OC90

Chr 8

otoconin 90

Also known as: PLA2L

NCBI Gene: 729330 ENSG00000253117 UniProt: Q02509 OMIM: 601658

The protein is a major component of otoconia (calcium carbonate structures in the inner ear) that acts as a scaffold for biomineralization by sequestering calcium and forming interconnecting fibrils between otoconia crystals. Mutations cause autosomal recessive benign recurrent vertigo, characterized by episodes of vertigo due to defective otoconia formation in the vestibular system. The gene shows minimal constraint against loss-of-function variants, consistent with its role in a non-life-threatening vestibular condition.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable calcium ion binding activity; calcium-dependent phospholipase A2 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, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 1.27

Clinical Summary— OC90

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

86 VUS of 93 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.27LOEUF

pLI 0.000

Z-score 0.57

OE 0.87 (0.60–1.27)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.01Z-score

OE missense 1.18 (1.07–1.30)

301 obs / 255.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.87 (0.60–1.27)

0≤0.351.4

Missense OE?1.18 (1.07–1.30)

0≤0.61.4

Synonymous OE?1.28

0≤1.21.6

LoF obs/exp: 19 / 21.9Missense obs/exp: 301 / 255.5Syn Z: -2.15

ClinVar Variant Classifications

93 submitted variants in ClinVar

ClinVar

Classification Summary

VUS86

Likely Benign6

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	86	86
Likely Benign	6	6
Benign	0	0
Total	92	92

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

55 pathogenic / likely-pathogenic (of 68) ClinVar copy-number / structural variants overlap OC90 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →