PCP2

protein-coding

Purkinje cell protein 2

Gene summary

Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to act upstream of or within G protein-coupled opsin signaling pathway. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_174895.3

Inheritance

—

ClinVar variants

U:32B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr19:7,631,611-7,633,719

External References & Databases

Ensembl (ENSG00000174788)

Transcript & Mutation Effects

hg38 • Region Span ~2.1 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 PCP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174895.3. 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			1 clinvar			1
missense			30 clinvar	4 clinvar	1 clinvar	35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	32	4	1	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174895.3	RefSeq	NP_777555.1	4	MANE Select
ENST00000311069.6	Ensembl	ENSP00000310585.4	4	MANE Select
NM_001271830.2	RefSeq	NP_001258759.1	4	Standard
ENST00000598935.5	Ensembl	ENSP00000472761.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
G alpha (i) signalling events
GPCR downstream signalling

Biological Process

rhodopsin mediated signaling pathway
regulation of catalytic activity

Molecular Function

guanyl-nucleotide exchange factor activity
GTPase regulator activity

Cellular Component

neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311069
Coding exons: 4
Length: 2138
Individuals with no LoFs: 125663
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125686
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.167	78	82.3	0.948	0.00000523	871
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.00033	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as a cell-type specific modulator for G protein-mediated cell signaling. {ECO:0000250}.;

Recessive Scores

pRec: 0.162

Intolerance Scores

LoFtool: 0.484
RVIS EVS: 0.13
RVIS percentile EVS: 63.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.128

Gene Damage Prediction

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