PRG2

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

Basic information

Region (hg38): 11:57386779-57390650

Links

ENSG00000186652 ∙ NCBI:5553 ∙ OMIM:605601 ∙ HGNC:9362 ∙ Uniprot:P13727 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (12 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.

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					1	1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	1

Variants in PRG2

This is a list of pathogenic ClinVar variants found in the PRG2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-57387499-T-A		not specified	Uncertain significance (Aug 15, 2023)
11-57387518-C-G		not specified	Uncertain significance (Jun 30, 2022)
11-57387805-C-A		not specified	Uncertain significance (Nov 01, 2022)
11-57387849-A-T		not specified	Uncertain significance (May 24, 2023)
11-57387853-G-A		not specified	Uncertain significance (Mar 11, 2024)
11-57387861-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-57388588-T-A		not specified	Uncertain significance (Jan 04, 2022)
11-57388623-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-57388656-T-C		not specified	Likely benign (Jan 17, 2024)
11-57388663-T-A		not specified	Uncertain significance (Dec 14, 2021)
11-57388669-T-C		not specified	Uncertain significance (Jun 11, 2021)
11-57389053-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-57389054-G-A		not specified	Uncertain significance (Feb 02, 2024)
11-57389093-T-G		not specified	Uncertain significance (Jul 28, 2021)
11-57389117-G-C		not specified	Uncertain significance (Aug 29, 2022)
11-57389185-C-T		not specified	Uncertain significance (Nov 05, 2021)
11-57389189-C-T		not specified	Uncertain significance (Oct 20, 2023)
11-57389208-T-C			Benign (Jun 30, 2017)
11-57389228-G-T		not specified	Uncertain significance (Dec 27, 2023)
11-57389230-G-T		not specified	Uncertain significance (Jan 09, 2024)
11-57389258-C-T		not specified	Uncertain significance (Nov 22, 2021)
11-57389272-A-T		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

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: 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

	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