PBK

PDZ binding kinase

Basic information

Region (hg38): 8:27809624-27838082

Links

ENSG00000168078 ∙ NCBI:55872 ∙ OMIM:611210 ∙ HGNC:18282 ∙ Uniprot:Q96KB5 ∙ 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 PBK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBK 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			12		1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	2

Variants in PBK

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

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

Position	Type	Phenotype	Significance	ClinVar
8-27810310-C-A		not specified	Uncertain significance (Nov 26, 2024)
8-27810346-A-C		not specified	Uncertain significance (Jun 10, 2022)
8-27810351-C-T		not specified	Uncertain significance (Feb 28, 2023)
8-27810433-T-C		not specified	Likely benign (Nov 12, 2024)
8-27810447-C-T		not specified	Uncertain significance (Nov 07, 2022)
8-27810478-A-C		not specified	Uncertain significance (Feb 12, 2024)
8-27811070-C-G			Benign (May 24, 2018)
8-27820589-G-T		not specified	Uncertain significance (Dec 19, 2023)
8-27820619-T-C		not specified	Uncertain significance (May 23, 2024)
8-27820643-C-T		not specified	Uncertain significance (Mar 01, 2023)
8-27820684-T-A		not specified	Uncertain significance (Jun 17, 2024)
8-27822332-G-T		not specified	Uncertain significance (May 20, 2024)
8-27822371-A-C		not specified	Uncertain significance (May 27, 2022)
8-27822404-A-G		not specified	Uncertain significance (Nov 10, 2024)
8-27822449-C-T		not specified	Uncertain significance (Nov 13, 2023)
8-27823131-C-G		not specified	Uncertain significance (Dec 08, 2023)
8-27823150-A-G		not specified	Uncertain significance (Jul 20, 2021)
8-27823201-G-A		not specified	Uncertain significance (May 15, 2024)
8-27823203-G-A		not specified	Uncertain significance (Dec 07, 2021)
8-27828118-A-G		not specified	Uncertain significance (Aug 27, 2024)
8-27828125-T-C			Benign (May 24, 2018)
8-27828168-G-A		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBK	protein_coding	protein_coding	ENST00000301905	7	28476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000122	0.601	125672	0	75	125747	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.663	143	167	0.856	0.00000791	2128
Missense in Polyphen		52	57.874	0.89851		752
Synonymous	-0.402	59	55.2	1.07	0.00000262	581
Loss of Function	0.958	11	15.0	0.733	7.90e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000686	0.000686
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000345	0.000334
Middle Eastern	0.000224	0.000217
South Asian	0.000462	0.000425
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates MAP kinase p38. Seems to be active only in mitosis. May also play a role in the activation of lymphoid cells. When phosphorylated, forms a complex with TP53, leading to TP53 destabilization and attenuation of G2/M checkpoint during doxorubicin-induced DNA damage. {ECO:0000269|PubMed:10781613, ECO:0000269|PubMed:17482142}.
• Pathway: 4-hydroxytamoxifen, Dexamethasone, and Retinoic Acids Regulation of p27 Expression;VEGFA-VEGFR2 Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.334

Intolerance Scores

• loftool: 0.625
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.487
• hipred: Y
• hipred_score: 0.637
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbk
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: mitotic cell cycle;protein phosphorylation;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of stress-activated MAPK cascade;cellular response to UV;negative regulation of inflammatory response
• Cellular component: nucleus
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding