PARD6A

par-6 family cell polarity regulator alpha, the group of PDZ domain containing

Basic information

Region (hg38): 16:67660945-67662774

Links

ENSG00000102981 ∙ NCBI:50855 ∙ OMIM:607484 ∙ HGNC:15943 ∙ Uniprot:Q9NPB6 ∙ 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 PARD6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARD6A gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	2

Variants in PARD6A

This is a list of pathogenic ClinVar variants found in the PARD6A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-67660954-G-GGCGGC			Benign (Mar 29, 2019)
16-67661070-G-A		not specified	Uncertain significance (Mar 31, 2023)
16-67661469-C-T		PARD6A-related disorder	Likely benign (Aug 26, 2019)
16-67661495-C-T		not specified	Uncertain significance (Dec 09, 2023)
16-67661580-T-C			Benign (Dec 31, 2019)
16-67661909-C-A		not specified	Uncertain significance (Jan 26, 2022)
16-67661983-G-A		not specified	Uncertain significance (Jul 15, 2021)
16-67662025-G-T		not specified	Uncertain significance (Sep 07, 2022)
16-67662029-G-C		not specified	Uncertain significance (Oct 26, 2022)
16-67662082-G-A		not specified	Uncertain significance (Apr 17, 2024)
16-67662137-G-T		not specified	Uncertain significance (May 26, 2023)
16-67662154-C-G		PARD6A-related disorder	Likely benign (Jan 28, 2020)
16-67662186-A-G		not specified	Uncertain significance (Oct 27, 2022)
16-67662226-G-C		not specified	Uncertain significance (Jan 12, 2024)
16-67662236-G-A		PARD6A-related disorder	Likely benign (Aug 16, 2019)
16-67662316-C-T		not specified	Uncertain significance (Apr 28, 2022)
16-67662326-T-A		not specified	Uncertain significance (Oct 13, 2023)
16-67662361-G-A		not specified	Uncertain significance (Dec 15, 2023)
16-67662443-C-G		not specified	Uncertain significance (Nov 21, 2023)
16-67662462-G-A		PARD6A-related disorder	Benign (Oct 17, 2019)
16-67662475-G-A		not specified	Uncertain significance (Apr 20, 2024)
16-67662493-A-G		not specified	Uncertain significance (Jun 22, 2023)
16-67662541-G-A		not specified	Uncertain significance (Apr 27, 2023)
16-67662555-C-T		not specified	Uncertain significance (Sep 20, 2023)
16-67662607-G-A		not specified	Uncertain significance (Jan 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARD6A	protein_coding	protein_coding	ENST00000219255	3	1833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00647	0.920	125717	0	16	125733	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	162	235	0.689	0.0000150	2199
Missense in Polyphen		51	80.593	0.63281		699
Synonymous	1.04	84	97.0	0.866	0.00000536	800
Loss of Function	1.54	5	10.3	0.483	7.87e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000589	0.0000462
European (Non-Finnish)	0.0000884	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein involved in asymmetrical cell division and cell polarization processes. Probably involved in the formation of epithelial tight junctions. Association with PARD3 may prevent the interaction of PARD3 with F11R/JAM1, thereby preventing tight junction assembly. The PARD6-PARD3 complex links GTP-bound Rho small GTPases to atypical protein kinase C proteins (PubMed:10873802). Regulates centrosome organization and function. Essential for the centrosomal recruitment of key proteins that control centrosomal microtubule organization (PubMed:20719959). {ECO:0000269|PubMed:10873802, ECO:0000269|PubMed:20719959}.
• Pathway: Endocytosis - Homo sapiens (human);Tight junction - Homo sapiens (human);Axon guidance - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Intracellular Signalling Through Adenosine Receptor A2b and Adenosine;Intracellular Signalling Through Adenosine Receptor A2a and Adenosine;Regulation of Microtubule Cytoskeleton;TGF-beta Signaling Pathway;Signaling by WNT;Signal Transduction;Asymmetric localization of PCP proteins;TGF_beta_Receptor;PCP/CE pathway;Beta-catenin independent WNT signaling;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;Insulin Pathway;CDC42 signaling events;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Nephrin/Neph1 signaling in the kidney podocyte;TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition);TGF-beta receptor signaling;RhoA signaling pathway (Consensus)

Recessive Scores

• pRec: 0.259

Intolerance Scores

• loftool: 0.353
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.385
• hipred: Y
• hipred_score: 0.728
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.651

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pard6a
• Phenotype: immune system phenotype; skeleton phenotype; hematopoietic system phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of protein phosphorylation;centrosome cycle;establishment or maintenance of cell polarity;transforming growth factor beta receptor signaling pathway;viral process;cell-cell junction maintenance;cell division;Wnt signaling pathway, planar cell polarity pathway;regulation of cellular localization;bicellular tight junction assembly;positive regulation of protein localization to centrosome
• Cellular component: ruffle;nucleus;centrosome;cytosol;plasma membrane;bicellular tight junction;cell cortex;apical plasma membrane;centriolar satellite
• Molecular function: protein kinase C binding;protein binding;transcription factor binding;Rho GTPase binding;GTP-dependent protein binding