GENE REFERENCE / HGNC:9016

PKHD1

PKHD1 ciliary IPT domain containing fibrocystin/polyductin

protein-coding gene6p12.3-p12.2Gene information

What does this gene do?

The PKHD1 gene provides instructions for making a protein called fibrocystin (sometimes known as polyductin). This protein is present in fetal and adult kidney cells, and is also present at low levels in the liver and pancreas.

Fibrocystin spans the cell membrane of kidney cells, so that one end of the protein remains inside the cell and the other end projects from the outer surface of the cell. Based on its structure, fibrocystin may act as a receptor, interacting with molecules outside the cell and receiving signals that help the cell respond to its environment. This protein also may be involved in connecting cells together (adhesion), keeping cells apart (repulsion), and promoting the growth and division of cells (proliferation).

Fibrocystin is also found in cell structures called primary cilia. Primary cilia are tiny, fingerlike projections that line the small tubes where urine is formed (renal tubules). Researchers believe that primary cilia play an important role in maintaining the size and structure of these tubules; however, the function of fibrocystin in primary cilia remains unclear.

Source: MedlinePlus, National Library of Medicine. Source publication: 2022-06-27. Source review: 2006-06.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
autosomal recessive polycystic kidney diseaseMONDO:0009889 · Evaluated 2020-11-11	Autosomal recessive	DefinitiveKidney Cystic and Ciliopathy Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 7,029
Submissions for variants in or overlapping this gene: 12,944
Submissions explicitly reporting this gene: 12,819
Alleles reported pathogenic / likely pathogenic: 1,752
VariationIDs with uncertain significance: 2,189
VariationIDs with conflicting classifications: 471

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about PKHD1?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 1,752 alleles in PKHD1 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in PKHD1.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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