GNLY

granulysin

Basic information

Region (hg38): 2:85685175-85698852

Previous symbols: [ "LAG2" ]

Links

ENSG00000115523 ∙ NCBI:10578 ∙ OMIM:188855 ∙ HGNC:4414 ∙ Uniprot:P22749 ∙ 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 GNLY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNLY 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			8		1	9
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	3

Variants in GNLY

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

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

Position	Type	Phenotype	Significance	ClinVar
2-85694426-C-T			Benign (May 08, 2018)
2-85694429-G-A			Benign (Apr 28, 2020)
2-85694432-C-T		not specified	Uncertain significance (Dec 02, 2022)
2-85695332-C-G		not specified	Uncertain significance (Aug 12, 2024)
2-85695345-T-C			Benign (Apr 24, 2018)
2-85695346-G-A		not specified	Uncertain significance (Jun 26, 2024)
2-85695348-G-C		not specified	Uncertain significance (Jul 02, 2024)
2-85695356-A-G		not specified	Uncertain significance (Jan 23, 2024)
2-85695381-T-G		not specified	Uncertain significance (Jun 05, 2023)
2-85695398-C-T		not specified	Uncertain significance (Aug 09, 2021)
2-85695413-A-T		not specified	Uncertain significance (Dec 09, 2024)
2-85695959-G-T		not specified	Uncertain significance (Jun 18, 2021)
2-85696016-T-C		not specified	Uncertain significance (Sep 14, 2022)
2-85697540-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-85697633-C-G		not specified	Uncertain significance (Oct 11, 2024)
2-85697633-C-T		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNLY	protein_coding	protein_coding	ENST00000263863	5	13680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.69e-9	0.0497	125355	0	393	125748	0.00156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.137	87	90.7	0.960	0.00000561	922
Missense in Polyphen		17	25.187	0.67494		267
Synonymous	0.383	35	38.0	0.921	0.00000239	298
Loss of Function	-0.707	11	8.74	1.26	4.70e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00108
Ashkenazi Jewish	0.00142	0.00139
East Asian	0.0000544	0.0000544
Finnish	0.000562	0.000554
European (Non-Finnish)	0.00286	0.00279
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.00215	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Antimicrobial protein that kills intracellular pathogens. Active against a broad range of microbes, including Gram-positive and Gram-negative bacteria, fungi, and parasites. Kills Mycobacterium tuberculosis.
• Pathway: Allograft Rejection;Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Intolerance Scores

• loftool: 0.833
• rvis_EVS: 1.1
• rvis_percentile_EVS: 91.96

Haploinsufficiency Scores

• pHI: 0.358
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000137

Gene ontology

• Biological process: intracellular defense response;antimicrobial humoral response;killing of cells of other organism;defense response to bacterium;defense response to fungus;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: extracellular region;extracellular space;cytolytic granule;phagocytic vesicle lumen