Hyperlipidemia Panel

Is a 20 gene panel that includes assessment of non-coding variants.

Is ideal for patients with a clinical suspicion of inherited dyslipidemia including familial hypercholesterolemia due to LDL receptor mutation or ligand-defective apoB, any type of hypertriglyceridemia and sitosterolemia. The genes on the Hyperlipidemia Core Panel are included on this panel.

Analysis methods
  • PLUS
4 weeks
Number of genes
Test code
Panel tier
Tier 2
CPT Code *
81405, 81406 x2, 81407, 81479
* The CPT codes provided are based on AMA guidelines and are for informational purposes only. CPT coding is the sole responsibility of the billing party. Please direct any questions regarding coding to the payer being billed.


The Blueprint Genetics Hyperlipidemia Panel (test code CA1101):

Read about our accreditations, certifications and CE-marked IVD medical devices here.

ICD Codes

Refer to the most current version of ICD-10-CM manual for a complete list of ICD-10 codes.

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Please see Sample Requirements for accepted saliva kits)

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

We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.

Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.

Read more about our sample requirements here.

Familial lipid disorders such as familial hypercholesterolemia (FH) are inborn errors of metabolism that result in high levels of blood cholesterol and predispose to myocardial infarctions at an early age. In addition to lethal cardiovascular complications, inherited forms of hypercholesterolemia can also cause health problems related to the buildup of excess cholesterol in other tissues. If cholesterol accumulates in tendons, it causes characteristic growths called tendon xanthomas. These growths most often affect the Achilles tendons and tendons in the hands and fingers. Yellowish cholesterol deposits under the skin of the eyelids are known as xanthelasmata. Cholesterol can also accumulate at the edges of the clear, front surface of the eye (the cornea), leading to a gray-colored ring called an arcus cornealis. Familial hypercholesterolemia is usually an autosomal dominant/recessive disorder caused by mutations in LDLR, APOB, PCSK9 or LDLRAP1. Both APOB and PCSK9 related FH are clinically indistinguishable from heterozygous FH (HeFH) caused by LDLR mutations. Recessive forms of hypercholesterolemia are rare. Of these, FH associated with LDLRAP1 is clinically similar to HeFHs. On the contrary, sitosterolemia, which is caused by ABCG5 and ABCG8 mutations, is a specific form of hyperlipidemia that manifests as hypercholesterolemia and high levels (30-100x normal) of plant sterols (phytosterols) in blood and other tissues. Clinical presentation of sitosterolemia includes xanthomas and coronary artery disease at an early age with conflict between the standard risk factor profile and the disease presentation. The familial lipoprotein lipase (LPL) deficiency (also called type 1 hyperlipoproteinemia) is an autosomal recessive condition distinct from other hyperlipidemias. It usually presents in childhood with very severe hypertriglyceridemia and episodic abdominal pain, recurrent acute pancreatitis, eruptive cutaneous xanthomata, and hepatosplenomegaly.

Genes in the Hyperlipidemia Panel and their clinical significance

To view complete table content, scroll horizontally.

Gene Associated phenotypes Inheritance ClinVar HGMD
ABCA1 Tangier disease, ABCA1 deficiency, HDL deficiency, Familial hypoalphalipoproteinemia AD/AR 25 218
ABCG5 Sitosterolemia AR 13 42
ABCG8 Sitosterolemia AR 18 44
ALMS1* Alström syndrome AR 197 302
APOA1 Amyloidosis, systemic nonneuronopathic, Hypoalphalipoproteinemia AD/AR 28 71
APOA5 Hyperchylomicronemia AD/AR 3 61
APOB Hypobetalipoproteinemia, Hypercholesterolemia AD/AR 69 306
APOC2 Hyperlipoproteinemia, type Ib AR 13 22
APOC3 Apolipoprotein C-III deficiency AD 6 8
APOE Sea-blue histiocyte disease, Dysbetalipoproteinemia, familial (Hyperlipoproteinemia), Lipoprotein glomerulopathy AD/AR 31 55
CREB3L3 Hypertriglyceridaemia AD 9
CYP27A1 Cerebrotendinous xanthomatosis AR 69 110
GPD1 Hypertriglyceridemia, transient infantile AR 4 10
GPIHBP1 Hyperlipoproteinemia, type ID AR 10 31
LDLR Hypercholesterolemia AD/AR 1719 2180
LDLRAP1 Hypercholesterolemia AR 10 23
LIPA Wolman disease, Cholesterol ester storage disease AR 27 93
LMF1 Combined lipase deficiency AR 4 14
LPL Lipoprotein lipase deficiency, Hyperlipoproteinemia, Combined hyperlipidemia, familial AD/AR 44 209
PCSK9 Hypercholesterolemia AD 29 89

The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads.


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

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#). Due to possible limitations these genes may not be available as single gene tests.

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), 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 Mitomap databases.

Non-coding variants covered by Hyperlipidemia Panel

To view complete table content, scroll horizontally.

Gene Genomic location HG19 HGVS RefSeq RS-number
ABCA1 Chr9:107549295 c.6205-39delT NM_005502.3 rs572405590
ABCA1 Chr9:107567035 c.4465-34A>G NM_005502.3
ABCA1 Chr9:107571856 c.4176-11T>G NM_005502.3
ABCA1 Chr9:107599404 c.1195-27G>A NM_005502.3 rs200563809
ABCA1 Chr9:107690213 c.-93+2dupT NM_005502.3
APOA1 Chr11:116708299 c.-21+22G>A NM_000039.1
APOA1 Chr11:116708365 c.-65A>C NM_000039.1
APOC3 Chr11:116701284 c.-13-2A>C NM_000040.1
LDLR Chr19:11199939 NM_000527.4
LDLR Chr19:11199958 c.-267A>G NM_000527.4
LDLR Chr19:11199997 c.-228G>C NM_000527.4 rs376713337
LDLR Chr19:11200000 NM_000527.4
LDLR Chr19:11200019 c.-206C>T NM_000527.4 rs549995837
LDLR Chr19:11200031 NM_000527.4 rs1270618112
LDLR Chr19:11200032 NM_000527.4 rs879254362
LDLR Chr19:11200032 NM_000527.4
LDLR Chr19:11200034 c.-191C>A NM_000527.4
LDLR Chr19:11200037 c.-188C>T NM_000527.4
LDLR Chr19:11200038 c.-185_-183delCTT NM_000527.4
LDLR Chr19:11200053 c.-172G>A NM_000527.4
LDLR Chr19:11200057 c.-168A>G NM_000527.4
LDLR Chr19:11200062 c.-163T>C NM_000527.4
LDLR Chr19:11200064 c.-161A>C NM_000527.4
LDLR Chr19:11200069 c.-155_-150delACCCCA NM_000527.4
LDLR Chr19:11200069 c.-155_-154delACinsTTCTGCAAACTCCT NM_000527.4
LDLR Chr19:11200069 c.-156C>T NM_000527.4
LDLR Chr19:11200070 c.-155_-150delACCCCAinsTT NM_000527.4
LDLR Chr19:11200070 c.-155_-154delACinsTTCTGCAAACTCCT NM_000527.4 rs879254365
LDLR Chr19:11200071 c.-154C>T NM_000527.4
LDLR Chr19:11200072 c.-153C>T NM_000527.4
LDLR Chr19:11200073 c.-152C>T NM_000527.4
LDLR Chr19:11200074 c.-151C>G NM_000527.4
LDLR Chr19:11200075 c.-150A>G NM_000527.4
LDLR Chr19:11200076 c.-149C>A NM_000527.4
LDLR Chr19:11200079 c.-146C>A NM_000527.4
LDLR Chr19:11200083 c.-142C>G/T NM_000527.4
LDLR Chr19:11200084 c.-139_-130delCTCCCCCTGC NM_000527.4
LDLR Chr19:11200085 c.-140C>A/G/T NM_000527.4 rs875989887
LDLR Chr19:11200086 c.-139C>A/G NM_000527.4
LDLR Chr19:11200086 c.-138delT NM_000527.4 rs387906307
LDLR Chr19:11200087 c.-138T>C NM_000527.4
LDLR Chr19:11200088 c.-137C>T NM_000527.4
LDLR Chr19:11200089 c.-136C>G NM_000527.4 rs879254374
LDLR Chr19:11200089 c.-136C>G/T NM_000527.4
LDLR Chr19:11200089 c.-136C>T NM_000527.4
LDLR Chr19:11200090 c.-135C>G NM_000527.4
LDLR Chr19:11200091 c.-134C>T NM_000527.4
LDLR Chr19:11200098 c.-124dupA NM_000527.4
LDLR Chr19:11200105 c.-120C>T NM_000527.4 rs875989886
LDLR Chr19:11200124 c.-101T>C NM_000527.4 rs747068848
LDLR Chr19:11200126 c.-99A>G NM_000527.4
LDLR Chr19:11200127 c.-98C>T NM_000527.4
LDLR Chr19:11200202 c.-23A>C NM_000527.4 rs763282380
LDLR Chr19:11200202 c.-22delC NM_000527.4 rs879254379
LDLR Chr19:11200211 c.-14C>A NM_000527.4
LDLR Chr19:11218203 c.940+14delC NM_000527.4 rs879254730
LDLR Chr19:11221315 c.941-13T>A NM_000527.4
LDLR Chr19:11224179 c.1359-31_1359-23delGCGCTGATGinsCGGCT NM_000527.4
LDLR Chr19:11224186 c.1359-25A>G NM_000527.4
LDLR Chr19:11227685 c.1845+11C>G NM_000527.4
LDLR Chr19:11227689 c.1845+15C>A NM_000527.4
LDLR Chr19:11231284 c.2140+86C>G NM_000527.4
LDLR Chr19:11231301 c.2140+103G>T NM_000527.4
LDLR Chr19:11242035 c.*43G>A NM_000527.4 rs879254527
LDLRAP1 Chr1:25870164 c.-17_-12dupGGCGGC NM_015627.2
LDLRAP1 Chr1:25891056 c.748-608G>A NM_015627.2
LPL Chr8:19796711 c.-241G>C NM_000237.2 rs540525285
LPL Chr8:19796725 c.-227T>C NM_000237.2
PCSK9 Chr1:55505180 c.-331C>A NM_174936.3 rs778796405

Test Strengths

The strengths of this test include:

  • CAP accredited laboratory
  • 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
  • Some of the panels include the whole mitochondrial genome (please see the Panel Content section)
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
  • Our rigorous 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
  • Some of the panels include the whole mitochondrial genome but not all (please see the Panel Content section)
  • 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 in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Low level heteroplasmy in mtDNA (>90% are detected at 5% level)
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments
  • Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis.

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.

The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

The performance metrics listed below are from an initial validation performed at our main laboratory in Finland. The performance metrics of our laboratory in Marlborough, MA, are equivalent.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999%
Insertions, deletions and indels by sequence analysis
1-10 bps 99.2% (7,745/7,806) >99.9999%
11-50 bps 99.13% (2,524/2,546) >99.9999%
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (25/25)
The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics
Mean sequencing depth 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Performance of Blueprint Genetics Mitochondrial Sequencing Assay.

Sensitivity % Specificity %
Single nucleotide variants
Heteroplasmic (45-100%) 100.0% (50/50) 100.0%
Heteroplasmic (35-45%) 100.0% (87/87) 100.0%
Heteroplasmic (25-35%) 100.0% (73/73) 100.0%
Heteroplasmic (15-25%) 100.0% (77/77) 100.0%
Heteroplasmic (10-15%) 100.0% (74/74) 100.0%
Heteroplasmic (5-10%) 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 50.0% (2/4) 100.0%
All types
Single nucleotide variants n=2026 SNVs
Heteroplasmic (45-100%) 100.0% (1940/1940) 100.0%
Heteroplasmic (35-45%) 100.0% (4/4) 100.0%
Heteroplasmic (25-35%) 100.0% (3/3) 100.0%
Heteroplasmic (15-25%) 100.0% (3/3) 100.0%
Heteroplasmic (10-15%) 100.0% (9/9) 100.0%
Heteroplasmic (5-10%) 92.3% (12/13) 99.98%
Heteroplasmic (<5%) 88.9% (48/54) 99.93%
Insertions and deletions by sequence analysis n=40 indels
Heteroplasmic (45-100%) 1-10bp 100.0% (32/32) 100.0%
Heteroplasmic (5-45%) 1-10bp 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 1-10bp 100.0% (5/5) 99,997%
SIMULATION DATA /(mitomap mutations)
Insertions, and deletions 1-24 bps by sequence analysis; n=17
Homoplasmic (100%) 1-24bp 100.0% (17/17) 99.98%
Heteroplasmic (50%) 100.0% (17/17) 99.99%
Heteroplasmic (25%) 100.0% (17/17) 100.0%
Heteroplasmic (20%) 100.0% (17/17) 100.0%
Heteroplasmic (15%) 100.0% (17/17) 100.0%
Heteroplasmic (10%) 94.1% (16/17) 100.0%
Heteroplasmic (5%) 94.1% (16/17) 100.0%
Copy number variants (separate artifical mutations; n=1500)
Homoplasmic (100%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (50%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (30%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (20%) 500 bp, 1kb, 5 kb 99.7% 100.0%
Heteroplasmic (10%) 500 bp, 1kb, 5 kb 99.0% 100.0%
The performance presented above reached by following coverage metrics at assay level (n=66)
Mean of medians Median of medians
Mean sequencing depth MQ0 (clinical) 18224X 17366X
Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical) 100%
rho zero cell line (=no mtDNA), mean sequencing depth 12X

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 and regulatory 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. If the test includes the mitochondrial genome the target region gene list contains the mitochondrial genes. 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 including, 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, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with suboptimal coverage (<20X for nuclear genes and <1000X for mtDNA) if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

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 cornerstone of clinical interpretation and resulting patient management decisions. Our classifications follow the ACMG guideline 2015.

The final step in the analysis is orthogonal confirmation. Sequence and copy number variants classified as pathogenic, likely pathogenic, and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing or by orthogonal methods such as qPCR/ddPCR when they do not meet our stringent NGS quality metrics for a true positive call.

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, abstracts, and variant databases used to help ordering providers 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. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. 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 healthcare provider at no additional cost, according to our latest follow-up reporting policy.