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
31
clinvar
3
clinvar
34
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 31 3 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PRG2protein_codingprotein_codingENST00000311862 53864
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001910.7301255190631255820.000251
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3151151250.9210.000007171422
Missense in Polyphen2832.3210.8663422
Synonymous0.01944545.20.9960.00000253426
Loss of Function0.966710.40.6765.09e-7117

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003480.00348
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008840.00000880
Middle Eastern0.000.00
South Asian0.00009830.0000980
Other0.0003290.000327

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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