PGLYRP2

protein-coding

peptidoglycan recognition protein 2, the group of Peptidoglycan recognition proteins

Gene summary

This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. This protein hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in bacterial cell wall glycopeptides, and thus may play a scavenger role by digesting biologically active peptidoglycan into biologically inactive fragments. [provided by RefSeq, Sep 2011]

MANE transcript

NM_052890.4

Inheritance

—

ClinVar variants

U:68B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr19:15,468,645-15,498,956

External References & Databases

Ensembl (ENSG00000161031)

Transcript & Mutation Effects

hg38 • Region Span ~30.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PGLYRP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052890.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			67 clinvar	6 clinvar	1 clinvar	74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	68	6	1	75

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052890.4	RefSeq	NP_443122.3	5	MANE Select
ENST00000340880.5	Ensembl	ENSP00000345968.4	5	MANE Select
NM_001363546.1	RefSeq	NP_001350475.1	4	Standard
ENST00000292609.8	Ensembl	ENSP00000292609.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Antimicrobial peptides
Innate Immune System
Immune System

Biological Process

peptide amidation
pattern recognition receptor signaling pathway
peptidoglycan catabolic process
detection of bacterium
antimicrobial humoral response

Molecular Function

zinc ion binding
N-acetylmuramoyl-L-alanine amidase activity
peptidoglycan receptor activity
peptidoglycan binding

Cellular Component

extracellular region
extracellular space
membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340880
Coding exons: 5
Length: 30312
Individuals with no LoFs: 125682
Homozygous LoFs: 1
Heterozygous LoFs: 65
Defined: 125748
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.07	276	331	0.835	0.0000187	3614
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00079	0.00075	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.146

Intolerance Scores

LoFtool: 0.841
RVIS EVS: 1.47
RVIS percentile EVS: 95.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.128

Gene Damage Prediction

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