PCDHB14

protocadherin beta 14, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141223343-141227759

Links

ENSG00000120327 ∙ NCBI:56122 ∙ OMIM:606340 ∙ HGNC:8685 ∙ Uniprot:Q9Y5E9 ∙ 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 PCDHB14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB14 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				4		4
missense			87	4		91
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	87	8	0

Variants in PCDHB14

This is a list of pathogenic ClinVar variants found in the PCDHB14 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141223522-C-T		not specified	Uncertain significance (Mar 04, 2024)
5-141223603-A-G		not specified	Uncertain significance (Aug 11, 2022)
5-141223606-C-T		not specified	Uncertain significance (Dec 06, 2022)
5-141223656-G-C		not specified	Uncertain significance (Oct 22, 2024)
5-141223668-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-141223668-G-C		not specified	Uncertain significance (May 20, 2024)
5-141223798-C-A		not specified	Uncertain significance (May 30, 2022)
5-141223798-C-G		not specified	Uncertain significance (Sep 17, 2021)
5-141223897-C-T		not specified	Uncertain significance (Aug 09, 2021)
5-141224013-T-A		not specified	Uncertain significance (Dec 20, 2023)
5-141224055-G-C		not specified	Uncertain significance (Jan 24, 2024)
5-141224157-G-A		not specified	Uncertain significance (Jan 31, 2023)
5-141224182-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-141224200-T-C		not specified	Uncertain significance (Oct 19, 2024)
5-141224208-A-G		not specified	Uncertain significance (Jan 08, 2025)
5-141224259-C-T		not specified	Uncertain significance (Sep 11, 2024)
5-141224286-A-T		not specified	Uncertain significance (Nov 06, 2023)
5-141224289-G-C		not specified	Uncertain significance (Aug 14, 2023)
5-141224295-A-G		not specified	Likely benign (Nov 12, 2021)
5-141224351-C-T			Likely benign (Jul 01, 2022)
5-141224371-G-C		not specified	Uncertain significance (Nov 08, 2022)
5-141224380-T-A		not specified	Uncertain significance (Mar 11, 2022)
5-141224394-A-G		not specified	Uncertain significance (Mar 19, 2024)
5-141224401-G-A		not specified	Uncertain significance (Oct 22, 2021)
5-141224449-A-G		not specified	Uncertain significance (Oct 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB14	protein_coding	protein_coding	ENST00000239449	1	2928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.55e-14	0.00695	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.42	552	466	1.19	0.0000285	5136
Missense in Polyphen		181	162.2	1.1159		1926
Synonymous	-3.28	280	218	1.28	0.0000155	1728
Loss of Function	-0.577	19	16.5	1.15	7.98e-7	207

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: 0.832
• rvis_EVS: 1.03
• rvis_percentile_EVS: 91.11

Haploinsufficiency Scores

• pHI: 0.0331
• hipred: N
• hipred_score: 0.131
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhb20

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;protein binding