OC90
protein-codingotoconin 90
Gene summary
Predicted to enable calcium ion binding activity and phospholipid binding activity. Predicted to be involved in otolith mineralization; phosphatidylcholine metabolic process; and phosphatidylglycerol metabolic process. Predicted to be located in extracellular region. Predicted to be active in extracellular matrix. [provided by Alliance of Genome Resources, Jun 2026]
- PLA2L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~35.2 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 OC90 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080399.3. 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 | 86 | 6 | 92 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 86 | 6 | 0 | 92 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073868.2 | 13 | MANE Select | |
| Ensembl | ENSP00000254627.3 | 13 | MANE Select | |
| Ensembl | ENSP00000802728.1 | 13 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| oc90 | Danio rerio | Structure: otolith Quality: aplastic abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- phospholipases
Biological Process
- phospholipid metabolic process
- biological_process
- lipid catabolic process
- otolith mineralization
- otolith development
Molecular Function
- molecular_function
- phospholipase A2 activity
- structural molecule activity
- calcium ion binding
Cellular Component
- cellular_component
- extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254627
- Coding exons
- 13
- Length
- 35161
- Individuals with no LoFs
- 124510
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 136
- Defined
- 124647
- p
- 0.000550
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.01 | 301 | 256 | 1.18 | 0.0000128 | 3088 |
| Missense (PolyPhen) | 107 | 86.391 | 1.2386 | 1122 | ||
| Synonymous | -2.15 | 125 | 98.0 | 1.28 | 0.00000522 | 930 |
| Loss of Function | 0.573 | 19 | 21.9 | 0.868 | 0.00000108 | 264 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00036 | 0.00035 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00051 | 0.00051 | rare |
| European (Non-Finnish) | 0.00088 | 0.00087 | rare |
| South Asian | 0.00045 | 0.00039 | rare |
| Other | 0.00034 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Major protein of the otoconia, a calcium carbonate structure in the saccule and utricle of the ear. Together with OTOL1, acts as a scaffold for otoconia biomineralization: sequesters calcium and forms interconnecting fibrils between otoconia that are incorporated into the calcium crystal structure. Together with OTOL1, modulates calcite crystal morphology and growth kinetics. It is unlikely that this protein has phospholipase A2 activity. {ECO:0000250|UniProtKB:Q9Z0L3}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- LoFtool
- 0.373
- RVIS EVS
- 0.45
- RVIS percentile EVS
- 77.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0223
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |