- Is a 99 gene panel that includes assessment of non-coding variants
Is ideal for patients with a clinical suspicion of X-linked intellectual disability.
Is not ideal for patients suspected to have Fragile X syndrome before the repeat expansion in FMR1 has been excluded.
Number of genes99
CPT codesSEQ 81470
The Blueprint Genetics X-linked Intellectual Disability Panel (test code NE0601):
- Is a 99 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
- 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.
Intellectual disability (ID) is more common in males than females in the general population, presumed to be due to mutations in genes on the X chromosome. X-linked ID accounts for approximately 16% of males with intellectual disability. In addition to karyotype abnormalities and Fragile X syndrome, numerous X-linked genes exist where mutations have been described that result in either syndromic or non‐syndromic ID. Epileptic seizures accompany ID in almost half of these X-linked disorders.This panel allows for systematic screening of X-linked nonsyndromic and syndromic intellectual disability.
Genes in the X-linked Intellectual Disability Panel and their clinical significance
|AFF2||Premature ovarian failure, Mental retardation, X-linked, FRAXE type||XL||6||25|
|AP1S2*||Mental retardation, syndromic, Fried (Pettigrew syndrome)||XL||11||11|
|ARHGEF9||Epileptic encephalopathy, early infantile||XL||7||21|
|ARX||Lissencephaly, Epileptic encephalopathy, Corpus callosum, agenesis of, with abnormal genitalia, Partington syndrome, Proud syndrome, Hydranencephaly with abnormal genitalia, Mental retardation||XL||66||89|
|ATP6AP2||Mental retardation, syndromic, Hedera, Parkinsonism with spasticity||XL||3||4|
|ATP7A||Menkes disease, Occipital horn syndrome, Spinal muscular atrophy, distal, X-linked 3||XL||113||354|
|ATRX||Carpenter-Waziri syndrome, Alpha-thalassemia/mental retardation syndrome, Holmes-Gang syndrome, Juberg-Marsidi syndrome, Smith-Fineman-Myers syndrome, Mental retardation-hypotonic facies syndrome||XL||59||163|
|BCOR||Microphthalmia, syndromic, Oculofaciocardiodental syndrome||XL||38||50|
|CASK||Mental retardation and microcephaly with pontine and cerebellar hypoplasia, FG syndrome, Mental retardation||XL||80||104|
|CDKL5||Epileptic encephalopathy, early infantile, Rett syndrome, atypical, Angelman-like syndrome||XL||291||313|
|CLCN4||Mental retardation, X-linked 49||XL||21||9|
|CUL4B||Mental retardation, syndromic, Cabezas||XL||23||37|
|DCX||Lissencephaly, Subcortical laminal heterotopia||XL||131||142|
|DDX3X||Mental retardation, X-linked 102||XL||76||48|
|DKC1||Hoyeraal-Hreidarsson syndrome, Dyskeratosis congenita||XL||47||71|
|FGD1||Aarskog-Scott syndrome, Mental retardation, syndromic||XL||26||49|
|FLNA||Frontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defects||XL||119||235|
|FMR1||Premature ovarian failure, Fragile X syndrome, Fragile X tremor/ataxia syndrome||XL||13||76|
|GK*||Glycerol kinase deficiency||XL||11||35|
|HCCS||Linear skin defects with multiple congenital anomalies 1 (MIDAS syndrome)||XL||7||13|
|HPRT1||Lesch-Nyhan syndrome, Kelley-Seegmiller syndrome||XL||69||426|
|HSD17B10||17-beta-hydroxysteroid dehydrogenase X deficiency, Mental retardation, syndromic||XL||10||14|
|HUWE1||Mental retardation, syndromic, Turner||XL||37||37|
|IGBP1||Corpus callosum, agenesis of, with mental retardation, ocular coloboma and micrognathia||XL||1||1|
|KDM5C||Mental retardation, syndromic, Claes-Jensen||XL||43||54|
|L1CAM||Mental retardation, aphasia, shuffling gait, and adducted thumbs (MASA) syndrome, Hydrocephalus due to congenital stenosis of aqueduct of Sylvius, Spastic, CRASH syndrome, Corpus callosum, partial agenesis||XL||71||287|
|MAGT1||Immunodeficiency, with magnesium defect, Epstein-Barr virus infection and neoplasia, Mental retardation, X-linked 95||XL||5||14|
