GeneBe

PARD3

par-3 family cell polarity regulator, the group of PDZ domain containing|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 10:34109560-34815325

Links

ENSG00000148498 ∙ NCBI:56288 ∙ OMIM:606745 ∙ HGNC:16051 ∙ Uniprot:Q8TEW0 ∙ 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 PARD3 gene.

  • not_specified (161 variants)
  • PARD3-related_disorder (32 variants)
  • not_provided (14 variants)
  • Neural_tube_defect (6 variants)
  • Prostate_cancer (3 variants)
  • Premature_ovarian_failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001184785.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
17
clinvar
4
clinvar
 21
missense
2
clinvar
162
clinvar
10
clinvar
5
clinvar
 179
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 2 0 162 27 9
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PARD3protein_codingprotein_codingENST00000374789 25705766
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9560.04421257080401257480.000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.047027840.8950.00004508933
Missense in Polyphen260328.820.790713648
Synonymous0.3222792860.9760.00001692588
Loss of Function6.301471.50.1960.00000434762

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005930.000582
Ashkenazi Jewish0.0001040.0000992
East Asian0.00005510.0000544
Finnish0.0001850.000185
European (Non-Finnish)0.0001790.000176
Middle Eastern0.00005510.0000544
South Asian0.0001010.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Adapter protein involved in asymmetrical cell division and cell polarization processes (PubMed:27925688, PubMed:10954424). Seems to play a central role in the formation of epithelial tight junctions (PubMed:27925688). Targets the phosphatase PTEN to cell junctions (By similarity). Involved in Schwann cell peripheral myelination (By similarity). Association with PARD6B may prevent the interaction of PARD3 with F11R/JAM1, thereby preventing tight junction assembly (By similarity). The PARD6-PARD3 complex links GTP-bound Rho small GTPases to atypical protein kinase C proteins (PubMed:10934474). Required for establishment of neuronal polarity and normal axon formation in cultured hippocampal neurons (PubMed:19812038, PubMed:27925688). {ECO:0000250|UniProtKB:Q99NH2, ECO:0000250|UniProtKB:Q9Z340, ECO:0000269|PubMed:10934474, ECO:0000269|PubMed:10954424, ECO:0000269|PubMed:19812038, ECO:0000269|PubMed:27925688}.;
Disease
DISEASE: Neural tube defects (NTD) [MIM:182940]: Congenital malformations of the central nervous system and adjacent structures related to defective neural tube closure during the first trimester of pregnancy. Failure of neural tube closure can occur at any level of the embryonic axis. Common NTD forms include anencephaly, myelomeningocele and spina bifida, which result from the failure of fusion in the cranial and spinal region of the neural tube. NTDs have a multifactorial etiology encompassing both genetic and environmental components. {ECO:0000269|PubMed:27925688}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
Pathway
Adherens junction - Homo sapiens (human);Endocytosis - Homo sapiens (human);Tight junction - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Axon guidance - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Chemokine signaling pathway;Signal Transduction;TCR;EGFR1;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Cell-Cell communication;TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) (Consensus)

Recessive Scores

pRec
0.298

Intolerance Scores

loftool
0.683
rvis_EVS
-0.92
rvis_percentile_EVS
9.81

Haploinsufficiency Scores

pHI
0.511
hipred
Y
hipred_score
0.652
ghis
0.545

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.743

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pard3
Phenotype
embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name
pard3ab
Affected structure
retinal ganglion cell
Phenotype tag
abnormal
Phenotype quality
decreased process quality

Gene ontology

Biological process
microtubule cytoskeleton organization;protein targeting to membrane;cell cycle;cell adhesion;establishment or maintenance of cell polarity;transforming growth factor beta receptor signaling pathway;protein kinase C-activating G protein-coupled receptor signaling pathway;axonogenesis;protein localization;asymmetric cell division;negative regulation of peptidyl-threonine phosphorylation;myelination in peripheral nervous system;establishment of cell polarity;positive regulation of myelination;establishment or maintenance of epithelial cell apical/basal polarity;establishment of centrosome localization;regulation of cellular localization;protein-containing complex assembly;bicellular tight junction assembly;establishment of epithelial cell polarity
Cellular component
cytoplasm;cytosol;cytoskeleton;plasma membrane;cell-cell junction;adherens junction;cell-cell adherens junction;bicellular tight junction;cell cortex;endomembrane system;apical plasma membrane;cell junction;protein-containing complex;internode region of axon;neuronal cell body;apical junction complex;axonal growth cone
Molecular function
protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;protein phosphatase binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol binding;identical protein binding