PCDHGB1

protocadherin gamma subfamily B, 1, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141350099-141512975

Links

ENSG00000254221 ∙ NCBI:56104 ∙ OMIM:606299 ∙ HGNC:8708 ∙ Uniprot:Q9Y5G3 ∙ 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 PCDHGB1 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 PCDHGB1 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	1	5
missense			54	2		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	3	826	69	15	914
Total	1	3	880	75	16

Variants in PCDHGB1

This is a list of pathogenic ClinVar variants found in the PCDHGB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141350282-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-141350326-G-T		not specified	Uncertain significance (Nov 08, 2022)
5-141350375-C-G		not specified	Uncertain significance (Jan 06, 2023)
5-141350390-C-G		not specified	Uncertain significance (Aug 13, 2021)
5-141350449-A-C		not specified	Uncertain significance (Aug 09, 2021)
5-141350451-T-C		not specified	Uncertain significance (Oct 18, 2021)
5-141350480-G-A		not specified	Uncertain significance (Jun 07, 2023)
5-141350498-G-T		not specified	Uncertain significance (Feb 03, 2022)
5-141350568-T-C		not specified	Uncertain significance (Apr 08, 2024)
5-141350582-G-A		not specified	Uncertain significance (Jan 04, 2022)
5-141350687-G-T		not specified	Uncertain significance (Jan 06, 2023)
5-141350693-C-A		not specified	Uncertain significance (Apr 12, 2022)
5-141350895-T-C		not specified	Uncertain significance (Jul 21, 2022)
5-141350907-A-G		not specified	Uncertain significance (Mar 25, 2024)
5-141350933-A-G		not specified	Uncertain significance (Jun 07, 2024)
5-141350943-G-C		not specified	Uncertain significance (Dec 22, 2023)
5-141350958-A-G		not specified	Uncertain significance (Dec 19, 2022)
5-141351026-A-G		not specified	Uncertain significance (Jun 27, 2023)
5-141351093-T-C		not specified	Uncertain significance (May 23, 2023)
5-141351131-A-G		not specified	Uncertain significance (Jul 08, 2022)
5-141351194-G-A		not specified	Likely benign (Jul 25, 2023)
5-141351276-A-G		not specified	Uncertain significance (Dec 16, 2023)
5-141351445-G-C		not specified	Uncertain significance (May 30, 2024)
5-141351467-G-T		not specified	Uncertain significance (Jan 29, 2024)
5-141351482-C-A			Likely benign (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGB1	protein_coding	protein_coding	ENST00000523390	4	162719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000948	0.997	124466	1	228	124695	0.000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.104	561	568	0.988	0.0000360	6022
Missense in Polyphen		208	209.07	0.99489		2319
Synonymous	-2.02	294	253	1.16	0.0000184	1970
Loss of Function	2.63	11	25.3	0.435	0.00000136	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00211	0.00209
Ashkenazi Jewish	0.00	0.00
East Asian	0.00423	0.00418
Finnish	0.00	0.00
European (Non-Finnish)	0.000622	0.000610
Middle Eastern	0.00423	0.00418
South Asian	0.000425	0.000425
Other	0.000827	0.000825

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: 0.400
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.92

Haploinsufficiency Scores

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

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhgb1

Gene ontology

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