Test Code: 5261

Autosomal Recessive Polycystic Kidney Disease: PKHD1 Gene Deletion/Duplication
Test Code: 5261
Turnaround time: 3 weeks


The majority of individuals with autosomal recessive polycystic kidney disease (ARPKD) present in the neonatal period with enlarged echogenic kidneys. Clinical diagnostic criteria of autosomal recessive polycystic kidney disease (ARPKD) are:

Typical findings on renal imaging AND One or more of the following:

  • Clinical/laboratory signs of hepatic fibrosis that leads to portal hypertension and may be manifested by hepato-splenomegaly and/or esophageal varices
  • Hepatic pathology demonstrating a developmental ductal plate abnormality Absence of renal cysts in both parents, as demonstrated by ultrasound examination Pathoanatomical proof of ARPKD in an affected sib
  • Parental consanguinity suggesting autosomal recessive inheritance

At initial presentation, approximately 45% of infants have liver abnormalities, including hepatomegaly, dilated intrahepatic biliary ducts, and increased echogenicity. Pulmonary hypoplasia resulting from oligohydramnios occurs in a number of affected infants. Approximately 30% of affected neonates die, primarily of respiratory insufficiency. More than 50% of affected children progress to end-stage renal disease (ESRD), usually in the first decade of life. With neonatal respiratory support and renal replacement therapies, the ten-year survival of those who live beyond the first year of life has improved to 82%. Fifteen-year survival is estimated to be 67%-79%. A minority of individuals present as older children, usually with hepatosplenomegaly as the presenting feature.

PKHD1 (6p21.1-p12) is the only gene known to be associated with ARPKD. Mutation detection rates for sequence analysis of the coding region and flanking intronic regions have not been reported; they are expected to be as high or higher than those reported for mutation scanning analyses. Mutation scanning by denaturing high-performance liquid chromatography (DHPLC) has demonstrated an overall mutation detection rate of 82%-85% when diagnostic criteria of ARPKD are met either prenatally or postnatally.

The incidence of ARPKD is estimated at 1:10,000 to 1:40,000. The true incidence may be underestimated because children may die in the neonatal period without a definitive diagnosis, and previously undetected young adults are being diagnosed by molecular genetic testing. The carrier frequency for a PKHD1 mutation in the general population is estimated to be 1:70.

For patients with suspected ARPKD, sequence analysis is recommended as the first step in mutation identification. For patients in whom mutations are not identified by full gene sequencing, deletion/duplication analysis is appropriate.


This test is indicated for:

  • Confirmation of a clinical diagnosis of ARPKD in individuals who have tested negative for sequence analysis
  • Carrier testing in adults with a family history of ARPKD who have tested negative for sequence analysis


DNA isolated from peripheral blood is hybridized to a CGH array to detect deletions and duplications. The targeted CGH array has overlapping probes which cover the entire genomic region.

Please note that a “backbone” of probes across the entire genome are included on the array for analytical and quality control purposes. Rarely, off- target copy number variants causative of disease may be identified that may or may not be related to the patient’s phenotype. Only known pathogenic off-target copy number variants will be reported. Off-target copy number variants of unknown clinical significance will not be reported.


Detection is limited to duplications and deletions. The CGH array will not detect point or intronic mutations. Results of molecular analysis must be interpreted in the context of the patient’s clinical and/or biochemical phenotype.


Submit only 1 of the following specimen types
* Preferred specimen type: Whole Blood

Type: Whole Blood
Specimen Requirements:
In EDTA (purple top) or ACD (yellow top) tube: Infants (2 years): 3-5 ml
Older Children & Adults: 5-10 ml

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample within 5 days of collection at room temperature with overnight delivery.

Type: Saliva
Specimen Requirements:
OrageneTM Saliva Collection kit (available through CEN4GEN) used according to manufacturer instructions.

Specimen Collection and Shipping: Store sample at room temperature. Ship sample within 5 days of collection at room temperature with overnight delivery.

Submit copies of diagnostic biochemical test results with the sample, if appropriate.
Sequence analysis is required before deletion/duplication analysis by targeted CGH array. If sequencing is performed by another third party provider, please submit a copy of the sequencing report with the test requisition.


  • Sequencing analysis of the PKHD1 gene is available (test code: 6401) and is required before deletion/duplication analysis.