C22orf39
protein-codingchromosome 22 open reading frame 39
Gene summary
Predicted to be involved in negative regulation of long-term synaptic potentiation. Located in mitochondrion. [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 ~96.3 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 C22orf39 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_173793.5. 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_776154.4 | 3 | MANE Select | |
| Ensembl | ENSP00000382474.5 | 3 | MANE Select | |
| RefSeq | NP_001159714.2 | 3 | Standard | |
| Ensembl | ENSP00000382478.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000399562
- Coding exons
- 3
- Length
- 96865
- Individuals with no LoFs
- 125302
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 393
- Defined
- 125695
- p
- 0.00156
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.204 | 78 | 73.1 | 1.07 | 0.00000400 | 877 |
| Missense (PolyPhen) | 23 | 22.9 | 1.0044 | 306 | ||
| Synonymous | -0.674 | 34 | 29.4 | 1.16 | 0.00000149 | 266 |
| Loss of Function | -0.0656 | 7 | 6.82 | 1.03 | 3.90e-7 | 73 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0043 | 0.0038 | notable |
| Latino/Admixed American | 0.0038 | 0.0037 | notable |
| Ashkenazi Jewish | 0.0018 | 0.0017 | notable |
| East Asian | 0.000058 | 0.000054 | rare |
| Finnish | 0.00039 | 0.00037 | rare |
| European (Non-Finnish) | 0.0016 | 0.0015 | notable |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.0019 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |