PCP2

Purkinje cell protein 2

Basic information

Region (hg38): 19:7631611-7633719

Links

ENSG00000174788 ∙ NCBI:126006 ∙ OMIM:619344 ∙ HGNC:30209 ∙ Uniprot:Q8IVA1 ∙ 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 PCP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCP2 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
missense			18	3	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	2

Variants in PCP2

This is a list of pathogenic ClinVar variants found in the PCP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7631729-C-T		not specified	Uncertain significance (Sep 25, 2024)
19-7631742-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-7631792-C-T			Likely benign (Aug 03, 2018)
19-7632404-C-T		not specified	Uncertain significance (May 23, 2023)
19-7632415-C-A		not specified	Uncertain significance (Oct 01, 2024)
19-7632440-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-7632449-C-T		not specified	Uncertain significance (Oct 18, 2021)
19-7632458-G-A		not specified	Uncertain significance (Jul 26, 2024)
19-7632479-T-C		not specified	Uncertain significance (May 13, 2024)
19-7632500-C-T		not specified	Uncertain significance (May 31, 2023)
19-7632502-G-A		not specified	Uncertain significance (May 06, 2024)
19-7632513-G-C		not specified	Uncertain significance (Aug 14, 2023)
19-7632516-C-G		not specified	Uncertain significance (Nov 17, 2023)
19-7632742-G-T		not specified	Uncertain significance (Oct 04, 2024)
19-7632773-G-A		not specified	Uncertain significance (May 16, 2024)
19-7632786-G-C		not specified	Uncertain significance (Aug 06, 2024)
19-7632826-C-A			Benign (Jun 26, 2018)
19-7632827-C-A		not specified	Uncertain significance (Jul 14, 2024)
19-7633409-C-G		not specified	Uncertain significance (May 12, 2024)
19-7633409-C-T		not specified	Likely benign (Oct 28, 2023)
19-7633412-C-T		not specified	Likely benign (Jun 21, 2023)
19-7633417-G-C		not specified	Uncertain significance (Jul 30, 2023)
19-7633434-C-T		not specified	Benign (Mar 29, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCP2	protein_coding	protein_coding	ENST00000311069	4	2138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000300	0.352	125663	0	23	125686	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.167	78	82.3	0.948	0.00000523	871
Missense in Polyphen		40	41.132	0.97248		454
Synonymous	0.562	29	33.1	0.876	0.00000226	265
Loss of Function	0.125	7	7.37	0.950	4.68e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000489	0.000489
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a cell-type specific modulator for G protein-mediated cell signaling. {ECO:0000250}.
• Pathway: Signaling by GPCR;Signal Transduction;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.484
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.170
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcp2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype

Gene ontology

• Biological process: rhodopsin mediated signaling pathway;regulation of catalytic activity
• Cellular component: neuronal cell body
• Molecular function: guanyl-nucleotide exchange factor activity;GTPase regulator activity