PGLYRP2

peptidoglycan recognition protein 2, the group of Peptidoglycan recognition proteins

Basic information

Region (hg38): 19:15468645-15498956

Links

ENSG00000161031 ∙ NCBI:114770 ∙ OMIM:608199 ∙ HGNC:30013 ∙ Uniprot:Q96PD5 ∙ 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 PGLYRP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGLYRP2 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			21	2	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	1

Variants in PGLYRP2

This is a list of pathogenic ClinVar variants found in the PGLYRP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15468716-T-C		not specified	Uncertain significance (Aug 23, 2021)
19-15468726-A-C		not specified	Likely benign (Aug 16, 2021)
19-15469700-G-T		not specified	Uncertain significance (Dec 14, 2023)
19-15469781-T-C		not specified	Uncertain significance (Oct 04, 2022)
19-15469826-C-T		not specified	Uncertain significance (Nov 01, 2022)
19-15469873-C-T		not specified	Uncertain significance (Aug 22, 2022)
19-15471938-A-C		not specified	Uncertain significance (Nov 30, 2022)
19-15471996-A-G		not specified	Uncertain significance (May 24, 2024)
19-15472034-A-G		not specified	Uncertain significance (Jan 18, 2022)
19-15475615-T-C		not specified	Uncertain significance (Oct 24, 2023)
19-15475645-A-C		not specified	Uncertain significance (Jul 25, 2023)
19-15475714-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-15475793-G-A		not specified	Uncertain significance (Apr 13, 2022)
19-15475903-C-T		not specified	Uncertain significance (Jun 16, 2024)
19-15475969-C-A			Benign (Mar 29, 2018)
19-15475972-C-G		not specified	Uncertain significance (Oct 27, 2021)
19-15475996-C-T		not specified	Uncertain significance (Apr 12, 2022)
19-15476075-C-T		not specified	Uncertain significance (May 26, 2022)
19-15476177-C-T		not specified	Uncertain significance (May 23, 2023)
19-15476231-C-A		not specified	Uncertain significance (Dec 20, 2023)
19-15476240-T-C		not specified	Uncertain significance (Nov 06, 2023)
19-15476266-C-T		not specified	Likely benign (Feb 16, 2023)
19-15476267-G-T		not specified	Uncertain significance (May 13, 2024)
19-15476345-C-A		not specified	Uncertain significance (Jun 12, 2023)
19-15476345-C-G		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGLYRP2	protein_coding	protein_coding	ENST00000340880	5	30312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.68e-11	0.146	125682	1	65	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	276	331	0.835	0.0000187	3614
Missense in Polyphen		74	104.6	0.70749		1164
Synonymous	1.90	115	144	0.798	0.00000818	1305
Loss of Function	0.603	18	21.0	0.858	0.00000126	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000666	0.000666
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000789	0.000752
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a scavenger role by digesting biologically active peptidoglycan (PGN) into biologically inactive fragments. Has no direct bacteriolytic activity. {ECO:0000269|PubMed:14506276}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.841
• rvis_EVS: 1.47
• rvis_percentile_EVS: 95.25

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.188

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pglyrp2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; immune system phenotype; skeleton phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: peptide amidation;pattern recognition receptor signaling pathway;peptidoglycan catabolic process;detection of bacterium;antimicrobial humoral response;negative regulation of interferon-gamma production;negative regulation of natural killer cell differentiation involved in immune response;growth of symbiont in host;innate immune response;regulation of inflammatory response;defense response to Gram-positive bacterium
• Cellular component: extracellular region;extracellular space;membrane;extracellular exosome
• Molecular function: zinc ion binding;N-acetylmuramoyl-L-alanine amidase activity;peptidoglycan receptor activity;peptidoglycan binding