LYG1

protein-coding

lysozyme g1, the group of Lysozymes, g-type

Gene summary

Predicted to enable lysozyme activity. Predicted to be involved in defense response to Gram-positive bacterium. Predicted to be active in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_174898.3

Inheritance

—

ClinVar variants

U:21B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr2:99,284,238-99,304,742

External References & Databases

Ensembl (ENSG00000144214)

Transcript & Mutation Effects

hg38 • Region Span ~20.5 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 LYG1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 24

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174898.3. 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						0
missense			19 clinvar	5 clinvar		24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	21	5	0	26

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174898.3	RefSeq	NP_777558.1	5	MANE Select
ENST00000308528.9	Ensembl	ENSP00000311320.4	5	MANE Select
NM_001371380.1	RefSeq	NP_001358309.1	5	Standard
ENST00000409448.1	Ensembl	ENSP00000386923.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidoglycan catabolic process
cell wall macromolecule catabolic process

Molecular Function

lysozyme activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409448
Coding exons: 5
Length: 20505
Individuals with no LoFs: 125489
Homozygous LoFs: 1
Heterozygous LoFs: 256
Defined: 125746
p: 0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.579	92	109	0.844	0.00000554	1260
Missense (PolyPhen)		25	34.214	0.73069		439
Synonymous	0.692	36	41.7	0.864	0.00000221	386
Loss of Function	0.727	8	10.5	0.758	5.34e-7	112

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0024	0.0024	notable
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.0016	0.0016	notable
South Asian	0.000033	0.000033	rare
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.545
RVIS EVS: -0.05
RVIS percentile EVS: 49.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.134

Gene Damage Prediction

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