GNL2
protein-codingG protein nucleolar 2
Gene summary
Enables RNA binding activity. Predicted to be involved in ribosome biogenesis. Located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.1 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 GNL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013285.3. 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 | 109 | 3 | 112 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 112 | 4 | 0 | 116 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037417.1 | 16 | MANE Select | |
| Ensembl | ENSP00000362153.3 | 16 | MANE Select | |
| RefSeq | NP_001310552.1 | 17 | Standard | |
| RefSeq | NP_001310553.1 | 12 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gnl2 | Danio rerio | Structure: Muller cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ribosome biogenesis in eukaryotes - Homo sapiens (human)
Biological Process
- biological_process
- ribosome biogenesis
Molecular Function
- RNA binding
- GTPase activity
- GTP binding
Cellular Component
- nucleus
- nucleolus
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373062
- Coding exons
- 16
- Length
- 29120
- Individuals with no LoFs
- 125679
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 69
- Defined
- 125748
- p
- 0.000274
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.276 | 394 | 410 | 0.962 | 0.0000230 | 4811 |
| Missense (PolyPhen) | 122 | 146.31 | 0.83385 | 1694 | ||
| Synonymous | -0.0909 | 139 | 138 | 1.01 | 0.00000722 | 1358 |
| Loss of Function | 3.85 | 15 | 41.9 | 0.358 | 0.00000239 | 480 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00057 | 0.00055 | rare |
| Latino/Admixed American | 0.00050 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00025 | 0.00025 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: GTPase that associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation (By similarity). May promote cell proliferation possibly by increasing p53/TP53 protein levels, and consequently those of its downstream product CDKN1A/p21, and decreasing RPL23A protein levels (PubMed:26203195). {ECO:0000250, ECO:0000269|PubMed:26203195}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.771
- RVIS EVS
- -1
- RVIS percentile EVS
- 8.54
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.0619
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |