LYG1

lysozyme g1, the group of Lysozymes, g-type

Basic information

Region (hg38): 2:99284238-99304742

Links

ENSG00000144214 ∙ NCBI:129530 ∙ ∙ HGNC:27014 ∙ Uniprot:Q8N1E2 ∙ 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 LYG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYG1 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						0
missense			8	2		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	8	2	0

Variants in LYG1

This is a list of pathogenic ClinVar variants found in the LYG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-99284460-T-C		not specified	Uncertain significance (Jan 03, 2024)
2-99284468-G-T		not specified	Uncertain significance (Sep 23, 2023)
2-99284472-C-T		not specified	Likely benign (Feb 21, 2024)
2-99284763-T-G		not specified	Uncertain significance (Dec 27, 2023)
2-99284799-T-C		not specified	Likely benign (Mar 25, 2024)
2-99291307-C-A		not specified	Uncertain significance (Jul 12, 2023)
2-99291389-C-T		not specified	Uncertain significance (Feb 03, 2022)
2-99292556-C-T		not specified	Likely benign (Jun 16, 2023)
2-99292557-G-A		not specified	Uncertain significance (Jul 20, 2021)
2-99292584-G-C		not specified	Uncertain significance (Oct 26, 2022)
2-99292636-C-G		not specified	Uncertain significance (Apr 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYG1	protein_coding	protein_coding	ENST00000409448	5	20505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000313	0.581	125489	1	256	125746	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.579	92	109	0.844	0.00000554	1260
Missense in Polyphen		25	34.214	0.73069		439
Synonymous	0.692	36	41.7	0.864	0.00000221	386
Loss of Function	0.727	8	10.5	0.758	5.34e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000326
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00245	0.00245
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.00164	0.00163
Middle Eastern	0.00245	0.00245
South Asian	0.0000327	0.0000327
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.545
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.0516
• hipred: N
• hipred_score: 0.112
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyg1

Gene ontology

• Biological process: peptidoglycan catabolic process;cell wall macromolecule catabolic process
• Cellular component: extracellular region
• Molecular function: lysozyme activity