PCP4

Purkinje cell protein 4

Basic information

Region (hg38): 21:39867438-39929397

Links

ENSG00000183036

∙ NCBI:5121 ∙ OMIM:601629 ∙ HGNC:8742 ∙ Uniprot:P48539 ∙ 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 PCP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCP4 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						0
missense			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in PCP4

This is a list of pathogenic ClinVar variants found in the PCP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-39929004-G-A		not specified	Uncertain significance (Dec 05, 2023)	3210424

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCP4	protein_coding	protein_coding	ENST00000328619	3	62080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00217	0.534	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.613	24	34.1	0.704	0.00000180	409
Missense in Polyphen		5	9.2612	0.53989		121
Synonymous	0.628	8	10.6	0.755	5.41e-7	106
Loss of Function	0.204	4	4.47	0.896	2.74e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Functions as a modulator of calcium-binding by calmodulin. Thereby, regulates calmodulin activity and the different processes it controls (PubMed:19106096, PubMed:23204517, PubMed:27876793). For instance, may play a role in neuronal differentiation through activation of calmodulin-dependent kinase signaling pathways (PubMed:21491429). {ECO:0000269|PubMed:19106096, ECO:0000269|PubMed:21491429, ECO:0000269|PubMed:23204517, ECO:0000269|PubMed:27876793}.;

Intolerance Scores

loftool
rvis_EVS: 0.08
rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

pHI: 0.223
hipred: N
hipred_score: 0.278
ghis: 0.569

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.283

Mouse Genome Informatics

Gene name: Pcp4
Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: positive regulation of neuron differentiation;calmodulin dependent kinase signaling pathway
Cellular component: nucleus;cytosol;protein-containing complex
Molecular function: calcium ion binding;protein binding;calmodulin binding