PCDHB8

protocadherin beta 8, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141177790-141182369

Links

ENSG00000120322 ∙ NCBI:56128 ∙ OMIM:606334 ∙ HGNC:8693 ∙ Uniprot:Q9UN66 ∙ 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 PCDHB8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB8 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				10	1	11
missense			81	12	6	99
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	81	22	7

Variants in PCDHB8

This is a list of pathogenic ClinVar variants found in the PCDHB8 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141178099-G-A		not specified	Uncertain significance (Aug 27, 2024)
5-141178140-G-C		not specified	Uncertain significance (Jun 07, 2024)
5-141178141-T-C		not specified	Uncertain significance (Aug 20, 2024)
5-141178157-G-C		not specified	Uncertain significance (Mar 16, 2022)
5-141178165-C-T		not specified	Uncertain significance (Sep 24, 2024)
5-141178177-A-G		not specified	Likely benign (Aug 28, 2024)
5-141178178-T-C		not specified	Likely benign (May 06, 2024)
5-141178183-C-G		not specified	Uncertain significance (Mar 28, 2024)
5-141178198-T-C			Benign (Aug 03, 2017)
5-141178290-T-C			Likely benign (Mar 01, 2023)
5-141178306-T-C		not specified	Uncertain significance (Sep 04, 2024)
5-141178348-T-C		not specified	Uncertain significance (Aug 20, 2024)
5-141178357-A-C		not specified	Uncertain significance (Jun 05, 2023)
5-141178359-G-A		not specified	Uncertain significance (Jul 12, 2023)
5-141178398-C-G		not specified	Uncertain significance (Sep 19, 2022)
5-141178451-G-T		not specified	Likely benign (Sep 19, 2022)
5-141178461-G-A		not specified	Likely benign (Nov 18, 2023)
5-141178488-G-A		not specified	Likely benign (Jan 04, 2024)
5-141178489-C-A		not specified	Uncertain significance (Mar 16, 2022)
5-141178592-C-T			Likely benign (Nov 01, 2022)
5-141178665-T-G		not specified	Uncertain significance (Mar 23, 2023)
5-141178684-A-G		not specified	Uncertain significance (Dec 04, 2024)
5-141178739-T-C			Likely benign (Nov 01, 2022)
5-141178783-T-C		not specified	Uncertain significance (Aug 04, 2023)
5-141178787-G-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB8	protein_coding	protein_coding	ENST00000239444	1	2711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000132	0.619	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.75	532	430	1.24	0.0000280	4947
Missense in Polyphen		119	99.266	1.1988		1159
Synonymous	-3.96	279	207	1.35	0.0000163	1658
Loss of Function	0.987	11	15.1	0.726	7.93e-7	192

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: Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain. {ECO:0000250|UniProtKB:Q91XZ2}.

Intolerance Scores

• loftool: 0.886
• rvis_EVS: 2.74
• rvis_percentile_EVS: 98.96

Haploinsufficiency Scores

• pHI: 0.0342
• hipred: N
• hipred_score: 0.172
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.206

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhb16

Gene ontology

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