GON7
protein-codingGON7 subunit of KEOPS complex, the group of KEOPS complex
Gene summary
Involved in tRNA threonylcarbamoyladenosine modification. Located in nucleolus and nucleoplasm. Part of EKC/KEOPS complex. Implicated in Galloway-Mowat syndrome. [provided by Alliance of Genome Resources, Jun 2026]
- C14orf142
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0030471
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Neurologic; Renal
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
Comments: Renal transplant has been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GON7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032490.5. 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 | 2 | 2 | ||||
| missense | 1 | 1 | 2 | |||
| nonsense | 1 | 1 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 0 | 1 | 4 | 0 | 7 |
Highest pathogenic variant AF is 0.000004106141
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115879.2 | 2 | MANE Select | |
| Ensembl | ENSP00000306320.4 | 2 | MANE Select | |
| Ensembl | ENSP00000451114.1 | 2 | Standard | |
| Ensembl | ENSP00000540097.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- EKC/KEOPS complex
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000306954
- Coding exons
- 2
- Length
- 4201
- Individuals with no LoFs
- 124724
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 124730
- p
- 0.0000241
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.305 | 54 | 60.7 | 0.890 | 0.00000297 | 652 |
| Missense (PolyPhen) | 16 | 15.36 | 1.0417 | 177 | ||
| Synonymous | 0.613 | 23 | 27.1 | 0.850 | 0.00000140 | 198 |
| Loss of Function | 0.147 | 3 | 3.29 | 0.912 | 1.39e-7 | 39 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the EKC/KEOPS complex that is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. The complex is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. GON7 likely plays a supporting role to the catalytic subunit OSGEP in the complex. {ECO:0000250|UniProtKB:P46984, ECO:0000305|PubMed:27903914}.;
Intolerance Scores
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 56.25
Essentials
- Essential (gene trap)
- N