PCDHB11

protein-coding

protocadherin beta 11, the group of Clustered protocadherins

Gene summary

This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018931.3

Inheritance

—

ClinVar variants

U:186B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr5:141,199,610-141,203,779

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~4.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCDHB11 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 197
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018931.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
186
clinvar
11
clinvar
197
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00186130199
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_018931.3RefSeqNP_061754.11MANE Select
ENST00000354757.5EnsemblENSP00000346802.31MANE Select
ENST00000624887.1EnsemblENSP00000485553.11Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • cell adhesion
  • homophilic cell adhesion via plasma membrane adhesion molecules
  • chemical synaptic transmission
  • nervous system development
  • synapse assembly

Molecular Function

  • calcium ion binding

Cellular Component

  • integral component of plasma membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000354757
Coding exons
1
Length
3436
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-2.155914611.280.00002995138
Missense (PolyPhen)155139.711.10941701
Synonymous-5.023132191.430.00001701697
Loss of Function-0.08961413.61.036.02e-7189

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec
0.148

Intolerance Scores

LoFtool
0.860
RVIS EVS
1.01
RVIS percentile EVS
90.8

Essentials

Essential (CRISPR)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.0875

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerHighMediumHigh
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