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PCDHGB6 protocadherin gamma subfamily B, 6 [ Homo sapiens (human) ]

Gene ID: 56100, updated on 11-Apr-2024

Summary

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Official Symbol
PCDHGB6provided by HGNC
Official Full Name
protocadherin gamma subfamily B, 6provided by HGNC
Primary source
HGNC:HGNC:8713
See related
Ensembl:ENSG00000253305 MIM:606303; AllianceGenome:HGNC:8713
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCDH-GAMMA-B6
Summary
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
Orthologs
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Genomic context

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See PCDHGB6 in Genome Data Viewer
Location:
5q31.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141408021..141512975)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141933860..142038959)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140787588..140892542)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23293 Neighboring gene solute carrier family 25 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23294 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140713237-140713466 Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene TATA-box binding protein associated factor 7 Neighboring gene protocadherin gamma cluster Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140745768-140745946 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily B, 3 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23295 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23296 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140821493-140821993 Neighboring gene protocadherin gamma subfamily B, 8 pseudogene Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 9 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140855840-140856383 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140864468-140864695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23299 Neighboring gene RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140888408-140888908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23303 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893101-140893726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893727-140894352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140894353-140894978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140895605-140896230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140896231-140896856 Neighboring gene uncharacterized LOC124901091 Neighboring gene Sharpr-MPRA regulatory region 13534 Neighboring gene diaphanous related formin 1 Neighboring gene MPRA-validated peak5501 silencer Neighboring gene Sharpr-MPRA regulatory region 13738 Neighboring gene DIAPH1 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Analysis of RTEL1 and PCDHGB6 promoter methylation in circulating-free DNA of lung cancer patients using liquid biopsy: A pilot study. Powrózek T, et al. Exp Lung Res, 2016 Aug. PMID 27485611
  2. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. Sandoval J, et al. J Clin Oncol, 2013 Nov 10. PMID 24081945
  3. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. Nollet F, et al. J Mol Biol, 2000 Jun 9. PMID 10835267
  4. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. Yagi T, et al. Genes Dev, 2000 May 15. PMID 10817752
  5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Wu Q, et al. Genome Res, 2001 Mar. PMID 11230163, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. promoter methylation found in 41.4% of lung cancer patients and in 1.3% of healthy individuals
    Title: Analysis of RTEL1 and PCDHGB6 promoter methylation in circulating-free DNA of lung cancer patients using liquid biopsy: A pilot study.
  2. hypermethylation of HIST1H4F, PCDHGB6, NPBWR1, ALX1, and HOXA9 was significantly associated with shorter survival in stage 1 Non-small-cell lung cancer
    Title: A prognostic DNA methylation signature for stage I non-small-cell lung cancer.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protocadherin gamma-B6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_000012.2 

    Range
    118400..223176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001386906.1 → NP_001373835.1  protocadherin gamma-B6 isoform 3 precursor

    Status: REVIEWED

    Source sequence(s)
    AC005618
    Conserved Domains (3) summary
    cd11304
    Location:246 → 343
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:32 → 112
    Cadherin_2; Cadherin-like
    pfam16492
    Location:687 → 768
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

  2. NM_018926.3 → NP_061749.1  protocadherin gamma-B6 isoform 1 precursor

    See identical proteins and their annotated locations for NP_061749.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AC005618, AC008781
    Consensus CDS
    CCDS54929.1
    UniProtKB/Swiss-Prot
    Q9Y5C5, Q9Y5F9
    Related
    ENSP00000428603.1, ENST00000520790.2
    Conserved Domains (4) summary
    cd11304
    Location:246 → 343
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:32 → 112
    Cadherin_2; Cadherin-like
    pfam15974
    Location:807 → 903
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
    pfam16492
    Location:687 → 768
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

  3. NM_032100.1 → NP_115271.1  protocadherin gamma-B6 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115271.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes the shorter isoform (2).
    Source sequence(s)
    AF152522
    Consensus CDS
    CCDS75342.1
    UniProtKB/Swiss-Prot
    Q9Y5F9
    Related
    ENSP00000479143.1, ENST00000616430.1
    Conserved Domains (3) summary
    cd11304
    Location:246 → 343
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:32 → 112
    Cadherin_2; Cadherin-like
    pfam16492
    Location:687 → 768
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    141408021..141512975
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    141933860..142038959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5F9.1 GenPept UniProtKB/Swiss-Prot:Q9Y5F9

Gene LinkOut

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