|MBTPS2||Keratosis follicularis spinulosa decalvans, IFAP syndrome, Palmoplantar keratoderma, mutilating, with periorificial keratotic plaques||XL||10||24|
|MECP2||Angelman-like syndrome, Autism, Rett syndrome, Encephalopathy, Mental retardation||XL||471||984|
|MED12||Ohdo syndrome, Mental retardation, with Marfanoid habitus, FG syndrome, Opitz-Kaveggia syndrome, Lujan-Fryns syndrome||XL||29||27|
|MID1*||Opitz GBBB syndrome||XL||19||94|
|NDP||Exudative vitreoretinopathy, Norrie disease||XL||31||165|
|NDUFA1||Mitochondrial complex I deficiency||XL||3||4|
|NHS||Nance-Horan syndrome, Cataract||XL||28||48|
|NLGN3||Autism, Asperger syndrome||XL||2||9|
|NLGN4X||Autism, Asperger syndrome, Mental retardation||XL||7||35|
|NSDHL||Congenital hemidysplasia with ichthyosiform erythroderma and limb defects (CHILD syndrome), CK syndrome||XL||15||28|
|NXF5*||Familial heart block and focal segmental glomerulosclerosis, Mental retardation, syndromic, X-linked||XL||5|
|OCRL||Lowe syndrome, Dent disease||XL||42||260|
|OFD1||Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome||XL||142||157|
|OPHN1||Mental retardation, with cerebellar hypoplasia and distinctive facial appearance||XL||25||36|
|OTC||Ornithine transcarbamylase deficiency||XL||342||505|
|PCDH19||Epileptic encephalopathy, early infantile||XL||104||160|
|PDHA1||Leigh syndrome, Pyruvate dehydrogenase E1-alpha deficiency||XL||62||191|
|PGK1||Phosphoglycerate kinase 1 deficiency||XL||15||26|
|PHF8||Mental retardation syndrome, Siderius||XL||13||15|
|PLP1||Spastic paraplegia, Pelizaeus-Merzbacher disease||XL||55||337|
|PORCN||Focal dermal hypoplasia||XL||15||119|
|PRPS1*||Deafness, Phosphoribosylpyrophosphate synthetase I superactivity, Arts syndrome, Charcot-Marie-Tooth disease, X-linked recessive, 5, Nonsyndromic sensorineural deafness, 2, X-linked||XL||27||31|
|PTCHD1||Autism susceptibility, X-linked 4||XL||9||46|
|RAB39B||Waisman parkinsonism-mental retardation syndrome, Mental retardation||XL||6||17|
|RPS6KA3||Coffin-Lowry syndrome, Mental retardation||XL||55||170|
|SHROOM4||Stocco dos Santos mental retardation syndrome||XL||3||9|
|SLC6A8*||Creatine deficiency syndrome||XL||32||128|
|SLC9A6||Mental retardation, syndromic, Christianson||XL||24||21|
|SMC1A||Cornelia de Lange syndrome||XL||56||87|
|SMS||Mental retardation, Snyder-Robinson||XL||11||14|
|SRPX2||Rolandic epilepsy, mental retardation, and speech dyspraxia||XL||3||3|
|SYN1||Epilepsy, with variable learning disabilities and behavior disorders||XL||11||7|
|TAF1||Dystonia 3, torsion, X-linked, Mental retardation, X-linked, syndromic 33||XL||12||14|
|TIMM8A*||Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementia||XL||10||21|
|UBE2A||Mental retardation, syndromic, Nascimento||XL||8||25|
|UPF3B||Mental retardation, syndromic||XL||9||18|
|USP9X||Mental retardation, X-linked 99, Mental retardation, X-linked 99, syndromic, female restricted||XL||27||26|
|ZDHHC9||Mental retardation, syndromic, Raymond||XL||8||13|
* 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|
Test strengthThe 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
- ~1,500 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 limitationsThis 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 (variant with a minor allele fraction of 14.6% is detected with 90% probability)
- 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 x-linked intellectual disability panel covers classical genes associated with x-linked mental retardation. 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.
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 the following criteria are not Sanger confirmed: the variant quality score is above the internal threshold for a true positive call, and visual check-up of the variant at IGV is in-line with the variant call. 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.
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.