X-linked Intellectual Disability Panel

Last modified: Mar 01, 2019

Summary

  • 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.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

4 weeks

Number of genes

99

Test code

NE0601

Panel size

Large

CPT codes

SEQ 81470
DEL/DUP 81471

Summary

The Blueprint Genetics X-linked Intellectual Disability Panel (test code NE0601):

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

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. Read more about our sample requirements here.

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

Gene Associated phenotypes Inheritance ClinVar HGMD
ABCD1* Adrenoleukodystrophy XL 95 663
ACSL4 Mental retardation XL 6 7
AFF2 Premature ovarian failure, Mental retardation, X-linked, FRAXE type XL 6 25
AP1S2* Mental retardation, syndromic, Fried (Pettigrew syndrome) XL 11 12
ARHGEF6 Mental retardation XL 2 5
ARHGEF9 Epileptic encephalopathy, early infantile XL 10 23
ARX Lissencephaly, Epileptic encephalopathy, Corpus callosum, agenesis of, with abnormal genitalia, Partington syndrome, Proud syndrome, Hydranencephaly with abnormal genitalia, Mental retardation XL 66 93
ATP6AP2 Mental retardation, syndromic, Hedera, Parkinsonism with spasticity XL 3 6
ATP7A Menkes disease, Occipital horn syndrome, Spinal muscular atrophy, distal, X-linked 3 XL 116 354
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 65 165
BCOR Microphthalmia, syndromic, Oculofaciocardiodental syndrome XL 40 53
BRWD3 Mental retardation XL 9 17
CASK Mental retardation and microcephaly with pontine and cerebellar hypoplasia, FG syndrome, Mental retardation XL 87 112
CDKL5 Epileptic encephalopathy, early infantile, Rett syndrome, atypical, Angelman-like syndrome XL 312 331
CLCN4 Mental retardation, X-linked 49 XL 21 17
CUL4B Mental retardation, syndromic, Cabezas XL 23 38
DCX Lissencephaly, Subcortical laminal heterotopia XL 131 142
DDX3X Mental retardation, X-linked 102 XL 84 51
DKC1 Hoyeraal-Hreidarsson syndrome, Dyskeratosis congenita XL 48 74
DLG3 Mental retardation XL 11 17
ELK1* Intellectual disability XL 3
FANCB Fanconi anemia XL 11 21
FGD1 Aarskog-Scott syndrome, Mental retardation, syndromic XL 29 51
FLNA Frontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defects XL 133 257
FMR1 Premature ovarian failure, Fragile X syndrome, Fragile X tremor/ataxia syndrome XL 13 76
FTSJ1 Mental retardation XL 5 10
GDI1 Mental retardation XL 7 11
GK* Glycerol kinase deficiency XL 11 35
GPC3 Simpson-Golabi-Behmel syndrome XL 33 75
GRIA3 Mental retardation XL 12 23
HCCS Linear skin defects with multiple congenital anomalies 1 (MIDAS syndrome) XL 7 13
HPRT1 Lesch-Nyhan syndrome, Kelley-Seegmiller syndrome XL 72 427
HSD17B10 17-beta-hydroxysteroid dehydrogenase X deficiency, Mental retardation, syndromic XL 10 15
HUWE1 Mental retardation, syndromic, Turner XL 37 54
IDS* Mucopolysaccharidosis XL 85 637
IGBP1 Corpus callosum, agenesis of, with mental retardation, ocular coloboma and micrognathia XL 1 2
IL1RAPL1 Mental retardation XL 17 41
IQSEC2 Mental retardation XL 55 56
KDM5C Mental retardation, syndromic, Claes-Jensen XL 47 55
KIAA2022 Mental retardation XL 42 40
KLF8 Intellectual disability XL 1 2
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 80 292
LAMP2 Danon disease XL 62 101
MAGT1 Immunodeficiency, with magnesium defect, Epstein-Barr virus infection and neoplasia, Mental retardation, X-linked 95 XL 8 14
MAOA Brunner syndrome XL 7 14
MBTPS2 Keratosis follicularis spinulosa decalvans, IFAP syndrome, Palmoplantar keratoderma, mutilating, with periorificial keratotic plaques XL 12 25
MECP2 Angelman-like syndrome, Autism, Rett syndrome, Encephalopathy, Mental retardation XL 506 1039
MED12 Ohdo syndrome, Mental retardation, with Marfanoid habitus, FG syndrome, Opitz-Kaveggia syndrome, Lujan-Fryns syndrome XL 29 30
MID1* Opitz GBBB syndrome XL 30 96
MTM1 Myopathy, centronuclear XL 158 301
NDP Exudative vitreoretinopathy, Norrie disease XL 31 167
NDUFA1 Mitochondrial complex I deficiency XL 3 4
NHS Nance-Horan syndrome, Cataract XL 36 52
NLGN3 Autism, Asperger syndrome XL 2 10
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 47 264
OFD1 Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome XL 153 160
OPHN1 Mental retardation, with cerebellar hypoplasia and distinctive facial appearance XL 28 42
OTC Ornithine transcarbamylase deficiency XL 343 513
PAK3 Mental retardation XL 9 13
PCDH19 Epileptic encephalopathy, early infantile XL 116 200
PDHA1 Leigh syndrome, Pyruvate dehydrogenase E1-alpha deficiency XL 66 192
PGK1 Phosphoglycerate kinase 1 deficiency XL 16 26
PHF6 Borjeson-Forssman-Lehmann syndrome XL 22 29
PHF8 Mental retardation syndrome, Siderius XL 13 15
PLP1 Spastic paraplegia, Pelizaeus-Merzbacher disease XL 60 348
PORCN Focal dermal hypoplasia XL 16 121
PQBP1 Renpenning syndrome XL 14 18
PRPS1* Phosphoribosylpyrophosphate synthetase I superactivity, Arts syndrome, Charcot-Marie-Tooth disease, X-linked recessive, 5, Deafness, X-linked 1 XL 27 32
PTCHD1 Autism susceptibility, X-linked 4 XL 9 47
RAB39B Waisman parkinsonism-mental retardation syndrome, Mental retardation XL 6 17
RBM10 TARP syndrome XL 12 10
RPL10 Autism XL 4 5
RPS6KA3 Coffin-Lowry syndrome, Mental retardation XL 65 171
SHROOM4 Stocco dos Santos mental retardation syndrome XL 4 9
SLC16A2 Allan-Herndon-Dudley syndrome XL 39 84
SLC6A8* Creatine deficiency syndrome XL 38 133
SLC9A6 Mental retardation, syndromic, Christianson XL 24 28
SMC1A Cornelia de Lange syndrome XL 73 87
SMS Mental retardation, Snyder-Robinson XL 11 14
SOX3 Panhypopituitarism XL 4 26
SRPX2 Rolandic epilepsy, mental retardation, and speech dyspraxia XL 3 4
SYN1 Epilepsy, with variable learning disabilities and behavior disorders XL 12 8
SYP Mental retardation XL 4 8
TAF1 Dystonia 3, torsion, X-linked, Mental retardation, X-linked, syndromic 33 XL 13 14
TIMM8A* Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementia XL 11 21
TSPAN7 Mental retardation XL 4 12
UBE2A Mental retardation, syndromic, Nascimento XL 9 25
UPF3B Mental retardation, syndromic XL 9 21
USP9X Mental retardation, X-linked 99, Mental retardation, X-linked 99, syndromic, female restricted XL 30 27
ZC4H2 Wieacker-Wolff syndrome XL 20 16
ZCCHC12 Intellectual disability XL 2
ZDHHC9 Mental retardation, syndromic, Raymond XL 9 14
ZNF41 Mental retardation XL 6
ZNF674 Mental retardation XL 7
ZNF711 Mental retardation XL 6 8
ZNF81 Mental retardation XL 3 3

* 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 X-linked Intellectual Disability Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ATP7A ChrX:77279056 c.2916+2480T>G NM_000052.5
ATP7A ChrX:77287843 c.3294+763C>G NM_000052.5
CDKL5 ChrX:18525053 c.-162-2A>G NM_003159.2 rs786204973
DKC1 ChrX:153991099 c.-142C>G NM_001363.3 rs199422241
DKC1 ChrX:153991100 c.-141C>G NM_001363.3
DKC1 ChrX:153993704 c.85-15T>C NM_001363.3
DLG3 ChrX:69665038 c.-8dupG NM_021120.3
GK ChrX:30688489 c.259+2254G>A NM_001205019.1
HPRT1 ChrX:133594415 c.27+47C>T NM_000194.2
HPRT1 ChrX:133625464 c.402+1229A>G NM_000194.2
HPRT1 ChrX:133628822 c.485+1202T>A NM_000194.2
HPRT1 ChrX:133632625 c.533-13T>G NM_000194.2
IDS ChrX:148564764 c.1181-15C>A NM_000202.5
IDS ChrX:148578704 c.709-657G>A NM_000202.5
L1CAM ChrX:153128846 c.3531-12G>A NM_000425.4
L1CAM ChrX:153131293 c.2432-19A>C NM_000425.4
L1CAM ChrX:153133652 c.1704-75G>T NM_000425.4
L1CAM ChrX:153136500 c.523+12C>T NM_000425.4
LAMP2 ChrX:119604078 c.-1054A>C NM_001122606.1
MTM1 ChrX:149808833 c.529-909A>G NM_000252.2
MTM1 ChrX:149818176 c.868-13T>A NM_000252.2
NDP ChrX:43818099 c.-207-1G>A NM_000266.3
NDP ChrX:43832545 c.-208+5G>A NM_000266.3
NDP ChrX:43832548 c.-208+2T>G NM_000266.3
NDP ChrX:43832549 c.-208+1G>A NM_000266.3
OCRL ChrX:128674707 c.40-14A>G NM_000276.3
OCRL ChrX:128687279 c.239-4023A>G NM_000276.3
OCRL ChrX:128696350 c.940-11G>A NM_000276.3
OFD1 ChrX:13768358 c.935+706A>G NM_003611.2 rs730880283
OFD1 ChrX:13773245 c.1130-22_1130-19delAATT NM_003611.2 rs312262865
OTC ChrX:38260946 c.540+265G>A NM_000531.5
OTC ChrX:38269404 c.867+1126A>G NM_000531.5
OTC ChrX:38272343 c.1005+1091C>G NM_000531.5
PDHA1 ChrX:19372579 c.625-30G>A NM_001173454.1
PDHA1 ChrX:19373648 c.873+26G>A NM_001173454.1
PDHA1 ChrX:19377861 c.*79_*90dupAGTCAATGAAAT NM_001173454.1
PLP1 ChrX:103042405 c.454-322G>A NM_000533.3
PLP1 ChrX:103042413 c.454-314T>A/G NM_000533.3
PORCN ChrX:48370668 c.374-46T>A NM_203475.1
PORCN ChrX:48370699 c.374-15G>A NM_203475.1
RPS6KA3 ChrX:20191268 c.1228-279T>G NM_004586.2
RPS6KA3 ChrX:20213274 c.326-11A>G NM_004586.2
TIMM8A ChrX:100601671 c.133-23A>C NM_004085.3 rs869320666

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
  • ~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 limitations

This panel does not cover repeat expansion variants such as (CGG)n repeat expansion in FMR1 causing Fragile X syndrome. 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 (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%

Bioinformatics

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 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.