LYZL2

protein-coding

lysozyme like 2, the group of Lysozymes, c-type

Gene summary

Lysozymes (see LYZ; MIM 153450), especially C-type lysozymes, are well-recognized bacteriolytic factors widely distributed in the animal kingdom and play a mainly protective role in host defense. LYZL2 is a member of a family of lysozyme-like genes (Zhang et al., 2005 [PubMed 16014814]).[supplied by OMIM, Apr 2009]

MANE transcript

NM_183058.3

Inheritance

—

ClinVar variants

U:25B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.13

Max pathogenic AF

—

Genomic locus

chr10:30,611,779-30,629,762

External References & Databases

Ensembl (ENSG00000151033)

Transcript & Mutation Effects

hg38 • Region Span ~18.0 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 LYZL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_183058.3. 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				1 clinvar		1
missense			25 clinvar	2 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	3	0	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_183058.3	RefSeq	NP_898881.3	4	MANE Select
ENST00000647634.2	Ensembl	ENSP00000497408.1	4	MANE Select
ENST00000375318.4	Ensembl	ENSP00000364467.2	5	Standard
ENST00001091360.1	Ensembl	ENSP00000761166.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

metabolic process
defense response to Gram-negative 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: ENST00000375318
Coding exons: 5
Length: 17974
Individuals with no LoFs: 125043
Homozygous LoFs: 10
Heterozygous LoFs: 690
Defined: 125743
p: 0.00279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.771	139	116	1.20	0.00000681	1251
Missense (PolyPhen)		46	38.15	1.2058		462
Synonymous	-0.574	58	52.7	1.10	0.00000394	360
Loss of Function	-0.360	10	8.84	1.13	3.74e-7	104

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.022	0.021	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.942
RVIS EVS: 0.08
RVIS percentile EVS: 60.31

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.139

Gene Damage Prediction

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