OC90

otoconin 90

Basic information

Region (hg38): 8:132024216-132059382

Previous symbols: [ "PLA2L" ]

Links

ENSG00000253117 ∙ NCBI:729330 ∙ OMIM:601658 ∙ HGNC:8100 ∙ Uniprot:Q02509 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OC90 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OC90 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	0

Variants in OC90

This is a list of pathogenic ClinVar variants found in the OC90 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-132024497-G-A		not specified	Uncertain significance (Dec 30, 2023)
8-132024515-C-T		not specified	Uncertain significance (Mar 29, 2024)
8-132024527-C-T		not specified	Likely benign (Nov 10, 2022)
8-132024599-C-A		not specified	Uncertain significance (Jun 10, 2024)
8-132024626-T-G		not specified	Uncertain significance (May 08, 2023)
8-132024632-C-G		not specified	Uncertain significance (Dec 16, 2022)
8-132024633-T-C		not specified	Likely benign (Aug 02, 2021)
8-132024644-G-T		not specified	Uncertain significance (Nov 09, 2021)
8-132024650-G-A		not specified	Uncertain significance (Sep 12, 2023)
8-132024670-T-A		not specified	Uncertain significance (Nov 21, 2023)
8-132024687-G-A		not specified	Uncertain significance (May 03, 2024)
8-132024705-C-A		not specified	Uncertain significance (Sep 12, 2023)
8-132024748-C-G		not specified	Uncertain significance (Oct 26, 2021)
8-132029105-G-A		not specified	Uncertain significance (Dec 03, 2021)
8-132029132-C-G		not specified	Uncertain significance (Feb 03, 2022)
8-132029137-C-G		not specified	Uncertain significance (Mar 29, 2022)
8-132031903-C-T		not specified	Uncertain significance (Sep 26, 2023)
8-132031906-C-T		not specified	Uncertain significance (Jul 09, 2021)
8-132031954-G-A		not specified	Uncertain significance (Mar 12, 2024)
8-132031960-G-A		not specified	Uncertain significance (May 30, 2023)
8-132032019-C-G		not specified	Uncertain significance (Oct 10, 2023)
8-132033064-A-T		not specified	Uncertain significance (Jul 12, 2023)
8-132033102-T-A		not specified	Uncertain significance (Apr 07, 2022)
8-132033153-T-C		not specified	Uncertain significance (Dec 21, 2021)
8-132034826-G-A		not specified	Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OC90	protein_coding	protein_coding	ENST00000254627	13	35161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.68e-12	0.114	124510	1	136	124647	0.000550

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	301	256	1.18	0.0000128	3088
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000426	0.000426
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.000513	0.000511
European (Non-Finnish)	0.000878	0.000867
Middle Eastern	0.000112	0.000111
South Asian	0.000450	0.000392
Other	0.000335	0.000165

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: phospholipases (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.373
• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.98

Haploinsufficiency Scores

• pHI: 0.0490
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0223

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Oc90
• Phenotype: hearing/vestibular/ear phenotype; normal phenotype

Zebrafish Information Network

• Gene name: oc90
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: phospholipid metabolic process;biological_process;lipid catabolic process;otolith mineralization;otolith development;arachidonic acid secretion
• Cellular component: cellular_component;extracellular matrix
• Molecular function: molecular_function;phospholipase A2 activity;structural molecule activity;calcium ion binding