PCDH8

protocadherin 8, the group of Non-clustered protocadherins

Basic information

Region (hg38): 13:52842889-52848641

Links

ENSG00000136099 ∙ NCBI:5100 ∙ OMIM:603580 ∙ HGNC:8660 ∙ Uniprot:O95206 ∙ 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 PCDH8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH8 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				4	3	7
missense			87	4	3	94
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	87	8	6

Variants in PCDH8

This is a list of pathogenic ClinVar variants found in the PCDH8 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52844573-T-C		not specified	Uncertain significance (Oct 10, 2023)
13-52844591-G-A		not specified	Uncertain significance (Dec 14, 2023)
13-52844596-G-A			Benign (Dec 26, 2018)
13-52844628-C-T		not specified	Uncertain significance (Jan 25, 2023)
13-52844633-A-G		not specified	Uncertain significance (Aug 04, 2023)
13-52844719-A-G			Benign (Dec 31, 2019)
13-52844741-G-T		not specified	Uncertain significance (Mar 23, 2022)
13-52844743-C-G		not specified	Uncertain significance (Dec 25, 2024)
13-52844792-G-A		not specified	Uncertain significance (Feb 28, 2024)
13-52844817-T-C		not specified	Uncertain significance (Sep 22, 2023)
13-52844819-G-A		not specified	Uncertain significance (May 31, 2023)
13-52844835-G-T		not specified	Uncertain significance (Jan 03, 2024)
13-52844843-G-A		not specified	Uncertain significance (Jan 18, 2025)
13-52844862-C-T		not specified	Uncertain significance (Feb 09, 2023)
13-52844912-T-G		not specified	Uncertain significance (Oct 05, 2023)
13-52845463-T-C		not specified	Uncertain significance (Nov 29, 2021)
13-52845540-T-G		not specified	Uncertain significance (Aug 30, 2021)
13-52845628-T-C		not specified	Uncertain significance (Jan 07, 2025)
13-52845639-C-T			Likely benign (Jul 31, 2018)
13-52845808-C-T		not specified	Uncertain significance (Sep 08, 2024)
13-52845814-G-A		not specified	Uncertain significance (Sep 09, 2021)
13-52845823-G-A		not specified	Uncertain significance (May 18, 2022)
13-52845828-C-T		not specified	Uncertain significance (Feb 08, 2025)
13-52845842-G-C		not specified	Uncertain significance (Apr 07, 2023)
13-52845853-C-A		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH8	protein_coding	protein_coding	ENST00000377942	3	4667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000342	0.989	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	439	567	0.775	0.0000293	6634
Missense in Polyphen		87	156.15	0.55714		1836
Synonymous	0.581	244	256	0.954	0.0000141	2383
Loss of Function	2.26	11	22.6	0.487	9.77e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000920	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000126	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000538	0.0000527
Middle Eastern	0.000126	0.000109
South Asian	0.00121	0.00121
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent cell-adhesion protein (By similarity). May play a role in activity-induced synaptic reorganization underlying long term memory (By similarity). Could be involved in CDH2 internalization through TAOK2/p38 MAPK pathway. In hippocampal neurons, may play a role in the down-regulation of dendritic spines, maybe through its action on CDH2 endocytosis (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.173

Haploinsufficiency Scores

• pHI: 0.915
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.442

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh8
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: pcdh8
• Affected structure: pronephros
• Phenotype tag: abnormal
• Phenotype quality: cystic

Gene ontology

• Biological process: somitogenesis;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;cell-cell signaling;chemical synaptic transmission;morphogenesis of embryonic epithelium;regulation of synaptic membrane adhesion
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;dendrite;presynaptic membrane;glutamatergic synapse;integral component of postsynaptic membrane
• Molecular function: calcium ion binding