PCDHB3

protocadherin beta 3, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141100473-141103827

Links

ENSG00000113205 ∙ NCBI:56132 ∙ OMIM:606329 ∙ HGNC:8688 ∙ Uniprot:Q9Y5E6 ∙ 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 PCDHB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB3 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			60	2		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	2	0

Variants in PCDHB3

This is a list of pathogenic ClinVar variants found in the PCDHB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141100722-C-G		not specified	Uncertain significance (Apr 07, 2022)
5-141100737-T-A		not specified	Uncertain significance (Aug 19, 2024)
5-141100744-G-A		not specified	Uncertain significance (Nov 13, 2024)
5-141100789-A-G		not specified	Uncertain significance (Sep 20, 2024)
5-141100809-C-G		not specified	Uncertain significance (Mar 06, 2023)
5-141100986-C-A		not specified	Uncertain significance (Mar 25, 2024)
5-141100998-G-A		not specified	Likely benign (Nov 21, 2022)
5-141101025-G-A		not specified	Uncertain significance (Oct 27, 2021)
5-141101047-T-A		not specified	Uncertain significance (Dec 24, 2024)
5-141101064-C-T		not specified	Uncertain significance (Dec 24, 2024)
5-141101167-C-T		not specified	Uncertain significance (Dec 07, 2024)
5-141101226-G-A		not specified	Uncertain significance (Sep 26, 2024)
5-141101262-C-A		not specified	Uncertain significance (May 17, 2023)
5-141101299-G-A		not specified	Uncertain significance (Dec 04, 2024)
5-141101311-C-T		not specified	Uncertain significance (Nov 03, 2022)
5-141101370-G-A		not specified	Uncertain significance (Jul 02, 2024)
5-141101455-T-C		not specified	Uncertain significance (Dec 24, 2024)
5-141101472-G-A		not specified	Uncertain significance (Oct 04, 2022)
5-141101492-T-A		not specified	Uncertain significance (Jul 20, 2021)
5-141101514-C-A		not specified	Uncertain significance (Jul 06, 2021)
5-141101526-C-G		not specified	Uncertain significance (Jan 19, 2024)
5-141101619-G-A		not specified	Uncertain significance (Aug 19, 2024)
5-141101649-A-G		not specified	Uncertain significance (Nov 25, 2024)
5-141101671-A-G		not specified	Uncertain significance (Dec 09, 2024)
5-141101742-C-G		not specified	Likely benign (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB3	protein_coding	protein_coding	ENST00000231130	1	3173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.59e-7	0.409	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.158	468	478	0.980	0.0000306	5094
Missense in Polyphen		99	103.63	0.95537		1188
Synonymous	-0.752	252	237	1.06	0.0000189	1741
Loss of Function	0.716	12	15.0	0.800	6.87e-7	189

LoF frequencies by population

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

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: 0.104

Intolerance Scores

• loftool: 0.865
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.69

Haploinsufficiency Scores

• pHI: 0.125
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.362

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhb3

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;chemical synaptic transmission;nervous system development;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