LYZL4

lysozyme like 4, the group of Lysozymes, c-type

Basic information

Region (hg38): 3:42397083-42410610

Links

ENSG00000157093 ∙ NCBI:131375 ∙ OMIM:612750 ∙ HGNC:28387 ∙ Uniprot:Q96KX0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LYZL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYZL4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in LYZL4

This is a list of pathogenic ClinVar variants found in the LYZL4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-42397305-G-A		not specified	Uncertain significance (Apr 23, 2024)
3-42404049-G-A		not specified	Uncertain significance (May 18, 2023)
3-42404077-T-G		not specified	Uncertain significance (May 30, 2023)
3-42404110-T-C		not specified	Likely benign (Jul 05, 2023)
3-42404114-A-G			Benign (Mar 29, 2018)
3-42406903-G-A		not specified	Uncertain significance (Dec 15, 2023)
3-42406938-C-T		not specified	Uncertain significance (Jul 05, 2023)
3-42406939-G-A		not specified	Uncertain significance (May 04, 2023)
3-42406956-G-A		not specified	Uncertain significance (Jan 04, 2022)
3-42407142-T-A		not specified	Uncertain significance (Jun 18, 2021)
3-42407209-C-T		not specified	Uncertain significance (Jul 12, 2022)
3-42407212-C-G		not specified	Uncertain significance (Apr 08, 2024)
3-42407239-C-T		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYZL4	protein_coding	protein_coding	ENST00000287748	4	13523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.532	0.454	125740	0	2	125742	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.503	74	87.2	0.848	0.00000505	938
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0927
• hipred: N
• hipred_score: 0.146
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.208

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyzl4
• Phenotype: normal phenotype

Gene ontology

• Biological process: single fertilization;fertilization;defense response to bacterium;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
• Cellular component: acrosomal vesicle;extracellular space;nucleus;sperm flagellum
• Molecular function: lysozyme activity