GON4L
protein-codinggon-4 like, the group of Myb/SANT domain containing
Gene summary
Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within B cell differentiation. Located in nuclear body. [provided by Alliance of Genome Resources, Jul 2025]
- GON4
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~109.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0700092
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0100038
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GON4L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001282860.2. 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 | 4 | 28 | 1 | 33 | ||
| missense | 19 | 9 | 28 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | 3 | 5 | ||
| splice donor/acceptor (+/-2bp) | 1 | 11 | 12 | |||
| Total | 2 | 1 | 38 | 37 | 1 | 79 |
Highest pathogenic variant AF is 0.0001834246
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001269789.1 | 31 | MANE Select | |
| Ensembl | ENSP00000357315.1 | 31 | MANE Select | |
| RefSeq | NP_001269785.1 | 31 | Standard | |
| RefSeq | NP_001269787.1 | 31 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gon4l | Danio rerio | Structure: nucleate erythrocyte Quality: immature abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- B cell differentiation
- negative regulation of transcription, DNA-templated
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA binding
- transcription corepressor activity
Cellular Component
- nucleus
- nucleoplasm
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000437809
- Coding exons
- 31
- Length
- 109684
- Individuals with no LoFs
- 125694
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 54
- Defined
- 125748
- p
- 0.000215
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.65 | 984 | 1.14e+3 | 0.863 | 0.0000606 | 14719 |
| Missense (PolyPhen) | 278 | 335.93 | 0.82755 | 4402 | ||
| Synonymous | -0.513 | 435 | 422 | 1.03 | 0.0000217 | 4368 |
| Loss of Function | 7.13 | 19 | 93.3 | 0.204 | 0.00000501 | 1222 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00023 | 0.00023 | rare |
| Ashkenazi Jewish | 0.0014 | 0.0014 | notable |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00024 | 0.00023 | rare |
| European (Non-Finnish) | 0.00016 | 0.00015 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Has transcriptional repressor activity, probably as part of a complex with YY1, SIN3A AND HDAC1. Required for B cell lymphopoiesis. {ECO:0000250|UniProtKB:Q9DB00}.;
Recessive Scores
- pRec
- 0.0872
Intolerance Scores
- LoFtool
- 0.572
- RVIS EVS
- -1.36
- RVIS percentile EVS
- 4.54
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.237
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |