Cholestasis Panel

Last modified: Mar 21, 2018


  • Is a 46 gene panel that includes assessment of non-coding variants
  • Is ideal for patients who have any type of cholestasis including those with clinical suspicion of Alagille syndrome, citrullinemia type 2, Crigler-Najjar syndrome types 1 and 2, Dubin-Johnson syndrome, Gilbert syndrome, intrahepatic cholestasis of pregnancy type 3 or progressive familial intrahepatic cholestasis types 1-4.

Analysis methods

  • PLUS
  • SEQ


3-4 weeks

Number of genes


Test code


CPT codes

SEQ 81405
SEQ 81406
SEQ 81407
DEL/DUP 81479


The Blueprint Genetics Cholestasis Panel (test code GA0501):

  • Is a 46 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Cholestasis Panel

ICD-10 Disease
K83.1 Progressive familial intrahepatic cholestasis types 1-4
E80.6 Dubin-Johnson syndrome
E80.5 Crigler-Najjar syndrome types 1 and 2
E80.4 Gilbert syndrome
Q44.7 Alagille syndrome
K83.1 Intrahepatic cholestasis of pregnancy type 3
E72.20 Citrullinemia type 2

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

Cholestasis is characterized by jaundice and pruritus. It can present as the hallmark feature in progressive familial intrahepatic cholestasis (PFIC) or as a feature in other inherited disorders such as Alagille syndrome where cholestasis occur in 95% of cases in the neonatal period. PFIC is a group of autosomal recessive liver disorders caused by defects in bile secretion and is characterized by intrahepatic cholestasis with disease onset usually in infancy and childhood. PFIC patients usually develop fibrosis and end-stage liver disease before adulthood. Defects in PFIC-associated genes ATP8B1 and ABCB11 may also cause a milder disease called benign recurrent intrahepatic cholestasis. There are several other inherited disorders where cholestasis is frequent such as Alagille syndrome (JAG1 and NOTCH2), arthrogryposis, renal dysfunction, and cholestasis syndrome (ARC syndrome; VPS33B and VIPAS39), alpha-1-antitrypsin deficiency (SERPINA1), citrullinemia (SLC25A13), congenital defects of bile acid synthesis (HSD3B7 and AKR1D1), familial hypercholanemia (TJP2 and BAAT) and neonatal ichthyosis-sclerosing cholangitis syndrome (CLDN1). The prevalence of PFIC is unknown while the prevalence is as follows for other causes of cholestasis: Dubin-Johnson 1:1,300 in Iranian or Moroccan Jews, Alagille syndrome 1:30,000, Crigler-Najjar syndrome 1:1,000,000. The Gilbert syndrome prevalence is 3-7% but it does cause only abnormal laboratory findings but no clinical symptoms.

Genes in the Cholestasis Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ABCB4 Gallbladder disease, Low phospholipid-associated cholelithiasis, Cholestasis AD/AR 17 203
ABCB11 Cholestasis AD/AR 24 275
ABCC2 Dubin-Johnson syndrome AD/AR 17 41
AKR1D1 Bile acid synthesis defect, congenital, 2 AR 5 13
ATP8B1 Intrahepatic cholestasis of pregnancy, Familial intrahepatic cholestasis, recurrent, Cholestasis, progressive familial intrahepatic AD/AR 17 125
BAAT Hypercholanemia, familial AR 3 7
CFTR Cystic fibrosis AR 410 1765
CREB3L3 Hypertriglyceridaemia AD 9
CYP7B1 Bile acid synthesis defect AR 16 40
DCDC2 Deafness AR 9 9
DGUOK Mitochondrial DNA depletion syndrome AR 19 60
EPCAM Diarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposis AD/AR 20 69
FAH Tyrosinemia AR 39 100
HSD3B7 Bile acid synthesis defect, congenital, 1 AR 7 24
JAG1 Alagille syndrome AD 100 568
LCT Lactase deficiency AR 11 14
LMF1 Combined lipase deficiency AR 4 13
MKS1 Bardet-Biedl syndrome, Meckel syndrome AR 42 51
MYO5B* Diarrhea, with microvillus atrophy AR 12 68
NEUROG3 Diarrhea, malabsorptive, congenital AR 3 7
NOTCH2* Alagille syndrome, Hajdu-Cheney syndrome AD 25 61
NPC1 Niemann-Pick disease AR 107 447
NPC2 Niemann-pick disease AR 16 27
NPHP1 Nephronophthisis, Joubert syndrome, Senior-Loken syndrome AR 14 73
NPHP3 Nephronophthisis, Renal-hepatic-pancreatic dysplasia, Meckel syndrome AR 24 72
NPHP4 Nephronophthisis, Senior-Loken syndrome AR 12 108
NR1H4 Cholestasis, progressive familial intrahepatic 5 4 5
PEX1 Heimler syndrome AR 77 130
PEX2 Zellweger syndrome, Peroxisome biogenesis disorder AR 9 18
PEX5 Adrenoleukodystrophy, neonatal, Rhizomelic chondrodysplasia punctata, Zellweger syndrome, Peroxisome biogenesis disorder AR 7 14
PEX6 Heimler syndrome AR 25 105
PEX10 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder, Ataxia AR 18 29
PEX12 Zellweger syndrome, Peroxisome biogenesis disorder AR 19 37
PEX26 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder AR 11 24
SERPINA1 Alpha-1-antitrypsin deficiency AR 46 79
SLC25A13 Citrin deficiency AR 23 109
SLC26A3 Diarrhea, secretory chloride, congenital AR 55 82
SMPD1 Niemann-Pick disease AR 81 238
SPINT2 Diarrhea, secretory sodium, congenital AD 6 10
TJP2 Cholestasis, progressive familial intrahepatic, Hypercholanemia, familial AR 20 23
TMEM216 Joubert syndrome, Meckel syndrome AR 14 8
TRMU Liver failure, infantile, Reversible infantile respiratory chain deficiency AR 18 17
TTC37 Trichohepatoenteric syndrome AR 9 38
UGT1A1 Crigler-Najjar syndrome, Gilbert syndrome AD/AR 31 138
VIPAS39 Arthrogryposis, renal dysfunction, and cholestasis 2 AR 5 13
VPS33B Arthrogryposis - renal dysfunction - cholestasis AD/AR 12 56

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
CFTR Chr7:117119984 c.-165G>A NM_000492.3 rs145483167
CFTR Chr7:117119900 c.-249G>C NM_000492.3
CFTR Chr7:117120115 c.-34C>T NM_000492.3 rs756314710
CFTR Chr7:117119654 c.-495C>T NM_000492.3 rs397507565
CFTR Chr7:117120064 c.-85C>G NM_000492.3
CFTR Chr7:117199500 c.1393-18G>A NM_000492.3 rs397508199
CFTR Chr7:117227774 c.1585-19T>C NM_000492.3 rs778457306
CFTR Chr7:117218381 c.1585-9412A>G NM_000492.3 rs397508229
CFTR Chr7:117229530 c.1680-877G>T NM_000492.3 rs397508261
CFTR Chr7:117229524 c.1680-883A>G NM_000492.3
CFTR Chr7:117229521 c.1680-886A>G NM_000492.3 rs397508266
CFTR Chr7:117243855 c.2908+19G>C NM_000492.3 rs370683572
CFTR Chr7:117246713 c.2909-15T>G NM_000492.3 rs397508455
CFTR Chr7:117246840 c.2988+33G>T NM_000492.3
CFTR Chr7:117251624 c.3140-11A>G NM_000492.3
CFTR Chr7:117251609 c.3140-26A>G NM_000492.3 rs76151804
CFTR Chr7:117266272 c.3469-1304C>G NM_000492.3
CFTR Chr7:117267864 c.3717+40A>G NM_000492.3 rs397508595
CFTR Chr7:117280015 c.3718-2477C>T NM_000492.3 rs75039782
CFTR Chr7:117282680 c.3873+33A>G NM_000492.3 rs397508622
CFTR Chr7:117288374 c.3874-4522A>G NM_000492.3
CFTR Chr7:117120325 c.53+124T>C NM_000492.3
DGUOK Chr2:74177701 c.444-11C>G NM_080916.2 rs536746349
DGUOK Chr2:74177650 c.444-62C>A NM_080916.2
EPCAM Chr2:47606078 c.556-14A>G NM_002354.2 rs376155665
JAG1 Chr20:10629767 c.1349-12T>G NM_000214.2
MYO5B Chr18:47365503 c.4852+11A>G NM_001080467.2
NPC1 Chr18:21132700 c.1554-1009G>A NM_000271.4
NPC1 Chr18:21137182 c.882-28A>G/T NM_000271.4
PEX6 Chr6:42933952 c.2300+28G>A NM_000287.3 rs267608237
PEX6 Chr6:42933858 c.2301-15C>G NM_000287.3 rs267608236
SERPINA1 Chr14:94854896 c.-5+1G>A NM_000295.4 rs775786225
UGT1A1 Chr2:234668879 c.-41_-40dupTA NM_000463.2 rs34983651
VPS33B Chr15:91550814 c.499-11G>A NM_018668.3

Added and removed genes from the panel

Genes added Genes removed

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • 1479 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics cholestasis panel covers classical genes associated with progressive familial intrahepatic cholestasis types 1-4, Dubin-Johnson syndrome, Crigler-Najjar syndrome types 1 and 2, Gilbert syndrome, Alagille syndrome, intrahepatic cholestasis of pregnancy type 3, citrullinemia type 2, congenital bile acid synthesis defect type 3, emphysema, related to alpha-1-antitrypsin deficiency, transient infantile liver failure, arthrogryposis, renal dysfunction, and cholestasis 1 and tyrosinemia type 1. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
The performance presented above reached by WES with the following coverage metrics
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%


The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.