LYG2

protein-coding

lysozyme g2, the group of Lysozymes, g-type

Gene summary

The protein encoded by this gene contains a SLT domain, a protein domain present in bacterial lytic transglycosylase (SLT) and in eukaryotic lysozymes (GEWL). SLT domain catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyglucosamine (GlcNAc). [provided by RefSeq, Jul 2008]

MANE transcript

NM_175735.4

Inheritance

—

ClinVar variants

U:34B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.23

Max pathogenic AF

—

Genomic locus

chr2:99,242,246-99,255,666

External References & Databases

Ensembl (ENSG00000185674)

Transcript & Mutation Effects

hg38 • Region Span ~13.4 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 LYG2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_175735.4. 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			34 clinvar	1 clinvar		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	2	0	36

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_175735.4	RefSeq	NP_783862.2	5	MANE Select
ENST00000333017.7	Ensembl	ENSP00000327533.2	5	MANE Select
ENST00000409238.5	Ensembl	ENSP00000386939.1	5	Standard
ENST00000409679.5	Ensembl	ENSP00000386381.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidoglycan catabolic process
cell wall macromolecule catabolic process
defense response to bacterium
defense response to Gram-positive bacterium

Molecular Function

lysozyme activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333017
Coding exons: 5
Length: 13037
Individuals with no LoFs: 125619
Homozygous LoFs: 0
Heterozygous LoFs: 125
Defined: 125744
p: 0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.398	114	127	0.900	0.00000704	1400
Missense (PolyPhen)		38	43.603	0.8715		503
Synonymous	0.576	43	48.1	0.894	0.00000307	397
Loss of Function	-0.669	12	9.75	1.23	4.14e-7	109

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0027	0.0027	notable
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.00046	0.00046	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a potent antibacterial protein that may play a role in the innate immunity. {ECO:0000269|PubMed:21093056}.;

Intolerance Scores

LoFtool: 0.457
RVIS EVS: 0.44
RVIS percentile EVS: 77.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.268

Gene Damage Prediction

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