C10orf90
protein-codingchromosome 10 open reading frame 90
Gene summary
Predicted to enable histone deacetylase binding activity and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle process; and response to ionizing radiation. Located in actin cytoskeleton; centrosome; and cytosol. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~373.7 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 C10orf90 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001350921.2. 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 | 5 | 5 | ||||
| missense | 11 | 1 | 3 | 15 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 9 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001337850.1 | 10 | MANE Select | |
| Ensembl | ENSP00000474558.3 | 10 | MANE Select | |
| RefSeq | NP_001004298.2 | 9 | Standard | |
| RefSeq | NP_001337851.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein polyubiquitination
- protein ubiquitination
- regulation of centriole replication
- protein stabilization
Molecular Function
- alpha-actinin binding
- ubiquitin protein ligase activity
Cellular Component
- nucleoplasm
- cytoplasm
- centrosome
- centriole
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000284694
- Coding exons
- 9
- Length
- 245514
- Individuals with no LoFs
- 125653
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 95
- Defined
- 125748
- p
- 0.000378
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.448 | 432 | 407 | 1.06 | 0.0000232 | 4548 |
| Missense (PolyPhen) | 103 | 103.76 | 0.99263 | 1249 | ||
| Synonymous | 0.545 | 156 | 165 | 0.946 | 0.0000100 | 1399 |
| Loss of Function | 0.692 | 24 | 28.0 | 0.859 | 0.00000135 | 353 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00044 | 0.00043 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00032 | 0.00031 | rare |
| South Asian | 0.0010 | 0.0010 | notable |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tumor suppressor that is required to sustain G2/M checkpoint after DNA damage. Mediates CDKN1A/p21 protein stability in a ubiquitin-independent manner (By similarity). May have a role in the assembly of primary cilia. {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.950
- RVIS EVS
- 0.8
- RVIS percentile EVS
- 87.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |