PCDHGB7

protocadherin gamma subfamily B, 7, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141417645-141512975

Links

ENSG00000254122 ∙ NCBI:56099 ∙ OMIM:606304 ∙ HGNC:8714 ∙ Uniprot:Q9Y5F8 ∙ 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 PCDHGB7 gene.

• Neurodevelopmental disorder with poor growth and skeletal anomalies (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHGB7 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				3	1	4
missense			46	4		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	3	207	13	7	231
Total	1	3	253	20	8

Variants in PCDHGB7

This is a list of pathogenic ClinVar variants found in the PCDHGB7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141417959-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-141417980-C-A		not specified	Uncertain significance (Sep 17, 2021)
5-141418041-T-C		not specified	Uncertain significance (Jan 29, 2024)
5-141418041-T-G		not specified	Uncertain significance (Feb 06, 2023)
5-141418056-T-G		not specified	Uncertain significance (Dec 11, 2023)
5-141418085-A-C		not specified	Uncertain significance (Jun 18, 2024)
5-141418121-G-A		not specified	Uncertain significance (May 03, 2023)
5-141418244-C-T		not specified	Uncertain significance (Apr 08, 2024)
5-141418250-C-T		not specified	Uncertain significance (Sep 06, 2022)
5-141418416-C-G		not specified	Uncertain significance (Jan 18, 2022)
5-141418424-G-A		not specified	Uncertain significance (Mar 25, 2024)
5-141418490-G-A		not specified	Uncertain significance (Jan 12, 2024)
5-141418514-G-A		not specified	Uncertain significance (Jun 02, 2023)
5-141418520-C-A		not specified	Uncertain significance (Dec 01, 2022)
5-141418595-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-141418620-A-T		not specified	Uncertain significance (Aug 16, 2022)
5-141418763-C-G		not specified	Uncertain significance (Jan 09, 2024)
5-141418806-C-T		not specified	Uncertain significance (Dec 07, 2021)
5-141418814-A-G		not specified	Likely benign (Jun 12, 2023)
5-141418815-T-C		not specified	Uncertain significance (Mar 13, 2023)
5-141418848-G-A		not specified	Likely benign (Dec 03, 2021)
5-141418950-T-A		not specified	Uncertain significance (Jun 30, 2023)
5-141419063-T-A		not specified	Uncertain significance (Nov 22, 2022)
5-141419064-A-G		not specified	Uncertain significance (Jun 10, 2024)
5-141419169-C-T		not specified	Uncertain significance (Jun 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGB7	protein_coding	protein_coding	ENST00000398594	4	95120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000155	0.999	124930	1	81	125012	0.000328

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	506	576	0.879	0.0000350	6020
Missense in Polyphen		194	237.99	0.81516		2508
Synonymous	1.76	223	259	0.861	0.0000181	1987
Loss of Function	2.79	13	29.3	0.444	0.00000168	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00143
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000166
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000311	0.000309
Middle Eastern	0.000278	0.000166
South Asian	0.000229	0.000229
Other	0.000331	0.000329

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: 0.559
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.91

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.389
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhgb7

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