PRG3

proteoglycan 3, pro eosinophil major basic protein 2, the group of C-type lectin domain containing

Basic information

Region (hg38): 11:57376769-57381150

Links

ENSG00000156575 ∙ NCBI:10394 ∙ OMIM:606814 ∙ HGNC:9363 ∙ Uniprot:Q9Y2Y8 ∙ 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 PRG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRG3 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						0
missense			15	2		17
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in PRG3

This is a list of pathogenic ClinVar variants found in the PRG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57376857-G-A		not specified	Uncertain significance (Oct 12, 2022)
11-57376864-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-57376864-C-T		not specified	Likely benign (Nov 12, 2024)
11-57376881-T-C		not specified	Uncertain significance (May 10, 2023)
11-57376883-G-T			Likely benign (Dec 31, 2019)
11-57376908-C-T		not specified	Uncertain significance (Jul 12, 2022)
11-57377757-C-G		not specified	Uncertain significance (Sep 30, 2024)
11-57377770-G-T		not specified	Uncertain significance (Jul 09, 2024)
11-57378733-G-A		not specified	Uncertain significance (Dec 22, 2024)
11-57379559-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-57379574-C-T		not specified	Uncertain significance (Jun 02, 2024)
11-57379662-A-C		not specified	Uncertain significance (May 10, 2023)
11-57379682-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-57379711-G-T		not specified	Uncertain significance (Feb 06, 2024)
11-57379718-C-A		not specified	Uncertain significance (Apr 04, 2023)
11-57379723-T-A		not specified	Uncertain significance (Nov 20, 2024)
11-57379798-G-A		not specified	Likely benign (May 26, 2022)
11-57380653-T-C		not specified	Uncertain significance (Sep 03, 2024)
11-57380687-G-A		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRG3	protein_coding	protein_coding	ENST00000287143	5	4382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000334	0.833	125716	0	18	125734	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.451	133	119	1.12	0.00000606	1465
Missense in Polyphen		35	30.18	1.1597		392
Synonymous	-0.740	52	45.6	1.14	0.00000226	422
Loss of Function	1.23	7	11.5	0.608	4.90e-7	129

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	0.0000463	0.0000462
European (Non-Finnish)	0.000135	0.000132
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses similar cytotoxic and cytostimulatory activities to PRG2/MBP. In vitro, stimulates neutrophil superoxide production and IL8 release, and histamine and leukotriene C4 release from basophils. {ECO:0000269|PubMed:10318872}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.816
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.23

Haploinsufficiency Scores

• pHI: 0.0522
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0246

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Prg3
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: histamine biosynthetic process;negative regulation of translation;leukotriene biosynthetic process;neutrophil activation;superoxide anion generation;neutrophil degranulation;positive regulation of interleukin-8 biosynthetic process;basophil activation
• Cellular component: extracellular region;specific granule lumen;collagen-containing extracellular matrix;tertiary granule lumen
• Molecular function: extracellular matrix structural constituent conferring compression resistance;carbohydrate binding