PCDHB15

protocadherin beta 15, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141245395-141249365

Links

ENSG00000113248

∙ NCBI:56121 ∙ OMIM:606341 ∙ HGNC:8686 ∙ Uniprot:Q9Y5E8 ∙ 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 PCDHB15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB15 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			54 clinvar	3 clinvar		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	3	0

Variants in PCDHB15

This is a list of pathogenic ClinVar variants found in the PCDHB15 region.

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

Position	Phenotype	Significance	ClinVar
5-141245597-C-A	not specified	Uncertain significance (Feb 17, 2024)	3209674
5-141245627-C-A	not specified	Uncertain significance (Mar 28, 2023)	2530519
5-141245628-T-A	not specified	Uncertain significance (Jun 16, 2023)	2600087
5-141245640-T-C	not specified	Uncertain significance (Sep 29, 2023)	3209680
5-141245676-A-G	not specified	Uncertain significance (Dec 20, 2021)	3209684
5-141245750-G-A	not specified	Uncertain significance (Jun 17, 2024)	3304834
5-141245778-T-C	not specified	Uncertain significance (Jul 05, 2023)	2610014
5-141245792-G-A	not specified	Uncertain significance (Dec 01, 2022)	2330512
5-141245811-A-T	not specified	Uncertain significance (Nov 05, 2021)	2259017
5-141245814-T-C	not specified	Uncertain significance (Oct 28, 2023)	3209676
5-141245846-C-G	not specified	Uncertain significance (Jul 25, 2023)	2613550
5-141245847-T-G	not specified	Uncertain significance (Mar 28, 2024)	3304841
5-141245849-G-T	not specified	Uncertain significance (Nov 10, 2024)	3415172
5-141245900-G-C	not specified	Uncertain significance (May 23, 2024)	3304835
5-141245919-T-C	not specified	Uncertain significance (Sep 27, 2022)	2313914
5-141246021-T-C	not specified	Likely benign (Mar 25, 2024)	3304833
5-141246023-G-A	not specified	Uncertain significance (Dec 22, 2023)	3209677
5-141246047-G-A	not specified	Uncertain significance (Mar 04, 2024)	3209678
5-141246095-T-C	not specified	Uncertain significance (Oct 06, 2024)	3415170
5-141246096-C-A	not specified	Uncertain significance (Sep 16, 2021)	2386023
5-141246114-A-G	not specified	Uncertain significance (Jan 29, 2024)	3209679
5-141246132-G-T	not specified	Uncertain significance (Feb 28, 2023)	2471841
5-141246222-T-C	not specified	Uncertain significance (Feb 06, 2023)	2481320
5-141246227-G-A	not specified	Uncertain significance (Jun 26, 2023)	2598562
5-141246242-C-G	not specified	Uncertain significance (Dec 19, 2022)	2337519

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB15	protein_coding	protein_coding	ENST00000231173	1	2653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.74e-12	0.0826	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.611	503	466	1.08	0.0000313	5030
Missense in Polyphen		105	107.93	0.97289		1294
Synonymous	-2.49	276	228	1.21	0.0000184	1744
Loss of Function	0.374	18	19.8	0.909	0.00000125	201

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: 0.728
rvis_EVS: 1.58
rvis_percentile_EVS: 95.79

Haploinsufficiency Scores

pHI: 0.194
hipred: N
hipred_score: 0.291
ghis: 0.504

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pcdhb22
Phenotype

Gene ontology

Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;nervous system development
Cellular component: integral component of plasma membrane;photoreceptor connecting cilium
Molecular function: calcium ion binding