LYZL1

lysozyme like 1, the group of Lysozymes, c-type

Basic information

Region (hg38): 10:29289061-29318328

Links

ENSG00000120563 ∙ NCBI:84569 ∙ ∙ HGNC:30502 ∙ Uniprot:Q6UWQ5 ∙ 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 LYZL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYZL1 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			10	3		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1		1	2
Total	0	0	11	4	1

Variants in LYZL1

This is a list of pathogenic ClinVar variants found in the LYZL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-29289127-G-A		not specified	Uncertain significance (Sep 14, 2022)
10-29289170-C-T		not specified	Uncertain significance (Feb 09, 2022)
10-29291854-G-A		not specified	Likely benign (Nov 29, 2021)
10-29291858-G-T		not specified	Uncertain significance (Oct 05, 2023)
10-29291916-G-A		not specified	Likely benign (Jul 26, 2022)
10-29291919-G-A		not specified	Uncertain significance (May 06, 2024)
10-29291938-G-A		not specified	Uncertain significance (Apr 17, 2024)
10-29291938-G-C		not specified	Uncertain significance (Jan 23, 2023)
10-29291962-C-T		not specified	Uncertain significance (Mar 26, 2024)
10-29292004-A-C		not specified	Uncertain significance (May 11, 2022)
10-29292013-C-T			Benign (Aug 15, 2017)
10-29292015-C-A			Benign (Aug 15, 2017)
10-29292575-G-A		not specified	Uncertain significance (Aug 28, 2023)
10-29292595-T-C			Likely benign (Aug 01, 2022)
10-29292632-C-T		not specified	Uncertain significance (Jun 22, 2021)
10-29292633-G-A		not specified	Likely benign (Dec 03, 2021)
10-29292655-C-G		not specified	Uncertain significance (Oct 25, 2023)
10-29292665-G-A		not specified	Uncertain significance (May 28, 2024)
10-29292668-G-A		not specified	Uncertain significance (Nov 03, 2022)
10-29311040-A-T		not specified	Uncertain significance (Nov 29, 2023)
10-29311051-G-T		not specified	Uncertain significance (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYZL1	protein_coding	protein_coding	ENST00000375500	5	29268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.72e-7	0.190	125708	0	23	125731	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0209	112	111	1.01	0.00000645	1260
Missense in Polyphen		26	23.329	1.1145		320
Synonymous	-0.902	56	48.0	1.17	0.00000335	363
Loss of Function	-0.105	9	8.67	1.04	3.66e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000572	0.0000462
European (Non-Finnish)	0.0000550	0.0000528
Middle Eastern	0.000109	0.000109
South Asian	0.000206	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Endohydrolysis of 1,4-alpha-D-glucosidic linkages in polysaccharides by alpha-amylase (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.478
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

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