PCDHB4

protocadherin beta 4, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141121817-141125623

Links

ENSG00000081818 ∙ NCBI:56131 ∙ OMIM:606330 ∙ HGNC:8689 ∙ Uniprot:Q9Y5E5 ∙ 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 PCDHB4 gene.

• Inborn genetic diseases (39 variants)
• not provided (24 variants)
• Microcephaly;Intellectual disability;Epilepsy (1 variants)
• Seizure;Microcephaly;Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB4 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				7	4	11
missense			37	3	10	50
nonsense						0
start loss						0
frameshift			1		1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	10	15

Variants in PCDHB4

This is a list of pathogenic ClinVar variants found in the PCDHB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141122003-A-G		not specified	Uncertain significance (May 23, 2023)
5-141122015-G-A		not specified	Uncertain significance (Nov 05, 2021)
5-141122093-A-T		not specified	Uncertain significance (Mar 01, 2024)
5-141122123-C-A		not specified	Uncertain significance (Dec 22, 2023)
5-141122128-G-T			Benign (Dec 31, 2019)
5-141122177-C-T			Benign (Dec 31, 2019)
5-141122179-C-G		not specified	Uncertain significance (Dec 05, 2022)
5-141122215-C-G		not specified	Uncertain significance (Dec 17, 2023)
5-141122269-C-T		not specified	Uncertain significance (Dec 28, 2023)
5-141122489-A-G		not specified	Uncertain significance (Aug 09, 2021)
5-141122501-A-G			Benign (Dec 31, 2019)
5-141122584-G-A		not specified	Uncertain significance (Aug 13, 2021)
5-141122595-G-A			Benign (Oct 12, 2018)
5-141122628-C-T			Likely benign (Jan 08, 2018)
5-141122632-G-A		not specified	Likely benign (Apr 25, 2022)
5-141122636-C-G		not specified	Uncertain significance (Apr 25, 2022)
5-141122650-T-A		not specified	Uncertain significance (Feb 23, 2023)
5-141122676-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-141122761-C-T			Benign (Oct 12, 2018)
5-141122762-C-T			Benign (Oct 12, 2018)
5-141122770-T-C		not specified	Uncertain significance (Sep 27, 2022)
5-141122801-T-C		not specified	Uncertain significance (Jul 20, 2022)
5-141122851-G-C			Benign (Jun 16, 2018)
5-141122904-GA-G		Seizure;Microcephaly;Intellectual disability • Microcephaly;Intellectual disability;Epilepsy	Uncertain significance (Sep 23, 2020)
5-141122929-A-C		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB4	protein_coding	protein_coding	ENST00000194152	1	3621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.03e-12	0.0686	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.341	479	458	1.04	0.0000293	5107
Missense in Polyphen		129	138.23	0.93321		1648
Synonymous	-2.77	266	214	1.24	0.0000161	1728
Loss of Function	0.298	18	19.4	0.927	0.00000128	214

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.

Intolerance Scores

• loftool: 0.933
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.72

Haploinsufficiency Scores

• pHI: 0.197
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.145

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhb5

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