PARD6B

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

Basic information

Region (hg38): 20:50731580-50756795

Links

ENSG00000124171 ∙ NCBI:84612 ∙ OMIM:608975 ∙ HGNC:16245 ∙ Uniprot:Q9BYG5 ∙ 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 PARD6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARD6B 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						0
missense			22		1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	1

Variants in PARD6B

This is a list of pathogenic ClinVar variants found in the PARD6B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-50731812-C-T		not specified	Uncertain significance (Nov 25, 2024)
20-50737954-A-G		not specified	Uncertain significance (Sep 14, 2022)
20-50737956-G-A		not specified	Uncertain significance (Dec 03, 2021)
20-50737994-C-G		not specified	Uncertain significance (May 17, 2023)
20-50738075-G-T		not specified	Uncertain significance (Jul 19, 2023)
20-50749692-C-T			Benign (Jan 25, 2018)
20-50749711-T-G		not specified	Uncertain significance (Oct 10, 2023)
20-50749718-A-G		not specified	Uncertain significance (Feb 06, 2024)
20-50749830-C-T		not specified	Uncertain significance (Jun 16, 2023)
20-50749944-T-C		not specified	Uncertain significance (Jun 28, 2024)
20-50749952-T-C		not specified	Uncertain significance (Sep 07, 2022)
20-50750034-A-G		not specified	Uncertain significance (Oct 04, 2022)
20-50750087-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-50750101-A-G		not specified	Uncertain significance (Jan 07, 2022)
20-50750148-G-A		not specified	Uncertain significance (Jan 08, 2024)
20-50750154-C-G		not specified	Uncertain significance (Dec 03, 2021)
20-50750165-G-A		not specified	Uncertain significance (Sep 26, 2024)
20-50750169-A-G		not specified	Uncertain significance (Jan 23, 2024)
20-50750208-T-C		not specified	Uncertain significance (Mar 11, 2024)
20-50750210-G-A		not specified	Uncertain significance (Feb 03, 2022)
20-50750261-A-G		not specified	Uncertain significance (Dec 20, 2023)
20-50750297-G-A		not specified	Uncertain significance (Sep 14, 2023)
20-50750351-G-A		not specified	Uncertain significance (Nov 30, 2022)
20-50750360-C-A		not specified	Uncertain significance (Nov 14, 2024)
20-50750397-C-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARD6B	protein_coding	protein_coding	ENST00000371610	3	25252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.926	0.0738	125742	0	3	125745	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	147	203	0.726	0.0000112	2460
Missense in Polyphen		29	67.812	0.42765		751
Synonymous	0.155	75	76.7	0.977	0.00000452	733
Loss of Function	2.67	0	8.31	0.00	3.49e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein involved in asymmetrical cell division and cell polarization processes. Probably involved in 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.
• 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);Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.0877

Intolerance Scores

• loftool: 0.323
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.138
• hipred: Y
• hipred_score: 0.830
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pard6b

Gene ontology

• Biological process: cell-cell junction assembly;centrosome cycle;establishment or maintenance of cell polarity;axonogenesis;regulation of cell migration;cell division;regulation of cellular localization;protein-containing complex assembly;bicellular tight junction assembly
• Cellular component: nucleus;cytosol;plasma membrane;bicellular tight junction;cell cortex;apical plasma membrane;protein-containing complex;extracellular exosome
• Molecular function: protein kinase C binding;protein binding;Rho GTPase binding