PCDHB16

protocadherin beta 16, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141182387-141186226

Links

ENSG00000272674 ∙ NCBI:57717 ∙ OMIM:606345 ∙ HGNC:14546 ∙ Uniprot:Q9NRJ7 ∙ 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 PCDHB16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB16 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				3		3
missense			86	8		94
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	87	11	0

Variants in PCDHB16

This is a list of pathogenic ClinVar variants found in the PCDHB16 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141182572-T-A		not specified	Uncertain significance (Feb 19, 2025)
5-141182582-A-G		not specified	Likely benign (Mar 24, 2023)
5-141182624-G-A		not specified	Uncertain significance (Dec 21, 2022)
5-141182677-G-A		not specified	Uncertain significance (Nov 23, 2024)
5-141182690-T-C		not specified	Uncertain significance (Apr 12, 2024)
5-141182705-G-A		not specified	Likely benign (Dec 17, 2024)
5-141182728-A-T		not specified	Uncertain significance (Nov 10, 2022)
5-141182743-C-G		not specified	Uncertain significance (Jul 26, 2022)
5-141182754-G-T		not specified	Uncertain significance (Apr 04, 2024)
5-141182772-C-G		not specified	Uncertain significance (Nov 09, 2021)
5-141182813-T-C		not specified	Uncertain significance (Jul 22, 2024)
5-141182843-T-C		not specified	Uncertain significance (Jun 18, 2021)
5-141182874-T-G		not specified	Uncertain significance (Jan 19, 2025)
5-141182881-G-T		not specified	Uncertain significance (Dec 28, 2022)
5-141182897-C-T		not specified	Uncertain significance (Mar 31, 2022)
5-141182912-A-T		not specified	Uncertain significance (Dec 12, 2023)
5-141182987-C-A		not specified	Uncertain significance (Sep 17, 2021)
5-141183002-T-C		not specified	Uncertain significance (Jul 15, 2021)
5-141183047-G-T		not specified	Uncertain significance (Dec 22, 2024)
5-141183071-A-C		not specified	Uncertain significance (Jun 16, 2024)
5-141183079-C-G		not specified	Uncertain significance (May 13, 2024)
5-141183088-C-T		not specified	Uncertain significance (Mar 14, 2025)
5-141183156-G-C		not specified	Uncertain significance (Jun 06, 2023)
5-141183171-G-C		not specified	Uncertain significance (Feb 17, 2024)
5-141183200-C-T			Likely benign (Jan 01, 2025)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Recessive Scores

• pRec: 0.198

Intolerance Scores

• loftool: 0.706
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.71

Haploinsufficiency Scores

• pHI: 0.0799
• hipred: N
• hipred_score: 0.199

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Pcdhb17

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;chemical synaptic transmission;synapse assembly;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
• Cellular component: integral component of plasma membrane;integral component of membrane
• Molecular function: calcium ion binding