PCDHB13

protocadherin beta 13, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141213919-141218979

Links

ENSG00000187372 ∙ NCBI:56123 ∙ OMIM:606339 ∙ HGNC:8684 ∙ Uniprot:Q9Y5F0 ∙ 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 PCDHB13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB13 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			57			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	57	1	0

Variants in PCDHB13

This is a list of pathogenic ClinVar variants found in the PCDHB13 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141214149-G-A		not specified	Uncertain significance (Aug 14, 2024)
5-141214151-A-G		not specified	Uncertain significance (Oct 16, 2024)
5-141214263-C-G		not specified	Uncertain significance (Nov 18, 2022)
5-141214266-A-G		not specified	Uncertain significance (Aug 01, 2022)
5-141214281-T-C		not specified	Uncertain significance (Nov 10, 2024)
5-141214287-T-C		not specified	Uncertain significance (Sep 25, 2023)
5-141214326-T-C		not specified	Uncertain significance (Oct 29, 2024)
5-141214339-C-G		not specified	Uncertain significance (Dec 21, 2022)
5-141214406-G-C		not specified	Uncertain significance (Dec 20, 2023)
5-141214431-G-A		not specified	Uncertain significance (Sep 30, 2021)
5-141214433-G-A		not specified	Uncertain significance (Sep 02, 2024)
5-141214512-A-G		not specified	Uncertain significance (Jun 30, 2023)
5-141214530-A-G		not specified	Uncertain significance (Dec 16, 2022)
5-141214565-C-T		not specified	Uncertain significance (Aug 12, 2024)
5-141214607-G-C		not specified	Uncertain significance (Aug 01, 2024)
5-141214643-A-G		not specified	Uncertain significance (Jun 10, 2022)
5-141214719-A-C		not specified	Uncertain significance (Jun 16, 2023)
5-141214796-G-C		not specified	Uncertain significance (May 25, 2022)
5-141214817-G-C		not specified	Uncertain significance (Jun 18, 2021)
5-141214826-G-A		not specified	Uncertain significance (Jan 30, 2024)
5-141214844-C-T		not specified	Uncertain significance (May 26, 2023)
5-141214866-A-G		not specified	Uncertain significance (Dec 27, 2023)
5-141214869-G-C		not specified	Uncertain significance (Aug 13, 2021)
5-141214872-T-C		not specified	Uncertain significance (Dec 21, 2022)
5-141214894-G-A			Likely benign (Jul 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB13	protein_coding	protein_coding	ENST00000341948	1	3485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.48e-12	0.0145	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.92	578	462	1.25	0.0000299	5135
Missense in Polyphen		124	95.596	1.2971		1132
Synonymous	-4.04	299	222	1.34	0.0000171	1719
Loss of Function	-0.616	16	13.6	1.18	6.79e-7	175

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: 0.0901

Intolerance Scores

• loftool: 0.877
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.5

Haploinsufficiency Scores

• pHI: 0.0259
• hipred: N
• hipred_score: 0.187
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.282

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;photoreceptor connecting cilium;postsynaptic membrane;photoreceptor disc membrane
• Molecular function: calcium ion binding