PCDHB11

protocadherin beta 11, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141199609-141203779

Links

ENSG00000197479 ∙ NCBI:56125 ∙ OMIM:606337 ∙ HGNC:8682 ∙ Uniprot:Q9Y5F2 ∙ 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 PCDHB11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB11 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				2		2
missense			76	5	1	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	76	7	1

Variants in PCDHB11

This is a list of pathogenic ClinVar variants found in the PCDHB11 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141199823-C-G		not specified	Uncertain significance (Feb 01, 2023)
5-141199838-G-A		not specified	Uncertain significance (Mar 08, 2024)
5-141199878-T-C		not specified	Uncertain significance (Oct 05, 2022)
5-141199880-G-A		not specified	Uncertain significance (May 20, 2024)
5-141199938-A-T		not specified	Uncertain significance (Dec 07, 2021)
5-141199941-T-A		not specified	Uncertain significance (Dec 11, 2023)
5-141199952-T-C		not specified	Uncertain significance (May 04, 2022)
5-141199964-G-T		not specified	Uncertain significance (Sep 29, 2023)
5-141199977-C-T		not specified	Uncertain significance (Mar 06, 2023)
5-141200001-A-G		not specified	Uncertain significance (Feb 22, 2023)
5-141200009-A-G		not specified	Uncertain significance (Dec 03, 2021)
5-141200015-A-G		not specified	Uncertain significance (May 16, 2023)
5-141200064-G-C		not specified	Uncertain significance (Sep 22, 2023)
5-141200114-A-T		not specified	Uncertain significance (May 15, 2024)
5-141200115-C-A		not specified	Uncertain significance (Aug 01, 2022)
5-141200134-G-C		not specified	Uncertain significance (Oct 25, 2023)
5-141200163-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-141200165-C-T		not specified	Uncertain significance (Mar 07, 2024)
5-141200244-C-T		not specified	Uncertain significance (Dec 19, 2022)
5-141200321-A-G		not specified	Uncertain significance (Apr 25, 2022)
5-141200340-G-A		not specified	Uncertain significance (Mar 21, 2022)
5-141200422-T-G		not specified	Uncertain significance (Apr 15, 2024)
5-141200433-C-T		not specified	Uncertain significance (Aug 21, 2023)
5-141200442-C-T		not specified	Uncertain significance (Jan 08, 2024)
5-141200477-A-G		not specified	Likely benign (Jul 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB11	protein_coding	protein_coding	ENST00000354757	1	3436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.82e-10	0.0672	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.15	591	461	1.28	0.0000299	5138
Missense in Polyphen		155	139.71	1.1094		1701
Synonymous	-5.02	313	219	1.43	0.0000170	1697
Loss of Function	-0.0896	14	13.6	1.03	6.02e-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: 0.148

Intolerance Scores

• loftool: 0.860
• rvis_EVS: 1.01
• rvis_percentile_EVS: 90.8

Haploinsufficiency Scores

• pHI: 0.0303
• hipred: N
• hipred_score: 0.112
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhb21

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