PCDHB10

protocadherin beta 10, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141192353-141195647

Links

ENSG00000120324 ∙ NCBI:56126 ∙ OMIM:606336 ∙ HGNC:8681 ∙ Uniprot:Q9UN67 ∙ 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 PCDHB10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB10 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				1		1
missense			106	7		113
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	106	8	0

Variants in PCDHB10

This is a list of pathogenic ClinVar variants found in the PCDHB10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141192605-T-G		not specified	Uncertain significance (Jul 30, 2024)
5-141192613-T-G		not specified	Likely benign (Apr 25, 2022)
5-141192628-G-A		not specified	Uncertain significance (Sep 13, 2023)
5-141192672-G-C		not specified	Uncertain significance (May 17, 2023)
5-141192722-G-A		not specified	Uncertain significance (Oct 29, 2024)
5-141192730-G-A		not specified	Uncertain significance (Nov 18, 2022)
5-141192765-C-A		not specified	Uncertain significance (Sep 06, 2022)
5-141192793-A-G		not specified	Uncertain significance (Jun 26, 2024)
5-141192874-A-T		not specified	Uncertain significance (Mar 31, 2024)
5-141192883-G-T		not specified	Uncertain significance (Feb 14, 2023)
5-141192884-A-G		not specified	Uncertain significance (Apr 04, 2023)
5-141192905-G-C		not specified	Uncertain significance (May 30, 2024)
5-141192924-G-T		not specified	Uncertain significance (Dec 14, 2023)
5-141192953-A-G		not specified	Uncertain significance (Jan 26, 2022)
5-141192982-G-C		not specified	Uncertain significance (Sep 26, 2022)
5-141193010-G-A		not specified	Uncertain significance (May 04, 2023)
5-141193028-A-T		not specified	Uncertain significance (May 28, 2023)
5-141193030-C-A		not specified	Uncertain significance (Feb 10, 2025)
5-141193066-A-C		not specified	Uncertain significance (Sep 22, 2022)
5-141193072-C-T		not specified	Uncertain significance (Sep 01, 2021)
5-141193075-A-G		not specified	Uncertain significance (May 09, 2024)
5-141193076-A-G		not specified	Uncertain significance (Dec 17, 2023)
5-141193105-G-C		not specified	Uncertain significance (Oct 21, 2024)
5-141193108-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-141193115-G-C		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB10	protein_coding	protein_coding	ENST00000239446	1	3274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000131	0.848	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.39	609	464	1.31	0.0000287	5074
Missense in Polyphen		129	111.95	1.1523		1352
Synonymous	-3.86	289	217	1.33	0.0000154	1702
Loss of Function	1.39	10	16.0	0.624	8.36e-7	200

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: 0.107

Intolerance Scores

• loftool: 0.956
• rvis_EVS: 2.21
• rvis_percentile_EVS: 98.14

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.216
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0912

Gene Damage Prediction

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

Gene ontology

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