Intellectual Disability NGS Panel

  • Panel Description
  • Test Description
  • CPT Codes
  • Resources

Panel Description

Intellectual Disability

Intellectual disability (ID), also known as general learning disability, is a neurodevelopmental disorder characterized by impairments in intellectual and adaptive functioning. The defining limits of ID vary, but it is generally indicated by an IQ score under 70-75 in addition to deficits in two or more behaviors that affect conceptual skills, social skills, or activities of daily living. Intellectual disability may be part of a syndrome, involving genes that are associated with other clinical features, or may be non-syndromic with ID being the sole clinical feature. ID is often accompanied by related neurodevelopmental disorders such as autism spectrum disorder and/or epilepsy. The Intellectual Disability NGS Panel analyzes over 500 genes associated with intellectual disability with or without syndromic features.This panel may be appropriate for anyone with a personal or family history of ID or developmental delay. Patients with intellectual disability without a clear etiology and/or patients with low IQ scores may benefit from this test.ID is a complex condition that varies greatly from person to person. Treatment plans must be tailored to the individual. Confirmation of an ID diagnosis through genetic testing can reveal more information about the specific etiology present, prognosis, and may lead to more personalized treatment.

Identification of the underlying genetic etiology of intellectual disability can:
  • Confirm a clinical diagnosis or genetic syndrome
  • Allow easier access to early intervention and scholastic assistance
  • Help determine medical management and/or treatment
  • Provide information about the clinical course of disease or comorbidities
  • Provide information for at-risk relatives
  • Inform options for participation in clinical trials
  • Inclusion of clinical information is strongly recommended
.

