PROCA1

protein interacting with cyclin A1

Basic information

Region (hg38): 17:28703197-28711888

Links

ENSG00000167525 ∙ NCBI:147011 ∙ OMIM:617376 ∙ HGNC:28600 ∙ Uniprot:Q8NCQ7 ∙ 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 PROCA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PROCA1 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				1	1	2
missense			30	8	1	39
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	9	3

Variants in PROCA1

This is a list of pathogenic ClinVar variants found in the PROCA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28703565-A-G		not specified	Uncertain significance (Jan 09, 2025)
17-28703583-G-T		not specified	Uncertain significance (Nov 12, 2021)
17-28703589-G-T		not specified	Uncertain significance (Jan 04, 2025)
17-28703592-T-C		not specified	Uncertain significance (Feb 15, 2023)
17-28703611-T-TG			Benign (Dec 31, 2019)
17-28703656-T-G		not specified	Uncertain significance (Jan 26, 2025)
17-28703675-T-G			Likely benign (Jul 05, 2018)
17-28703688-A-G		not specified	Uncertain significance (Jan 17, 2024)
17-28703719-G-C		not specified	Uncertain significance (Jul 30, 2023)
17-28703722-C-T		not specified	Uncertain significance (Feb 22, 2023)
17-28703734-C-T		not specified	Uncertain significance (Jan 24, 2025)
17-28703743-C-G		not specified	Uncertain significance (Oct 12, 2024)
17-28703745-A-C		not specified	Uncertain significance (Nov 05, 2021)
17-28703815-C-T		not specified	Uncertain significance (Jul 30, 2023)
17-28703845-G-C		not specified	Uncertain significance (Jan 17, 2024)
17-28703851-T-C		not specified	Uncertain significance (Jun 27, 2023)
17-28703879-T-G		not specified	Uncertain significance (Feb 26, 2025)
17-28703886-T-G		not specified	Uncertain significance (Jul 21, 2021)
17-28703927-T-C			Benign (Jan 25, 2018)
17-28703928-T-C		not specified	Uncertain significance (Apr 24, 2024)
17-28703982-G-C		not specified	Uncertain significance (Dec 08, 2023)
17-28703992-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-28704033-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-28704052-C-T			Benign (Jan 25, 2018)
17-28704082-C-T		not specified	Uncertain significance (Nov 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PROCA1	protein_coding	protein_coding	ENST00000301039	4	8658

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.46e-8	0.217	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.418	207	191	1.09	0.0000107	2199
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000623	0.000614
Ashkenazi Jewish	0.000111	0.0000992
East Asian	0.000940	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000240	0.000237
Middle Eastern	0.000940	0.000925
South Asian	0.000163	0.000163
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.746
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.615

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Proca1

Gene ontology

• Biological process: phospholipid metabolic process;arachidonic acid secretion
• Molecular function: phospholipase A2 activity;cyclin binding