C2orf69
protein-codingchromosome 2 open reading frame 69
Gene summary
Involved in oxidative phosphorylation. Located in mitochondrion. Implicated in combined oxidative phosphorylation deficiency 53. [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 ~44.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0030378
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Biochemical; Cardiovascular; Gastrointestinal; Neurologic
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to C2orf69 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_153689.6. 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 | 14 | 14 | ||||
| missense | 9 | 5 | 14 | |||
| nonsense | 1 | 1 | 2 | |||
| start loss | 1 | 1 | ||||
| frameshift | 4 | 2 | 6 | |||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 5 | 2 | 11 | 19 | 0 | 37 |
Highest pathogenic variant AF is 0.000008682246
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_710156.3 | 2 | MANE Select | |
| Ensembl | ENSP00000312770.5 | 2 | MANE Select | |
| Ensembl | ENSP00000791475.1 | 3 | Standard | |
| Ensembl | ENSP00000793784.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000319974
- Coding exons
- 2
- Length
- 44680
- Individuals with no LoFs
- 124595
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 124601
- p
- 0.0000241
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.15 | 164 | 211 | 0.778 | 0.0000101 | 2544 |
| Missense (PolyPhen) | 30 | 59.781 | 0.50183 | 792 | ||
| Synonymous | 0.217 | 76 | 78.4 | 0.969 | 0.00000368 | 729 |
| Loss of Function | 2.07 | 5 | 13.1 | 0.383 | 6.36e-7 | 159 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000027 | 0.000027 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.144
- RVIS EVS
- 0.39
- RVIS percentile EVS
- 75.87
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 |