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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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PCDHGB6
protocadherin gamma subfamily B, 6
Chromosome 5 · 5q31.3
NCBI Gene: 56100Ensembl: ENSG00000253305.3HGNC: HGNC:8713UniProt: Q9Y5F9
12PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
cell adhesionplasma membranecell adhesion molecule bindingmembraneneurodevelopmental disorder with poor growth and skeletal anomaliesgenetic disorderNeurodevelopmental disorderatrial flutter
✦AI Summary

PCDHGB6 (protocadherin gamma subfamily B, 6) is a potential calcium-dependent cell-adhesion protein that may be involved in establishing and maintaining specific neuronal connections in the brain. However, its primary clinical significance lies in its role as a tumor suppressor gene marker through promoter hypermethylation across multiple cancer types. PCDHGB6 promoter methylation occurs frequently in lung cancer (41.4% of patients vs 1.3% of healthy controls) 1 and breast cancer (methylated in more than 10 of 21 primary breast cancers) 2. This hypermethylation likely silences PCDHGB6 expression, contributing to tumorigenesis. The methylation pattern serves as a valuable biomarker for cancer detection, with combined analysis of PCDHGB6 and other genes achieving up to 90% sensitivity for cancer detection 3. Notably, PCDHGB6 methylation can be detected non-invasively in oral epithelium for lung cancer risk stratification, particularly in smokers 4, and in bronchial brushing specimens with 80% sensitivity 5. Additionally, germline variants in PCDHGB6 may contribute to susceptibility for certain lymphomas 6 and methamphetamine dependence 7, though these associations require validation.

Sources cited
1
PCDHGB6 promoter methylation found in 41.4% of lung cancer patients vs 1.3% of healthy individuals
PMID: 27485611
2
PCDHGB6 methylated in more than 10 of 21 primary breast cancers and may serve as early-stage cancer marker
PMID: 15818620
3
Combined methylation analysis of PCDHGB6 with other genes achieved up to 90% sensitivity for cancer detection
PMID: 26446775
4
PCDHGB6 methylation in oral epithelium can be used for non-invasive lung cancer risk assessment, especially in smokers
PMID: 30417685
5
PCDHGB6 methylation detection in bronchial brushing specimens achieved 80% sensitivity for NSCLC diagnosis
PMID: 27240011
6
Germline variants in PCDHGB6 found as candidate susceptibility variants in angioimmunoblastic T-cell lymphoma
PMID: 30097855
7
PCDHGB6 region genetic polymorphisms associated with methamphetamine dependence vulnerability
PMID: 35669261
Disease Associationsⓘ20
neurodevelopmental disorder with poor growth and skeletal anomaliesOpen Targets
0.52Moderate
genetic disorderOpen Targets
0.19Weak
Neurodevelopmental disorderOpen Targets
0.12Weak
atrial flutterOpen Targets
0.06Suggestive
breast carcinomaOpen Targets
0.04Suggestive
atrial fibrillationOpen Targets
0.04Suggestive
Down syndromeOpen Targets
0.03Suggestive
neoplasmOpen Targets
0.02Suggestive
laryngotracheoesophageal cleftOpen Targets
0.01Suggestive
ataxia telangiectasiaOpen Targets
0.01Suggestive
non-small cell lung carcinomaOpen Targets
0.01Suggestive
lung cancerOpen Targets
0.01Suggestive
type 1 diabetes mellitusOpen Targets
0.01Suggestive
adenocarcinomaOpen Targets
0.01Suggestive
ulcerative colitisOpen Targets
0.01Suggestive
cancerOpen Targets
0.00Suggestive
lung adenocarcinomaOpen Targets
0.00Suggestive
breast cancerOpen Targets
0.00Suggestive
squamous cell carcinomaOpen Targets
0.00Suggestive
psoriasisOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
PCDH10Shared pathway100%PCDHA1Shared pathway100%PCDHA2Shared pathway100%PCDHA3Shared pathway100%PCDHA4Shared pathway100%PCDHA5Shared pathway100%
Tissue Expression6 tissues
Ovary
100%
Brain
58%
Heart
51%
Lung
30%
Liver
23%
Bone Marrow
4%
Gene Interaction Network
Click a node to explore
PCDHGB6PCDH10PCDHA1PCDHA2PCDHA3PCDHA4PCDHA5
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt Q9Y5F9
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.02LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.81 [0.65–1.02]
RankingsWhere PCDHGB6 stands among ~20K protein-coding genes
  • #16,532of 20,598
    Most Researched12
  • #10,059of 17,882
    Most Constrained (LOEUF)1.02
Genes detectedPCDHGB6
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Analysis of RTEL1 and PCDHGB6 promoter methylation in circulating-free DNA of lung cancer patients using liquid biopsy: A pilot study.
PMID: 27485611
Exp Lung Res · 2016
1.00
2
Identification of 20 genes aberrantly methylated in human breast cancers.
PMID: 15818620
Int J Cancer · 2005
0.90
3
Lung cancer risk stratification using methylation profile in the oral epithelium.
PMID: 30417685
Asian Cardiovasc Thorac Ann · 2019
0.80
4
Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method.
PMID: 26446775
Nanoscale · 2015
0.70
5
Absolute quantification of DNA methylation using microfluidic chip-based digital PCR.
PMID: 28525852
Biosens Bioelectron · 2017
0.60