LYZ

lysozyme, the group of Lysozymes, c-type

Basic information

Region (hg38): 12:69348380-69354234

Links

ENSG00000090382 ∙ NCBI:4069 ∙ OMIM:153450 ∙ HGNC:6740 ∙ Uniprot:P61626 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial visceral amyloidosis (Strong), mode of inheritance: AD
• ALys amyloidosis (Supportive), mode of inheritance: AD
• familial visceral amyloidosis (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amyloidosis, systemic nonneuropathic	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Gastrointestinal; Renal	8464497; 15745733; 21988333
The treatment of amyloidosis differs depending on the genetic cause (and genetic diagnosis may additionally help avoid relatively high-risk treatment regimens), and in lysozyme amyloidosis, liver and renal transplantation may be beneficial, but it is not clear that early (genetic) diagnosis would be beneficial

ClinVar

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

• Familial visceral amyloidosis, Ostertag type (50 variants)
• not provided (14 variants)
• not specified (3 variants)
• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYZ 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				2		2
missense	2		8	3	2	15
nonsense			1	1	1	3
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			23	2	13	38
Total	2	0	33	8	16

Variants in LYZ

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

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

Position	Type	Phenotype	Significance	ClinVar
12-69348408-C-T		Familial visceral amyloidosis, Ostertag type	Benign (Jan 13, 2018)
12-69348418-C-G		Familial visceral amyloidosis, Ostertag type	Benign (Jan 07, 2024)
12-69348448-G-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
12-69348493-AC-A		Familial visceral amyloidosis, Ostertag type	Uncertain significance (Oct 16, 2018)
12-69348498-G-C			Likely benign (Oct 18, 2022)
12-69348503-G-A		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
12-69348553-A-G			Likely benign (Oct 03, 2023)
12-69350122-A-T		Familial visceral amyloidosis, Ostertag type	Benign (Feb 26, 2018)
12-69350127-G-A		Familial visceral amyloidosis, Ostertag type • not specified	Conflicting classifications of pathogenicity (Jan 17, 2024)
12-69350146-C-T		not specified • Familial visceral amyloidosis, Ostertag type	Uncertain significance (Jan 17, 2024)
12-69350159-A-G			Uncertain significance (Dec 19, 2023)
12-69350170-G-C		AMYLOIDOSIS, HEREDITARY SYSTEMIC 5	Pathogenic (Nov 01, 1999)
12-69350180-C-G		not specified • Familial visceral amyloidosis, Ostertag type	Uncertain significance (Jan 14, 2023)
12-69350192-T-C		AMYLOIDOSIS, HEREDITARY SYSTEMIC 5	Pathogenic (Apr 08, 1993)
12-69350194-T-A		AMYLOIDOSIS, HEREDITARY SYSTEMIC 5	Pathogenic (May 01, 2003)
12-69350201-T-C			Uncertain significance (Feb 20, 2022)
12-69350215-T-A		Familial visceral amyloidosis, Ostertag type	Pathogenic (Dec 30, 2022)
12-69350215-T-C		Familial visceral amyloidosis, Ostertag type	Pathogenic (Apr 23, 2019)
12-69350234-C-A		Familial visceral amyloidosis, Ostertag type	Benign/Likely benign (Jan 24, 2024)
12-69350240-G-A		Familial visceral amyloidosis, Ostertag type	Uncertain significance (Mar 25, 2022)
12-69350243-C-G		Familial visceral amyloidosis, Ostertag type	Likely benign (Jan 13, 2018)
12-69350257-C-A		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
12-69352267-G-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
12-69353154-G-A			Uncertain significance (Jan 02, 2024)
12-69353164-G-C			Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYZ	protein_coding	protein_coding	ENST00000261267	4	5894

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000341	0.205	125672	0	74	125746	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.732	65	83.9	0.775	0.00000459	963
Missense in Polyphen		10	20.936	0.47764		272
Synonymous	0.0192	28	28.1	0.995	0.00000138	284
Loss of Function	-0.201	8	7.41	1.08	4.13e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000528	0.000528
Ashkenazi Jewish	0.00	0.00
East Asian	0.00212	0.00212
Finnish	0.00	0.00
European (Non-Finnish)	0.000149	0.000141
Middle Eastern	0.00212	0.00212
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte- macrophage system and enhance the activity of immunoagents.
• Disease: DISEASE: Amyloidosis 8 (AMYL8) [MIM:105200]: A form of hereditary generalized amyloidosis. Clinical features include extensive visceral amyloid deposits, renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash. There is no involvement of the nervous system. {ECO:0000269|PubMed:8464497}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Salivary secretion - Homo sapiens (human);Macrophage markers;Macrophage markers;Neutrophil degranulation;Antimicrobial peptides;Innate Immune System;Immune System;C-MYB transcription factor network (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.660
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.0521
• hipred: N
• hipred_score: 0.146
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyz2
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; neoplasm; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; hematopoietic system 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); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: retina homeostasis;inflammatory response;antimicrobial humoral response;cytolysis;killing of cells of other organism;defense response to bacterium;neutrophil degranulation;cellular protein metabolic process;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
• Cellular component: extracellular region;extracellular space;azurophil granule lumen;specific granule lumen;extracellular exosome;tertiary granule lumen
• Molecular function: lysozyme activity;identical protein binding