PROCA1

protein-coding

protein interacting with cyclin A1

Gene summary

Enables cyclin binding activity. Predicted to be involved in arachidonate secretion and phospholipid metabolic process. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001366301.1

Inheritance

—

ClinVar variants

U:55B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr17:28,703,197-28,711,888

External References & Databases

Ensembl (ENSG00000167525)

Transcript & Mutation Effects

hg38 • Region Span ~8.7 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 PROCA1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 62

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366301.1. 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				1 clinvar	1 clinvar	2
missense			54 clinvar	10 clinvar	1 clinvar	65
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	55	11	3	69

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366301.1	RefSeq	NP_001353230.1	5	MANE Select
ENST00000682792.1	Ensembl	ENSP00000507242.1	5	MANE Select
NM_001304949.2	RefSeq	NP_001291878.1	5	Standard
NM_001304951.2	RefSeq	NP_001291880.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

phospholipid metabolic process
arachidonic acid secretion

Molecular Function

phospholipase A2 activity
cyclin binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301039
Coding exons: 4
Length: 8658
Individuals with no LoFs: 125683
Homozygous LoFs: 0
Heterozygous LoFs: 65
Defined: 125748
p: 0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.418	207	191	1.09	0.0000107	2199
Missense (PolyPhen)		71	66.655	1.0652		846
Synonymous	-0.713	87	78.9	1.10	0.00000490	627
Loss of Function	0.328	12	13.3	0.903	7.34e-7	157

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00094	0.00092	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00016	0.00016	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.746
RVIS EVS: -0.16
RVIS percentile EVS: 41.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.615

Gene Damage Prediction

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