PARD3B

par-3 family cell polarity regulator beta, the group of PDZ domain containing

Basic information

Region (hg38): 2:204545474-205620162

Previous symbols: [ "ALS2CR19" ]

Links

ENSG00000116117 ∙ NCBI:117583 ∙ OMIM:619353 ∙ HGNC:14446 ∙ Uniprot:Q8TEW8 ∙ 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 PARD3B gene.

• Inborn genetic diseases (61 variants)
• not provided (7 variants)
• PARD3B-related condition (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARD3B 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					1	1
missense			68			68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2			2
non coding						0
Total	0	0	68	0	1

Variants in PARD3B

This is a list of pathogenic ClinVar variants found in the PARD3B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-204546016-G-A		not specified	Uncertain significance (Jan 12, 2024)
2-204546054-G-A		not specified	Uncertain significance (Jan 11, 2023)
2-204686205-C-G		not specified	Uncertain significance (Feb 17, 2022)
2-204686210-C-T			Benign (Jul 18, 2017)
2-204965192-T-C		not specified	Uncertain significance (Jun 23, 2023)
2-204965261-A-G		not specified	Uncertain significance (Jan 27, 2022)
2-204965294-T-C		PARD3B-related disorder	Likely benign (Apr 28, 2022)
2-204965303-C-A		not specified	Uncertain significance (Oct 02, 2023)
2-204965306-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-204965308-T-A		not specified	Uncertain significance (Jun 11, 2021)
2-205047649-G-A		not specified	Uncertain significance (Dec 13, 2021)
2-205047664-G-A		not specified	Uncertain significance (Nov 13, 2023)
2-205104433-C-T		not specified	Uncertain significance (Sep 15, 2021)
2-205113505-C-A			Uncertain significance (Sep 13, 2021)
2-205113512-G-T		not specified	Uncertain significance (Nov 08, 2022)
2-205113577-G-GGTA		PARD3B-related disorder	Uncertain significance (Jan 27, 2023)
2-205118973-G-A		not specified	Uncertain significance (Oct 25, 2022)
2-205118985-C-T		not specified	Uncertain significance (Jul 06, 2022)
2-205118988-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-205119027-G-A		not specified	Uncertain significance (Aug 10, 2021)
2-205119035-A-C		not specified	Uncertain significance (Mar 07, 2024)
2-205121605-T-C		not specified	Uncertain significance (Jan 10, 2023)
2-205121626-C-A		not specified	Uncertain significance (Nov 10, 2022)
2-205121637-C-T		not specified	Uncertain significance (Oct 28, 2023)
2-205121643-G-A		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARD3B	protein_coding	protein_coding	ENST00000358768	22	1074371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.28e-13	1.00	124677	0	119	124796	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.564	688	648	1.06	0.0000357	7402
Missense in Polyphen		254	246.3	1.0313		2819
Synonymous	0.122	240	242	0.990	0.0000136	2285
Loss of Function	3.22	29	54.7	0.530	0.00000303	655

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00112
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000390	0.000389
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000446	0.000441
Middle Eastern	0.000390	0.000389
South Asian	0.000924	0.000850
Other	0.000496	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative adapter protein involved in asymmetrical cell division and cell polarization processes. May play a role in the formation of epithelial tight junctions.

Recessive Scores

• pRec: 0.0951

Intolerance Scores

• loftool: 0.940
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.75

Haploinsufficiency Scores

• pHI: 0.486
• hipred: Y
• hipred_score: 0.542
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pard3b
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: microtubule cytoskeleton organization;cell cycle;cell adhesion;protein localization;establishment of cell polarity;establishment or maintenance of epithelial cell apical/basal polarity;cell division;establishment of centrosome localization
• Cellular component: nucleoplasm;cytoplasm;adherens junction;cell-cell adherens junction;bicellular tight junction;cell cortex;endomembrane system;apical plasma membrane;nuclear body;cell junction;protein-containing complex;apical junction complex
• Molecular function: protein binding;phosphatidylinositol binding