PCDHB12

protocadherin beta 12, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141208697-141212571

Links

ENSG00000120328 ∙ NCBI:56124 ∙ OMIM:606338 ∙ HGNC:8683 ∙ Uniprot:Q9Y5F1 ∙ 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 PCDHB12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB12 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			58	7		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	8	0

Variants in PCDHB12

This is a list of pathogenic ClinVar variants found in the PCDHB12 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141208939-T-C		not specified	Likely benign (Mar 22, 2023)
5-141208974-A-G		not specified	Uncertain significance (May 23, 2024)
5-141208976-G-A		not specified	Uncertain significance (Jan 24, 2023)
5-141208989-T-C		not specified	Uncertain significance (Oct 12, 2022)
5-141209016-G-A		not specified	Uncertain significance (Apr 06, 2022)
5-141209036-C-A		not specified	Uncertain significance (Aug 12, 2021)
5-141209049-T-G		not specified	Uncertain significance (Oct 04, 2022)
5-141209064-G-A		not specified	Uncertain significance (Dec 27, 2023)
5-141209117-T-A		not specified	Uncertain significance (Oct 12, 2021)
5-141209140-A-G		not specified	Uncertain significance (Nov 24, 2024)
5-141209154-G-T		not specified	Uncertain significance (Oct 26, 2021)
5-141209208-C-A		not specified	Uncertain significance (Aug 04, 2024)
5-141209229-G-T		not specified	Uncertain significance (May 04, 2023)
5-141209236-T-A		not specified	Uncertain significance (Jan 02, 2024)
5-141209372-A-C		not specified	Uncertain significance (Oct 21, 2021)
5-141209416-A-G		not specified	Uncertain significance (Dec 07, 2024)
5-141209431-A-G		not specified	Uncertain significance (Jul 15, 2024)
5-141209444-C-A		not specified	Uncertain significance (Jul 22, 2024)
5-141209455-G-A		not specified	Uncertain significance (Apr 06, 2022)
5-141209490-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-141209505-C-A		not specified	Uncertain significance (Dec 05, 2022)
5-141209520-C-T		not specified	Uncertain significance (Mar 28, 2023)
5-141209523-C-A		not specified	Uncertain significance (Nov 07, 2022)
5-141209581-C-T		not specified	Uncertain significance (Aug 20, 2024)
5-141209589-G-A		not specified	Uncertain significance (Jun 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB12	protein_coding	protein_coding	ENST00000239450	1	3428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-7	0.364	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.51	608	457	1.33	0.0000287	5119
Missense in Polyphen		170	136.54	1.245		1661
Synonymous	-5.06	320	224	1.43	0.0000175	1705
Loss of Function	0.638	12	14.6	0.820	7.33e-7	194

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: 0.879
• rvis_EVS: 2.48
• rvis_percentile_EVS: 98.63

Haploinsufficiency Scores

• pHI: 0.0444
• hipred: N
• hipred_score: 0.139
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• 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: Pcdhb19

Gene ontology

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