PCDHB6

protocadherin beta 6, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141150057-141153287

Links

ENSG00000113211

∙ NCBI:56130 ∙ OMIM:606332 ∙ HGNC:8691 ∙ Uniprot:Q9Y5E3 ∙ 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 PCDHB6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB6 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 clinvar		3
missense			52 clinvar	7 clinvar		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	10	0

Variants in PCDHB6

This is a list of pathogenic ClinVar variants found in the PCDHB6 region.

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

Position	Phenotype	Significance	ClinVar
5-141150298-C-T	not specified	Uncertain significance (Sep 06, 2022)	2310502
5-141150367-A-C	not specified	Uncertain significance (Apr 13, 2022)	2350594
5-141150394-A-G	not specified	Uncertain significance (Apr 13, 2022)	2317019
5-141150426-G-A	not specified	Uncertain significance (Mar 29, 2022)	2280879
5-141150436-C-T	not specified	Uncertain significance (Aug 04, 2021)	2373495
5-141150441-G-A	not specified	Uncertain significance (Sep 22, 2023)	3209772
5-141150457-T-A	not specified	Uncertain significance (Mar 31, 2023)	2512512
5-141150501-G-A	not specified	Uncertain significance (Jan 16, 2024)	3209777
5-141150555-C-T	not specified	Uncertain significance (Mar 01, 2023)	2492700
5-141150667-T-C	not specified	Uncertain significance (Jun 12, 2023)	2568545
5-141150757-A-G	not specified	Uncertain significance (Jun 27, 2022)	2297949
5-141150792-G-T	not specified	Uncertain significance (Aug 22, 2022)	2213076
5-141150799-C-A	not specified	Uncertain significance (Jun 04, 2024)	3304885
5-141150906-G-C	not specified	Uncertain significance (Dec 27, 2022)	2339273
5-141150919-G-T	not specified	Uncertain significance (Nov 03, 2022)	2355223
5-141150933-G-A	not specified	Uncertain significance (Jan 31, 2022)	2274666
5-141150961-A-G	not specified	Uncertain significance (Jun 18, 2021)	2365405
5-141151044-G-A	not specified	Uncertain significance (Feb 06, 2024)	3209778
5-141151053-A-G	not specified	Uncertain significance (Jun 27, 2022)	2213043
5-141151069-G-T	not specified	Uncertain significance (Mar 05, 2024)	3209779
5-141151072-C-G	not specified	Uncertain significance (Jun 27, 2023)	2596162
5-141151102-A-G	not specified	Uncertain significance (Dec 15, 2023)	3209780
5-141151268-C-A	not specified	Uncertain significance (Jul 06, 2021)	2234898
5-141151294-C-T	not specified	Uncertain significance (Dec 27, 2022)	2339272
5-141151296-A-T	not specified	Uncertain significance (Jan 05, 2022)	2352350

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB6	protein_coding	protein_coding	ENST00000231136	1	3186

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.77e-10	0.121	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.21	534	461	1.16	0.0000310	5084
Missense in Polyphen		112	106.25	1.0542		1263
Synonymous	-1.47	253	225	1.13	0.0000180	1713
Loss of Function	0.378	16	17.7	0.903	8.68e-7	215

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: Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain. {ECO:0000250|UniProtKB:Q91XZ4}.;

Intolerance Scores

loftool: 0.812
rvis_EVS: 2.63
rvis_percentile_EVS: 98.8

Haploinsufficiency Scores

pHI: 0.0733
hipred: N
hipred_score: 0.299
ghis: 0.515

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pcdhb13
Phenotype

Gene ontology

Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;chemical synaptic transmission;nervous system development;synapse assembly;cell-cell recognition;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;identical protein binding