Syndromic Hearing Loss Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: EA0401

The Blueprint Genetics Syndromic Hearing Loss Panel is a 70 gene test for genetic diagnostics of patients with clinical suspicion of Alport syndrome, branchio-oto-renal (BOR) syndrome, Pendred syndrome, Stickler syndrome, Usher syndrome or Waardenburg syndrome.

Inheritance of syndromes characterized by hearing loss and deafness varies from autosomal recessive and dominant to X-linked forms. Clinical utility of this Panel varies between syndromes, and is estimated to be for example >50% for Pendred syndrome, 80%-90% for Usher syndrome, >80% for Alport syndrome and >40% for branchio-oto-renal syndrome. In addition to main phenotypes, this Panel can be used for differential diagnostics of other rare phenotypes such as Jervell and Lange-Nielsen syndrome, Mohr-Tranebjaerg syndrome, Norrie disease, Treacher Collins syndrome and CHARGE syndrome. This Panel includes the Waardenburg Syndrome Panel, Pendred Syndrome Panel, Usher Syndrome Panel, Stickler Syndrome Panel, Alport Syndrome Panel and Branchio-Oto-Renal (BOR) Syndrome Panel. This Panel is included in the Comprehensive Hearing Loss and Deafness Panel.

About Syndromic Hearing Loss

Hearing loss is a genetically very heterogenous group of phenotypes varying in severity and causes. In syndromic hearing loss, symptoms affecting other parts of the body occur interlinked with hearing impairnment or deafness. Altogether syndromic hearing loss accounts for 20% to 30% of congenital hearing loss and deafness and the combined prevalence of syndromic hearing loss is approximately 1-2:10000.


Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more.

Genes in the Syndromic Hearing Loss Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ABHD12Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataractAR1015
ACTG1*Deafness, Baraitser-Winter syndromeAD1737
ADGRV1Usher syndromeAR/Digenic43153
ALMS1*Alström syndromeAR31281
ANKHCalcium pyrophosphate deposition disease (familial chondrocalcinosis type 2), Craniometaphyseal dysplasia autosomal dominant typeAD1221
ATP6V1B1Renal tubular acidosis with deafnessAR839
BCS1LBjornstad syndromeAR2032
BSNDSensorineural deafness with mild renal dysfunction, Bartter syndromeAR1021
BTDBiotinidase deficiencyAR165231
CACNA1DPrimary aldosteronism, seizures, and neurologic abnormalities, Sinoatrial node dysfunction and deafnessAD/AR45
CD151Raph blood groupBG14
CDH23Deafness, Usher syndromeAR/Digenic48294
CDKN1CBeckwith-Wiedemann syndrome, IMAGE syndromeAD2579
CHD7Isolated gonadotropin-releasing hormone deficiency, CHARGE syndromeAD128746
CHSY1Temtamy preaxial brachydactyly syndromeAR610
CIB2Deafness, Usher syndromeAR415
CLRN1Retinitis pigmentosa, Usher syndromeAR1432
COL2A1Avascular necrosis of femoral head, Rhegmatogenous retinal detachment, Epiphyseal dysplasia, with myopia and deafness, Czech dysplasia, Achondrogenesis type 2, Platyspondylic dysplasia Torrance type, Hypochondrogenesis, Spondyloepiphyseal dysplasia congenital (SEDC), Spondyloepimetaphyseal dysplasia (SEMD) Strudwick type, Kniest dysplasia, Spondyloperipheral dysplasia, Mild SED with premature onset arthrosis, SED with metatarsal shortening, Stickler syndrome type 1AD106537
COL4A3Alport syndromeAD/AR17225
COL4A4Alport syndromeAD/AR17170
COL4A5Alport syndromeXL627909
COL4A6Deafness, with cochlear malformationXL124
COL9A1Stickler syndrome recessive type, Multiple epiphyseal dysplasia type 6 (EDM6)AR34
COL9A2Stickler syndrome, Multiple epiphyseal dysplasia type 2 (EDM2)AR512
COL9A3Multiple epihyseal dysplasia type 3 (EDM3)AD316
COL11A1Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2AD/AR1876
COL11A2Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular)AD/AR1751
DFNB31Deafness, Usher syndromeAR928
DLX5Split-hand/foot malformation with sensorineural hearing lossAR38
EDN3Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndromeAD/AR621
EDNRBHirschsprung disease, ABCD syndrome, Waardenburg syndromeAD/AR562
EYA1Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndromeAD33186
FGF3Deafness, congenital with inner ear agenesis, microtia, and microdontiaAR1220
FOXI1Pendred syndrome, Enlarged vestibular aqueductAR18
GATA3Hypomagnesemia, renalAD1677
HARSUsher syndromeAR610
HOXB1Facial paresis, hereditary congenitalAR15
KCNE1Long QT syndrome, Jervell and Lange-Nielsen syndromeAD/AR/Digenic646
KCNJ10Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SESAME syndrome), Pendred syndrome, Enlarged vestibular aqueductAR/Digenic1426
KCNQ1Short QT syndrome, Long QT syndrome, Atrial fibrillation, Jervell and Lange-Nielsen syndromeAD/AR/Digenic237590
LRP2Donnai-Barrow syndrome, Faciooculoacousticorenal syndromeAR1528
MANBAMannosidosis, lysosomalAR918
MITFRenal cell carcinoma with or without malignant melanoma, Tietz albinism-deafness syndrome, Waardenburg syndrome, Melanoma, cutaneous malignantAD1550
MYH9Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafnessAD19113
MYO7ADeafness, Usher syndromeAR125402
NDPExudative vitreoretinopathy, Norrie diseaseXL25155
NLRP3Neonatal onset multisystem inflammatory disease (NOMID), Muckle-Wells syndrome, Chronic infantile neurologic cutaneous articular (CINCA) syndromeAD15125
PAX3Craniofacial-deafness-hand syndrome, Waardenburg syndromeAD/AR20135
PCDH15Deafness, Usher syndromeAR/Digenic2897
PDZD7Usher syndromeDigenic114
POLR1CTreacher Collins syndromeAR1318
POLR1DTreacher Collins syndromeAD/AR725
SIX1Deafness, Branchiootic syndrome, Branchiootorenal syndromeAD915
SIX5Branchiootorenal syndromeAD37
SLC19A2Thiamine-responsive megaloblastic anemia syndromeAR1047
SLC26A4Deafness, Pendred syndrome, Enlarged vestibular aqueductAR98521
SLITRK6Deafness and myopiaAR33
SMAD4Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasiaAD119128
SNAI2Waardenburg syndromeAR24
SOX10Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung diseaseAD31119
TCOF1Treacher Collins syndromeAD17303
TFAP2ABranchiooculofacial sydromeAD942
TIMM8A*Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementiaXL1121
TYR*Albinism, oculocutaneousAR46356
USH1CDeafness, Usher syndromeAR1345
USH1GUsher syndromeAR924
USH2AUsher syndromeAR147924
VCANWagner diseaseAD1119
WFS1Wolfram syndromeAR59343
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (; HGMD, refers to a 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 CDG ( or Orphanet ( databases.

Blueprint Genetics offers a comprehensive syndromic hearing loss panel that covers classical genes associated with Alport syndrome, branchio-oto-renal (BOR) syndrome, CHARGE syndrome, Jervell and Lange-Nielsen syndrome, Mohr-Tranebjaerg syndrome, Norrie disease, Pendred syndrome, Stickler syndrome, treacher Collins syndrome, Usher syndrome and Waardenburg syndrome. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

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. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (, the NHLBI GO Exome Sequencing Project (ESP;, the Exome Aggregation Consortium (ExAC;, ClinVar database of genotype-phenotype associations ( and the Human Gene Mutation Database ( The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (, Polyphen (, and Mutation Taster (

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes


ICD codes

Commonly used ICD-10 codes when ordering the Syndromic Hearing Loss Panel

E70.3Waardenburg syndrome
Q87.8Alport syndrome
E07.1Pendred syndrome
H35.50Usher syndrome
Q87.5Stickler syndrome
Q87.8Branchio-oto-renal (BOR) syndrome

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • 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.