PGLYRP4

peptidoglycan recognition protein 4, the group of Peptidoglycan recognition proteins

Basic information

Region (hg38): 1:153330119-153348841

Links

ENSG00000163218 ∙ NCBI:57115 ∙ OMIM:608198 ∙ HGNC:30015 ∙ Uniprot:Q96LB8 ∙ 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 PGLYRP4 gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGLYRP4 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in PGLYRP4

This is a list of pathogenic ClinVar variants found in the PGLYRP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153330806-C-G		not specified	Uncertain significance (Apr 08, 2022)
1-153330814-G-T		not specified	Uncertain significance (Jan 05, 2022)
1-153330826-A-C		not specified	Uncertain significance (Nov 09, 2021)
1-153330831-C-T		not specified	Likely benign (Apr 13, 2022)
1-153330850-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-153330888-A-G		not specified	Uncertain significance (Nov 14, 2023)
1-153330922-G-T		not specified	Uncertain significance (Sep 14, 2023)
1-153337277-C-T		not specified	Uncertain significance (Aug 22, 2023)
1-153340436-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-153340448-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-153340448-G-T		not specified	Uncertain significance (Jan 02, 2024)
1-153340507-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-153341637-G-T		not specified	Uncertain significance (Jan 23, 2023)
1-153341639-T-A		not specified	Uncertain significance (Oct 27, 2022)
1-153341708-G-C		not specified	Uncertain significance (Jun 02, 2023)
1-153341713-C-T		not specified	Uncertain significance (Nov 30, 2022)
1-153343101-C-T		not specified	Uncertain significance (Aug 30, 2022)
1-153343130-G-T		not specified	Uncertain significance (Nov 23, 2021)
1-153345192-G-C		not specified	Uncertain significance (Mar 06, 2023)
1-153345223-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-153345349-C-T		not specified	Uncertain significance (Dec 19, 2023)
1-153345358-G-A		not specified	Likely benign (Jul 11, 2023)
1-153346185-G-A		not specified	Uncertain significance (Nov 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGLYRP4	protein_coding	protein_coding	ENST00000359650	8	18721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.94e-15	0.00267	125402	1	345	125748	0.00138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00366	210	210	0.999	0.0000107	2409
Missense in Polyphen		67	73.778	0.90812		928
Synonymous	-0.730	98	89.2	1.10	0.00000488	770
Loss of Function	-0.897	20	16.1	1.24	6.86e-7	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00279	0.00279
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000166	0.000163
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.00197	0.00196
Middle Eastern	0.000166	0.000163
South Asian	0.000686	0.000653
Other	0.00163	0.00163

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: 0.0909

Intolerance Scores

• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.58

Haploinsufficiency Scores

• pHI: 0.0854
• hipred: N
• hipred_score: 0.112
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.425

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pglyrp4
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism 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

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;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 space;membrane;protein-containing complex
• Molecular function: zinc ion binding;N-acetylmuramoyl-L-alanine amidase activity;peptidoglycan receptor activity;peptidoglycan binding;protein heterodimerization activity