PDZK1

PDZ domain containing 1, the group of PDZ domain containing|NHERF family PDZ scaffold proteins

Basic information

Region (hg38): 1:145670852-145708148

Links

ENSG00000174827 ∙ NCBI:5174 ∙ OMIM:603831 ∙ HGNC:8821 ∙ Uniprot:Q5T2W1 ∙ 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 PDZK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZK1 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	1	1

Variants in PDZK1

This is a list of pathogenic ClinVar variants found in the PDZK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145672743-A-G		not specified	Uncertain significance (Nov 10, 2024)
1-145672804-G-A		not specified	Uncertain significance (Apr 24, 2024)
1-145672818-G-C		not specified	Uncertain significance (Mar 15, 2024)
1-145672976-C-G		not specified	Uncertain significance (Aug 12, 2024)
1-145673658-T-G		not specified	Uncertain significance (Aug 12, 2021)
1-145673685-C-T		not specified	Likely benign (Dec 09, 2024)
1-145673686-G-A		not specified	Uncertain significance (Sep 30, 2024)
1-145673730-A-G		not specified	Uncertain significance (Jan 07, 2022)
1-145673878-G-A		not specified	Uncertain significance (May 16, 2022)
1-145678570-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-145682510-A-G		not specified	Uncertain significance (Jun 26, 2023)
1-145682530-C-T			Likely benign (Jul 01, 2022)
1-145682538-T-C		not specified	Uncertain significance (Jul 14, 2024)
1-145682555-A-G		not specified	Uncertain significance (May 23, 2024)
1-145682585-C-T			Benign (Aug 16, 2017)
1-145686522-C-T		not specified	Uncertain significance (Aug 02, 2023)
1-145686536-C-T		not specified	Uncertain significance (May 03, 2023)
1-145686639-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-145686641-C-T		not specified	Likely benign (Nov 25, 2024)
1-145687824-T-G		not specified	Uncertain significance (Mar 02, 2023)
1-145687865-C-A		not specified	Uncertain significance (Jul 09, 2021)
1-145687882-G-A		not specified	Uncertain significance (Nov 23, 2021)
1-145687931-C-T		not specified	Uncertain significance (Nov 01, 2022)
1-145687960-C-T			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZK1	protein_coding	protein_coding	ENST00000344770	8	37157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.16e-9	0.0527	125621	0	126	125747	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0487	173	171	1.01	0.00000858	3367
Missense in Polyphen		40	48.012	0.83312		994
Synonymous	0.763	55	62.7	0.877	0.00000293	1001
Loss of Function	-0.345	13	11.7	1.11	6.62e-7	270

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000571	0.000571
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00277	0.00278
Finnish	0.00	0.00
European (Non-Finnish)	0.000370	0.000369
Middle Eastern	0.00277	0.00278
South Asian	0.000363	0.000359
Other	0.000661	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: A scaffold protein that connects plasma membrane proteins and regulatory components, regulating their surface expression in epithelial cells apical domains. May be involved in the coordination of a diverse range of regulatory processes for ion transport and second messenger cascades. In complex with SLC9A3R1, may cluster proteins that are functionally dependent in a mutual fashion and modulate the trafficking and the activity of the associated membrane proteins. May play a role in the cellular mechanisms associated with multidrug resistance through its interaction with ABCC2 and PDZK1IP1. May potentiate the CFTR chloride channel activity. Required for normal cell-surface expression of SCARB1. Plays a role in maintaining normal plasma cholesterol levels via its effects on SCARB1. Plays a role in the normal localization and function of the chloride-anion exchanger SLC26A6 to the plasma membrane in the brush border of the proximal tubule of the kidney. May be involved in the regulation of proximal tubular Na(+)-dependent inorganic phosphate cotransport therefore playing an important role in tubule function (By similarity). {ECO:0000250}.
• Pathway: downregulated of mta-3 in er-negative breast tumors (Consensus)

Recessive Scores

• pRec: 0.206

Haploinsufficiency Scores

• pHI: 0.339
• hipred: N
• hipred_score: 0.410
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.396

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzk1
• Phenotype: liver/biliary system phenotype; respiratory system phenotype; embryo 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); hematopoietic system phenotype; 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); skeleton phenotype; homeostasis/metabolism phenotype; immune system phenotype; muscle phenotype

Gene ontology

• Biological process: cell population proliferation;carnitine transport;drug transport;positive regulation of ion transmembrane transporter activity;regulation of anion transport;positive regulation of protein targeting to membrane;positive regulation of cation transmembrane transport
• Cellular component: plasma membrane;apical plasma membrane;brush border membrane;microvillus membrane;membrane raft;extracellular exosome
• Molecular function: scavenger receptor binding;transporter activity;protein binding;PDZ domain binding;protein-containing complex binding