PCDHB7

protocadherin beta 7, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141172644-141176383

Links

ENSG00000113212 ∙ NCBI:56129 ∙ OMIM:606333 ∙ HGNC:8692 ∙ Uniprot:Q9Y5E2 ∙ 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 PCDHB7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHB7 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			96	6		102
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	96	7	1

Variants in PCDHB7

This is a list of pathogenic ClinVar variants found in the PCDHB7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141172852-A-G		not specified	Uncertain significance (Sep 09, 2021)
5-141172924-C-T		not specified	Uncertain significance (Feb 06, 2023)
5-141172927-T-A		not specified	Uncertain significance (Dec 03, 2024)
5-141172938-G-C		not specified	Uncertain significance (Aug 26, 2024)
5-141172942-C-A		not specified	Uncertain significance (Dec 17, 2024)
5-141173008-A-T		not specified	Uncertain significance (Mar 10, 2025)
5-141173011-T-C		not specified	Uncertain significance (Jan 10, 2023)
5-141173016-G-A		not specified	Uncertain significance (Nov 14, 2024)
5-141173016-G-T		not specified	Uncertain significance (Apr 25, 2023)
5-141173048-C-G		not specified	Uncertain significance (Jan 27, 2025)
5-141173055-A-T		not specified	Likely benign (Dec 10, 2024)
5-141173112-G-A		not specified	Uncertain significance (Jan 08, 2025)
5-141173134-A-G		not specified	Uncertain significance (Nov 30, 2021)
5-141173240-C-G		not specified	Uncertain significance (Dec 11, 2023)
5-141173246-G-C		not specified	Uncertain significance (Jun 28, 2024)
5-141173254-T-C		not specified	Uncertain significance (Dec 14, 2023)
5-141173281-G-C		not specified	Uncertain significance (Nov 03, 2023)
5-141173284-C-T		not specified	Uncertain significance (Sep 22, 2023)
5-141173293-T-G		not specified	Uncertain significance (May 17, 2023)
5-141173316-G-T		not specified	Uncertain significance (Aug 09, 2021)
5-141173319-G-A		not specified	Uncertain significance (May 24, 2023)
5-141173341-A-G		not specified	Uncertain significance (Dec 23, 2022)
5-141173436-G-T		not specified	Uncertain significance (Mar 28, 2024)
5-141173484-G-T		not specified	Uncertain significance (May 23, 2024)
5-141173487-G-T		not specified	Uncertain significance (Jul 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHB7	protein_coding	protein_coding	ENST00000231137	1	3715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.08e-18	0.000592	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.66	636	473	1.34	0.0000317	4999
Missense in Polyphen		143	99.454	1.4378		1179
Synonymous	-3.65	301	231	1.31	0.0000184	1717
Loss of Function	-1.19	23	17.6	1.31	9.73e-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: 0.840
• rvis_EVS: 1.63
• rvis_percentile_EVS: 96.08

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.155
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.232

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhb15

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