PGLYRP3

protein-coding

peptidoglycan recognition protein 3, 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. These proteins are part of the innate immune system and recognize peptidoglycan, a ubiquitous component of bacterial cell walls. This antimicrobial protein binds to murein peptidoglycans of Gram-positive bacteria. [provided by RefSeq, Oct 2014]

MANE transcript

NM_052891.3

Inheritance

—

ClinVar variants

U:50B:7

Top phenotype

PGLYRP3-associated inflamatory bowel disease

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr1:153,297,116-153,312,952

External References & Databases

Ensembl (ENSG00000159527)

Transcript & Mutation Effects

hg38 • Region Span ~15.8 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 PGLYRP3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 6

PGLYRP3-associated inflamatory bowel diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052891.3. 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					3 clinvar	3
missense			49 clinvar	2 clinvar	2 clinvar	53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	50	2	5	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052891.3	RefSeq	NP_443123.1	7	MANE Select
ENST00000683862.1	Ensembl	ENSP00000507327.1	7	MANE Select
ENST00000290722.1	Ensembl	ENSP00000290722.1	7	Standard
ENST00000290722.2	Ensembl	ENSP00000290722.1	7	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

pattern recognition receptor signaling pathway
peptidoglycan catabolic process
detection of bacterium
antimicrobial humoral response
killing of cells of other organism

Molecular Function

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

Cellular Component

extracellular region
extracellular space
membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290722
Coding exons: 7
Length: 12857
Individuals with no LoFs: 125669
Homozygous LoFs: 0
Heterozygous LoFs: 79
Defined: 125748
p: 0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.544	177	199	0.891	0.0000104	2224
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00098	0.00098	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00067	0.00065	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.853
RVIS EVS: 1.2
RVIS percentile EVS: 92.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.180

Gene Damage Prediction

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