PGLYRP3

peptidoglycan recognition protein 3, the group of Peptidoglycan recognition proteins

Basic information

Region (hg38): 1:153297116-153312952

Links

ENSG00000159527

∙ NCBI:114771 ∙ OMIM:608197 ∙ HGNC:30014 ∙ Uniprot:Q96LB9 ∙ 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 PGLYRP3 gene.

not_specified (42 variants)
not_provided (6 variants)
PGLYRP3-associated_inflamatory_bowel_disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGLYRP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000052891.3. 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					3 clinvar	3
missense			40 clinvar	2 clinvar	2 clinvar	44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	2	5

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGLYRP3	protein_coding	protein_coding	ENST00000290722	7	12857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.61e-8	0.533	125669	0	79	125748	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.544	177	199	0.891	0.0000104	2224
Missense in Polyphen		60	67.844	0.88439		814
Synonymous	-0.678	94	86.0	1.09	0.00000537	681
Loss of Function	0.968	13	17.4	0.749	8.99e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000409	0.000409
Ashkenazi Jewish	0.00	0.00
East Asian	0.000980	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000980	0.000979
South Asian	0.000672	0.000653
Other	0.000657	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Pattern receptor that binds to murein peptidoglycans (PGN) of Gram-positive bacteria. Has bactericidal activity towards Gram-positive bacteria. May kill Gram-positive bacteria by interfering with peptidoglycan biosynthesis. Binds also to Gram- negative bacteria, and has bacteriostatic activity towards Gram- negative bacteria. Plays a role in innate immunity. {ECO:0000269|PubMed:16354652}.;
Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec: 0.105

Intolerance Scores

loftool: 0.853
rvis_EVS: 1.2
rvis_percentile_EVS: 92.98

Haploinsufficiency Scores

pHI: 0.109
hipred: N
hipred_score: 0.112
ghis: 0.409

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.180

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

Gene name: Pglyrp3
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); digestive/alimentary phenotype; immune system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: pattern recognition receptor signaling pathway;peptidoglycan catabolic process;detection of bacterium;antimicrobial humoral response;killing of cells of other organism;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;defense response to Gram-positive bacterium;positive regulation of cytolysis in other organism;antimicrobial humoral immune response mediated by antimicrobial peptide
Cellular component: extracellular region;extracellular space;membrane;protein-containing complex
Molecular function: zinc ion binding;N-acetylmuramoyl-L-alanine amidase activity;peptidoglycan receptor activity;peptidoglycan binding;protein heterodimerization activity