LYZL2

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

Basic information

Region (hg38): 10:30611779-30629762

Links

ENSG00000151033 ∙ NCBI:119180 ∙ OMIM:612748 ∙ HGNC:29613 ∙ Uniprot:Q7Z4W2 ∙ 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 LYZL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYZL2 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	12	3	0

Variants in LYZL2

This is a list of pathogenic ClinVar variants found in the LYZL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-30611971-T-C		not specified	Likely benign (Nov 15, 2021)
10-30611983-T-C		not specified	Uncertain significance (Jun 18, 2021)
10-30626122-C-A		not specified	Uncertain significance (Aug 10, 2023)
10-30626134-T-C		not specified	Uncertain significance (Jul 06, 2021)
10-30626149-C-T		not specified	Likely benign (May 03, 2023)
10-30626218-T-C		not specified	Uncertain significance (Jan 30, 2024)
10-30626218-T-G		not specified	Uncertain significance (Apr 17, 2024)
10-30626250-C-T			Likely benign (Jul 01, 2022)
10-30626251-G-A		not specified	Uncertain significance (Feb 16, 2023)
10-30626816-C-A		not specified	Uncertain significance (May 03, 2023)
10-30626821-G-A		not specified	Uncertain significance (Mar 27, 2023)
10-30626862-C-G		not specified	Uncertain significance (Jun 05, 2023)
10-30626864-C-T		not specified	Uncertain significance (Jan 20, 2023)
10-30626924-C-T		not specified	Uncertain significance (Dec 15, 2023)
10-30626940-C-A		not specified	Uncertain significance (Aug 30, 2021)
10-30629608-C-T		not specified	Uncertain significance (Aug 16, 2021)
10-30629658-A-C		not specified	Uncertain significance (Nov 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYZL2	protein_coding	protein_coding	ENST00000375318	5	17974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.12e-7	0.106	125043	10	690	125743	0.00279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.771	139	116	1.20	0.00000681	1251
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000709	0.000709
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.0217	0.0215
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.942
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.139

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyzl1
• Phenotype: normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: metabolic process;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
• Cellular component: extracellular region
• Molecular function: lysozyme activity