Test Description

Print
  • Sequencing
  • Del/Dup
  • Rush / STAT
  • Exclude VUS
  • MCC
  • Duo/Trio
3-5 weeks
Call for details
ABCD1, ACAT1, ACOX1, ACSL4, ACTB, ACTG1, ACY1, ADAR, ADNP, ADSL, AFF2, AGTR2, AHDC1, AHI1, AIFM1, ALDH18A1, ALDH4A1, ALDH5A1, ALG1, ALG11, ALG12, ALG13, ALG2, ALG3, ALG6, ALX4, AMER1, ANK3, ANKRD11, AP1S1, AP1S2, AP3B1, AP4B1, AP4E1, AP4M1, AP4S1, AR, ARG1, ARHGEF6, ARHGEF9, ARID1A, ARID1B, ARX, ASAH1, ASPM, ASS1, ASXL1, ASXL3, ATL1, ATP10A, ATP13A2, ATP1A2, ATP6AP2, ATP7A, ATRX, AUH, AUTS2, AVPR1A, AVPR2, BBIP1, BBS1, BBS10, BBS12, BBS2, BBS4, BBS7, BBS9, BCL11A, BCOR, BCS1L, BDNF, BIN1, BRAF, BRSK2, BRWD3, BUB1B, CA2, CACNA1A, CACNA1C, CACNG2, CAMTA1, CANT1, CASK, CBS, CC2D1A, CC2D2A, CCDC22, CCDC88C, CDC42, CDH15, CDK13, CDK16, CDKL5, CDKN1C, CEP290, CEP41, CEP57, CHAMP1, CHD2, CHD7, CHD8, CHRNA4, CIC, CLCN4, CLIC2, CLN3, CLN5, CLN6, CLN8, CNKSR2, CNTNAP2, CNTNAP5, COG5, COG7, COG8, COL4A3BP, CP, CPA6, CPS1, CRADD, CRBN, CREBBP, CSNK2A1, CTC1, CTCF, CTNNB1, CTNND2, CTSA, CTSD, CTSF, CUL4B, CYB5R3, CYP27A1, D2HGDH, DARS2, DBT, DCX, DDX3X, DHCR24, DHCR7, DKC1, DLG3, DLGAP2, DMD, DNM1, DNMT3A, DOCK4, DPP10, DPP6, DPYD, DYNC1H1, DYRK1A, EBP, EFNB1, EFTUD2, EHMT1, EIF2S3, ELOVL4, EP300, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, ERCC8, EZH2, FAAH2, FAM126A, FANCB, FANCG, FBN1, FBXO11, FGD1, FGF14, FGFR1, FGFR2, FGFR3, FKRP, FKTN, FLNA, FMR1, FOLR1, FOXG1, FOXP1, FOXP2, FRMPD4, FTO, FTSJ1, G6PC3, GABRB3, GABRG2, GALE, GAMT, GAN, GATAD2B, GBA, GBE1, GCK, GDI1, GFAP, GFM1, GHR, GK, GLI3, GLRA1, GLUL, GLYCTK, GM2A, GNAO1, GNAS, GNPAT, GNPTAB, GNPTG, GPC3, GRIA3, GRIK2, GRIN1, GRIN2A, GRIN2B, GRM1, GRN, GSPT2, GSS, GUSB, HAX1, HCCS, HCFC1, HDAC4, HDAC8, HECW2, HEPACAM, HEXB, HOXA1, HPD, HPRT1, HRAS, HSD17B10, HSPD1, HUWE1, IDS, IGBP1, IGF1, IGF1R, IL1RAPL1, IMMP2L, IMPA1, INSR, IQSEC2, IRX5, ITGA7, ITPR1, KAT6A, KAT6B, KATNAL2, KCNB1, KCNJ10, KCNJ11, KCNK9, KCNQ2, KCTD13, KCTD7, KDM5B, KDM5C, KDM6A, KIF11, KIF1A, KIF1BP, KIF21A, KIF5A, KIF7, KIRREL3, KLF8, KMT2A, KMT2D, KMT5B, KRAS, L1CAM, LAMA2, LAMC3, LAMP2, LARGE1, LAS1L, LHX3, LIG4, LMBRD1, LYST, MACF1, MAGEL2, MAGT1, MAN1B1, MAN2B1, MANBA, MAOA, MAPK8IP3, MAT1A, MBD5, MBTPS2, MCCC1, MCCC2, MCOLN1, MCPH1, MECP2, MED12, MED13L, MED17, MED23, MEF2C, MFSD8, MGAT2, MID1, MKKS, MMADHC, MOCS1, MOCS2, MRAP, MTFMT, MTHFR, MTOR, MTR, MYCN, MYO5A, MYT1L, NAA10, NAGA, NALCN, NBN, NDP, NDUFA1, NDUFAF5, NDUFS1, NEGR1, NEXMIF, NF1, NGF, NGLY1, NHEJ1, NHP2, NHS, NIPBL, NLGN3, NLGN4X, NPC1, NPC2, NPHP3, NR2F1, NRXN1, NSD1, NSDHL, NSUN2, NTNG1, OCRL, OFD1, OGT, OPHN1, ORC1, OTC, PACS1, PAFAH1B1, PAH, PAK3, PAX6, PCDH19, PCDH9, PCGF2, PCNT, PDE4D, PDHA1, PDHX, PDSS1, PEX7, PGK1, PHF6, PHF8, PHKA2, PHKG2, PIGA, PIGL, PIGO, PIGV, PIP5K1B, PLA2G6, PLP1, PMM2, PNKP, POGZ, POMGNT1, POMT1, POMT2, PON3, PORCN, POU1F1, PPOX, PPP1CB, PPP2R1A, PPP2R5D, PPT1, PQBP1, PRKAR1A, PRMT7, PRPS1, PRSS12, PTCHD1, PTEN, PTPN11, PURA, PYCR1, PYGL, RAB39B, RAI1, RAPSN, RBBP8, RBFOX1, RBM10, RELN, RIT1, RORA, RPGRIP1L, RPL10, RPS6KA3, SACS, SAMHD1, SATB2, SCN1A, SCN2A, SCN8A, SDCCAG8, SETBP1, SETD5, SGSH, SHANK2, SHANK3, SHOC2, SHROOM4, SIL1, SKI, SLC16A2, SLC20A2, SLC25A12, SLC25A13, SLC25A15, SLC2A1, SLC2A2, SLC35A2, SLC35C1, SLC46A1, SLC4A4, SLC5A5, SLC6A1, SLC6A4, SLC6A8, SLC7A7, SLC9A6, SLC9A9, SLX4, SMARCA2, SMARCA4, SMARCB1, SMC1A, SMG6, SMS, SNAP25, SNIP1, SNRPN, SOBP, SOS1, SOS2, SOX10, SOX2, SOX3, SOX5, SPAST, SPATA5, SPR, SPRED1, SPTAN1, SRD5A3, SRPX2, ST3GAL3, ST7, STAT5B, STK3, STRA6, STX11, STXBP1, SUCLG1, SYN1, SYNGAP1, SYP, SYT14, TAF1, TAF6, TBC1D24, TBCE, TBL1XR1, TBR1, TBX1, TCF4, TECR, TET3, TGIF1, TH, THOC2, THRB, TIMM8A, TINF2, TMCO1, TMEM165, TMEM216, TMEM231, TMEM67, TMEM70, TPH2, TPK1, TPP1, TRAPPC9, TRHR, TRIO, TRIP12, TSC1, TSC2, TSHR, TSPAN7, TTC37, TTC8, TUBA1A, TUBA8, TUBB2B, TUBB3, TUSC3, TWIST1, UBE2A, UBE3A, UNC80, UPB1, UPF3B, UROC1, USP9X, VLDLR, VPS13B, WAC, WDR13, WDR45, WDR62, WDR73, WDR81, XPNPEP3, ZBTB16, ZBTB24, ZC4H2, ZCCHC12, ZDHHC9, ZEB2, ZFP57, ZFYVE26, ZIC2, ZMYM3, ZNF41, ZNF507, ZNF674, ZNF711, ZNF804A, ZNF81, ZNHIT6 ( 563 genes )
96% at 20x
Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in EB buffer) or Buccal Swab or Saliva (kits available upon request)
All sequencing technologies have limitations. This analysis is performed by Next Generation Sequencing (NGS) and is designed to examine coding regions and splicing junctions. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the contribution of pseudogene sequences or other highly-homologous sequences, these may still occasionally interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Sanger sequencing is used to confirm variants with low quality scores and to meet coverage standards. If ordered, deletion/duplication analysis can identify alterations of genomic regions which include one whole gene (buccal swab specimens and whole blood specimens) and are two or more contiguous exons in size (whole blood specimens only); single exon deletions or duplications may occasionally be identified, but are not routinely detected by this test. Identified putative deletions or duplications are confirmed by an orthogonal method (qPCR or MLPA). This assay will not detect certain types of genomic alterations which may cause disease such as, but not limited to, translocations or inversions, repeat expansions (eg. trinucleotides or hexanucleotides), alterations in most regulatory regions (promoter regions) or deep intronic regions (greater than 20bp from an exon). This assay is not designed or validated for the detection of somatic mosaicism or somatic mutations.

Gene Notes
AFF2 The current testing method does not assess trinucleotide repeat expansions in this gene. Unless otherwise specified above, only sequence variants and copy number changes in this gene are tested.
MECP2 Currently available technologies (NGS and qPCR) are not amenable to detection of single exon deletions/duplications of exon 1 in the MECP2 gene.
MTHFR As recommended by ACMG, the two common polymorphisms in the MTHFR gene - c.1286A>C (p.Glu429Ala, also known as c.1298A>C) and c.665C>T (p.Ala222Val, also known as c.677C>T) - are not reported in this test due to lack of sufficient clinical utility to merit testing (PubMed: 23288205).
SOX3 The current testing method does not assess trinucleotide repeat expansions in this gene.
ZIC2 The current testing method does not assess trinucleotide repeat expansions in this gene.
CPT Code 81403, 81405, 81406, 81407, 81479

NOTE:  The CPT codes listed on the website are in accordance with Current Procedural Terminology, a publication of the American Medical Association. CPT codes are provided here for the convenience of our clients. Clients who bill for services should make the final decision on which codes to use.

Resources

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Intellectual Disability Information for Patients