PCDH20

protocadherin 20, the group of Non-clustered protocadherins

Basic information

Region (hg38): 13:61409685-61415849

Links

ENSG00000280165 ∙ NCBI:64881 ∙ OMIM:614449 ∙ HGNC:14257 ∙ Uniprot:Q8N6Y1 ∙ 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 PCDH20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH20 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			76	4		80
nonsense						0
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	76	5	0

Variants in PCDH20

This is a list of pathogenic ClinVar variants found in the PCDH20 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-61411259-T-A		not specified	Uncertain significance (Sep 14, 2022)
13-61411268-T-A		not specified	Uncertain significance (Jul 11, 2023)
13-61411305-G-T		not specified	Uncertain significance (Sep 12, 2023)
13-61411311-T-C		not specified	Uncertain significance (Mar 01, 2023)
13-61411388-A-G		not specified	Uncertain significance (Jan 12, 2024)
13-61411400-G-C		not specified	Uncertain significance (Jan 24, 2025)
13-61411436-G-A		not specified	Uncertain significance (Feb 06, 2023)
13-61411454-T-C		not specified	Uncertain significance (Aug 31, 2022)
13-61411472-G-A		not specified	Uncertain significance (Apr 01, 2024)
13-61411503-C-G		not specified	Uncertain significance (Jan 29, 2025)
13-61411505-A-G		not specified	Uncertain significance (Nov 17, 2023)
13-61411539-C-T		not specified	Uncertain significance (Aug 17, 2021)
13-61411556-C-T		not specified	Uncertain significance (Jan 09, 2024)
13-61411593-T-C		not specified	Uncertain significance (Mar 22, 2023)
13-61411608-C-T		not specified	Uncertain significance (Mar 10, 2025)
13-61411659-C-T		not specified	Uncertain significance (Feb 09, 2023)
13-61411673-G-A		not specified	Uncertain significance (Apr 15, 2024)
13-61411675-C-G		not specified	Uncertain significance (Jan 23, 2024)
13-61411764-C-T		not specified	Uncertain significance (Feb 22, 2025)
13-61411775-C-T		not specified	Uncertain significance (Apr 06, 2023)
13-61411880-G-A		not specified	Uncertain significance (Feb 28, 2023)
13-61411922-G-C		not specified	Uncertain significance (Oct 03, 2022)
13-61411928-G-A		not specified	Uncertain significance (Sep 24, 2024)
13-61411964-A-G		not specified	Uncertain significance (Nov 21, 2022)
13-61412050-A-T		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential calcium-dependent cell-adhesion protein.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.231
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.27

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.737

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.760

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh20

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules
• Cellular component: integral component of plasma membrane
• Molecular function: RNA binding;calcium ion binding