LYZL4

protein-coding

lysozyme like 4, 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. LYZL4 is a member of a family of lysozyme-like genes (Zhang et al., 2005 [PubMed 16014814]).[supplied by OMIM, Apr 2009]

MANE transcript

NM_144634.4

Inheritance

—

ClinVar variants

U:27B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr3:42,397,083-42,410,610

External References & Databases

Ensembl (ENSG00000157093)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 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 LYZL4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144634.4. 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			27 clinvar	2 clinvar		29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	2	1	30

Loading ClinVar variants...

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_144634.4	RefSeq	NP_653235.1	4	MANE Select
ENST00000287748.8	Ensembl	ENSP00000287748.3	4	MANE Select
NM_001304386.2	RefSeq	NP_001291315.1	4	Standard
ENST00000441172.1	Ensembl	ENSP00000387897.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

single fertilization
fertilization
defense response to bacterium
defense response to Gram-negative bacterium
defense response to Gram-positive bacterium

Molecular Function

lysozyme activity

Cellular Component

acrosomal vesicle
extracellular space
nucleus
sperm flagellum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000287748
Coding exons: 4
Length: 13523
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125742
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.503	74	87.2	0.848	0.00000505	938
Missense (PolyPhen)		28	31.623	0.88544		395
Synonymous	0.483	29	32.5	0.892	0.00000186	273
Loss of Function	1.97	1	6.38	0.157	2.69e-7	80

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in fertilization (By similarity). Has no detectable bacteriolytic and lysozyme activities in vitro (By similarity). {ECO:0000250|UniProtKB:D4ABW7, ECO:0000250|UniProtKB:Q9D925}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.454
RVIS EVS: -0.01
RVIS percentile EVS: 53.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.208

Gene Damage Prediction

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