C15orf40
protein-codingchromosome 15 open reading frame 40
Gene summary
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 ~23.2 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 C15orf40 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144597.3. 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 | 0 | |||||
| missense | 3 | 3 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 | 3 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653198.2 | 4 | MANE Select | |
| Ensembl | ENSP00000307071.6 | 4 | MANE Select | |
| RefSeq | NP_001153585.1 | 3 | Standard | |
| RefSeq | NP_001153586.1 | 4 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000451195
- Coding exons
- 5
- Length
- 23201
- Individuals with no LoFs
- 125586
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 162
- Defined
- 125748
- p
- 0.000644
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.625 | 106 | 89.4 | 1.19 | 0.00000428 | 1036 |
| Missense (PolyPhen) | 14 | 19.691 | 0.71097 | 262 | ||
| Synonymous | -1.39 | 46 | 35.5 | 1.30 | 0.00000182 | 364 |
| Loss of Function | 1.66 | 2 | 6.58 | 0.304 | 2.76e-7 | 88 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.0015 | 0.0015 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000072 | 0.000070 | rare |
| South Asian | 0.0033 | 0.0033 | notable |
| Other | 0.00034 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0807
Intolerance Scores
- LoFtool
- 0.223
- RVIS EVS
- 1.04
- RVIS percentile EVS
- 91.21
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |