PCDH20

protein-coding

protocadherin 20, the group of Non-clustered protocadherins

Gene summary

This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]

MANE transcript

NM_022843.4

Inheritance

—

ClinVar variants

U:131B:7

Top phenotype

—

Max pathogenic AF

—

Genomic locus

chr13:61,409,685-61,415,849

External References & Databases

Ensembl (ENSG00000280165)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 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 PCDH20 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022843.4. 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						0
missense			131 clinvar	6 clinvar		137
nonsense						0
start loss				1 clinvar		1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	131	7	0	138

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022843.4	RefSeq	NP_073754.2	2	MANE Select
ENST00000409204.5	Ensembl	ENSP00000387250.3	2	MANE Select
ENST00001131854.1	Ensembl	ENSP00000812453.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion
homophilic cell adhesion via plasma membrane adhesion molecules

Molecular Function

RNA binding
calcium ion binding

Cellular Component

integral component of plasma membrane

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.760

Gene Damage Prediction

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