PCDHB4 (protocadherin beta 4)

Gene

• Entrez ID: 56131
• Gene name: Protocadherin beta 4
• Gene symbol: PCDHB4
• Synonyms (NCBI Gene): PCDH-BETA4
• Chromosome: 5
• Chromosome location: 5q31.3
• 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.

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs372292910	A>-,AA	Likely-pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1217207	hsa-miR-3065-5p	CLIP-seq
MIRT1217208	hsa-miR-3158-3p	CLIP-seq
MIRT1217209	hsa-miR-4269	CLIP-seq
MIRT1217210	hsa-miR-4666-5p	CLIP-seq
MIRT1217211	hsa-miR-4721	CLIP-seq
MIRT1217212	hsa-miR-4802-3p	CLIP-seq
MIRT1217213	hsa-miR-548u	CLIP-seq
MIRT1217208	hsa-miR-3158-3p	CLIP-seq
MIRT2062708	hsa-miR-4477a	CLIP-seq
MIRT1217211	hsa-miR-4721	CLIP-seq
MIRT2062709	hsa-miR-548ag	CLIP-seq
MIRT2062710	hsa-miR-548ai	CLIP-seq
MIRT2062711	hsa-miR-624	CLIP-seq
MIRT2062712	hsa-miR-944	CLIP-seq
MIRT2291091	hsa-miR-142-3p	CLIP-seq
MIRT2291092	hsa-miR-3606	CLIP-seq
MIRT2291093	hsa-miR-3616-5p	CLIP-seq
MIRT2291094	hsa-miR-3647-5p	CLIP-seq
MIRT2291095	hsa-miR-4795-5p	CLIP-seq
MIRT2291096	hsa-miR-518a-5p	CLIP-seq
MIRT2291097	hsa-miR-519a	CLIP-seq
MIRT2291098	hsa-miR-519b-3p	CLIP-seq
MIRT2291099	hsa-miR-519c-3p	CLIP-seq
MIRT2291100	hsa-miR-527	CLIP-seq
MIRT2291101	hsa-miR-548c-3p	CLIP-seq
MIRT2291102	hsa-miR-556-3p	CLIP-seq
MIRT2291103	hsa-miR-573	CLIP-seq
MIRT2062712	hsa-miR-944	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005509	Function	Calcium ion binding	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	10380929
GO:0007155	Process	Cell adhesion	IBA
GO:0007155	Process	Cell adhesion	IEA
GO:0007155	Process	Cell adhesion	TAS	10380929
GO:0007156	Process	Homophilic cell adhesion via plasma membrane adhesion molecules	IEA
GO:0007268	Process	Chemical synaptic transmission	TAS	12231349
GO:0007399	Process	Nervous system development	IEA
GO:0007399	Process	Nervous system development	TAS	10380929
GO:0007416	Process	Synapse assembly	TAS	12231349
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	11322959
GO:0016339	Process	Calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	NAS	11322959
GO:0045202	Component	Synapse	IEA
GO:0050839	Function	Cell adhesion molecule binding	IBA

Other IDs

• MIM: 606330
• HGNC: 8689
• e!Ensembl: ENSG00000081818

Protein

• UniProt ID: Q9Y5E5
• Protein name: Protocadherin beta-4 (PCDH-beta-4)
• Protein function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08266	Cadherin_2	29 → 111	Cadherin-like	Domain
  PF00028	Cadherin	138 → 232	Cadherin domain	Domain
  PF00028	Cadherin	246 → 337	Cadherin domain	Domain
  PF00028	Cadherin	351 → 441	Cadherin domain	Domain
  PF00028	Cadherin	455 → 551	Cadherin domain	Domain
  PF00028	Cadherin	574 → 662	Cadherin domain	Domain
  PF16492	Cadherin_C_2	684 → 767	Cadherin cytoplasmic C-terminal	Family

• Sequence:

  MKKLGRIHPNRQVLAFILMVFLSQVRLEPIRYSVLEETESGSFVAHLAKDLGLGIGELAS
  RSARVLSDDDKQRLQLDRQTGDLLLREKLDREELCGPIEPCVLHFQVFLEMPVQFFQGEL
  LIQDINDHSPIFPEREVLLKILENSQPGTLFPLLIAEDLDVGSNGLQKYTISPNSHFHIL
  TRNHSEGKKYPDLVQDKPLDREEQPEFSLTLVALDGGSPPRSGTVMVRILIMDINDNAPE
  FVHTPYGVQVLENSPLDSPIVRVLARDIDAGNFGSVSYGLFQASDEIKQTFSINEVTGEI
  LLKKKLDFEKIKSYHVEIEATDGGGLSGKGTVVIEVVDVNDNPPELIISSLTSSIPENAP
  ETVVSIFRIRDRDSGENGKMICSIPDNLPFILKPTLKNFYTLVTERPLDRETSAEYNITI
  AVTDLGTPRLKTQQNITVQVSDVNDNAPAFTQTSYTLFVRENNSPALHIGSVSATDRDSG
  TNAQVTYSLLPPQDPHLPLASLVSINADNGHLFALRSLDYEALQAFEFRVGASDRGSPAL
  SSEALVRVLVLDTNDNSPFVLYPLQNGSAPCTELVPRAAEPGYLVTKVVAVDGDSGQNAW
  LSYQLLKATEPGLFGVWAHNGEVRTARLLSERDAAKHRLVVLVKDNGEPPRSATATLHVL
  LVDGFSQPYLPLPEAAPAQAQADSLTVYLVVALASVSSLFLFSVLLFVAVRLCRRSRAAS
  VGRCSVPEGPFPGHLVDVSGTGTLSQSYQYEVCLTGDSGTGEFKFLKPIFPNLLVQDTGR
  EVKENPKFRNSLVFS

• Sequence length: 795

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Epilepsy	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Microcephaly	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seizure	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Atlanto Axial Fusion	Associate	40225938	★☆☆☆☆ Found in Text Mining only
Fused Kidney	Associate	40225938	★☆☆☆☆ Found in Text Mining only
Klippel Feil Syndrome	Associate	40225938	★☆☆☆☆ Found in Text Mining only