OVCA2

protein-coding

OVCA2 serine hydrolase domain containing

Gene summary

Enables carboxylesterase activity. Involved in response to retinoic acid. Located in cytosol and nucleoplasm. Biomarker of ovarian cancer. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_080822.3

Inheritance

—

ClinVar variants

U:60B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.29

Max pathogenic AF

—

Genomic locus

chr17:2,042,022-2,043,425

External References & Databases

Ensembl (ENSG00000262664)

Transcript & Mutation Effects

hg38 • Region Span ~1.4 kb

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GenCC 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 OVCA2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080822.3. 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				4 clinvar		4
missense			60 clinvar	1 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	60	5	0	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080822.3	RefSeq	NP_543012.1	2	MANE Select
ENST00000572195.3	Ensembl	ENSP00000461388.1	2	MANE Select
ENST00001140332.1	Ensembl	ENSP00000814265.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to retinoic acid

Molecular Function

hydrolase activity

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000572195
Coding exons: 2
Length: 1398
Individuals with no LoFs: 124417
Homozygous LoFs: 0
Heterozygous LoFs: 98
Defined: 124515
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.38	166	123	1.35	0.00000654	1425
Missense (PolyPhen)		72	50.783	1.4178		589
Synonymous	-1.96	74	55.4	1.34	0.00000306	499
Loss of Function	-0.660	8	6.22	1.29	3.12e-7	69

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.0023	0.0018	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.00016	0.00016	rare
Other	0.00020	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.393
RVIS EVS: -0.21
RVIS percentile EVS: 38.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.131

Gene Damage Prediction

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