GNLY
protein-codinggranulysin
Gene summary
The product of this gene is a member of the saposin-like protein (SAPLIP) family and is located in the cytotoxic granules of T cells, which are released upon antigen stimulation. This protein is present in cytotoxic granules of cytotoxic T lymphocytes and natural killer cells, and it has antimicrobial activity against M. tuberculosis and other organisms. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
- LAG2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GNLY variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006433.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 28 | 1 | 1 | 30 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 29 | 1 | 3 | 33 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006424.2 | 5 | MANE Select | |
| Ensembl | ENSP00000263863.5 | 5 | MANE Select | |
| RefSeq | NP_001289687.1 | 6 | Standard | |
| RefSeq | NP_036615.2 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Allograft Rejection
- Antimicrobial peptides
- Innate Immune System
- Immune System
Biological Process
- intracellular defense response
- antimicrobial humoral response
- killing of cells of other organism
- defense response to bacterium
- defense response to fungus
Cellular Component
- extracellular region
- extracellular space
- cytolytic granule
- phagocytic vesicle lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263863
- Coding exons
- 5
- Length
- 13680
- Individuals with no LoFs
- 125355
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 393
- Defined
- 125748
- p
- 0.00156
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.137 | 87 | 90.7 | 0.960 | 0.00000561 | 922 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00052 | 0.00049 | rare |
| Latino/Admixed American | 0.00059 | 0.00058 | rare |
| Ashkenazi Jewish | 0.0014 | 0.0014 | notable |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00056 | 0.00055 | rare |
| European (Non-Finnish) | 0.0029 | 0.0028 | notable |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0.0022 | 0.0021 | notable |
dbNSFP Gene Annotations
Source:
- 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.;
Intolerance Scores
- LoFtool
- 0.833
- RVIS EVS
- 1.1
- RVIS percentile EVS
- 91.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0000137