Publications about genetic testing for neurological disorders
  1. Syndromic autism gene panel

Syndromic autism gene panel

June 15, 2018

Disease summary:

Autism spectrum disorders (ASD) are a clinically heterogeneous group of disorders that share common features of impaired social relationships, language and communication skills, as well as repetitive behaviors or a specific and very narrow range of interests. Symptoms develop gradually, and about 50-70% of children with autism are identified as intellectually disabled1 with lifelong disability requiring intensive parental, school, and social support 2, 3.

Autism can be associated with a syndromic phenotype, commonly characterized by dysmorphic features, microcephaly and seizures.

In 20-25% of cases with autism a genetic cause can be identified2-7. Chromosomal disorders (~5%), copy number variants (CNVs; chromosomal microdeletions and duplication syndromes) (10–20%), and single-gene disorders (~5%) 8. Pathogenic variants in many single genes have been associated with autism, including genes AP3B1, BLOC1S3, BLOC1S6, C10ORF11, DTNBP1, EDN3, EDNRB, GPR143, HPS1, HPS3, HPS4, HPS5, HPS6, KIT, LYST, MC1R, MITF, MLPH, MYO5A, OCA2, PAX3, RAB27A, SLC24A5, SLC45A2, SNAI2, SOX10, TYR, TYRP1 (Table 1) 9-19

X-linked, autosomal dominant, autosomal recessive

2-4/10,000 4 to 20/10,000 6

Major clinical symptoms 1, 2, 3:

  • Impaired social interaction
  • Impaired communication
  • Repetitive and stereotypic behaviors

Additional symptoms1, 2, 3:

  • Hyper- and hyposensitivity to sound and touch
  • Stereotypic behavior around food and their presentation
  • Abnormal sleep pattern (>60%)
  • Seizures (>25%)
  • Tantrums and/or self-injurious and aggressive behaviors
  • Impaired motor development with toe walking, hypotonia, general clumsiness
  • Catatonia syndrome (>15%)
  • Obesity
  • Presence of the specific behavioral changes and other autism-associated clinical feature
  • Positive family history of autism
  • Identification of a pathogenic variant in one of the associated genes (Table 1)

There is no cure for autism, however many symptomatic treatments can relieve symptoms1, 2, 3:

  • Psychosocial therapies, psychotherapy, cognitive behavioral psychotherapy, social skill interventions
  • Pharmacological treatments, including atypical antipsychotics, antidepressants, mood stabilizers
  • Supplements including vitamins, minerals, Omega-3 Fatty acids and others
  • Ongoing clinical trials investigating potential therapeutic effects of new drugs 
  • Developmental delay (global, language, intellectual or motor delay)
  • Intellectual disability
  • Attention deficit hyperactivity disorder
  • Mood disorders (anxiety disorder, obsessive compulsive disorder) or psychoses
  • Rett syndrome
  • Epileptic encephalopathy
  • Chromosomal abnormalities-associated syndromes (Angelman syndrome, trisomy 22)

To confirm/establish the diagnosis, CENTOGENE offers the following tests:

  • Syndromic autism NGS Panel Plus which includes sequencing of the genes ADNP, ADSL, ALDH5A1, AMT, ANKRD11, ARID1B, BRAF, CACNA1C, CDKL5, CHD2, CHD7, CNTNAP2, CREBBP, DHCR7, EHMT1, FOXG1, FOXP1, GRIP1, HDAC8, HOXA1, HPRT1, MAGEL2, MECP2, MED12, MID1, NHS, NIPBL, NRXN1, NSD1, PCDH19, POGZ, PQBP1, PTEN, PTPN11, RAD21, RAI1, SCN1A, SCN2A, SETD2, SLC6A1, SLC6A8, SMC1A, SMC3, TBL1XR1, TCF4, TSC1, TSC2, UBE3A, VPS13B, ZEB2
  • Syndromic autism NGS Panel Plus + CNV which includes sequencing and additionally detection of large deletions and duplications from the NGS data
  • Individuals with a positive family history of syndromic autism
  • Individuals with most common symptoms of syndromic autism (regardless of family history)

Confirmation of a clinical diagnosis through genetic testing of syndromic autism can allow for genetic counseling and may direct medical management.

Table 1. Overview of the genes in CENTOGENE´s syndromic autism panel:

Gene (OMIM)Locus Associated phenotype (OMIM)
ADNP (611386) 20q13.13 Helsmoortel-van der Aa syndrome (615873)
ADSL (608222) 22q13.1 Adenylosuccinase deficiency (103050)
ALDH5A1(610045) 6p22.3 SSADH deficiency  (271980)
AMT (238310) 3p21.31 Glycine encephalopathy (605899)
ANKRD11(611192) 16q24.3 KBG syndrome (148050)
ARID1B (614556) 6q25.3 Coffin-Siris syndrome 1 (135900)
BRAF (164757) 7q34 Cardiofaciocutaneous syndrome (115150)
CACNA1C (114205) 12p13.33 Timothy syndrome (601005)
CDKL5 (300203) Xp22.13 Early epileptic encephalopathy 2 (300672)
CHD2 (602119) 15q26.1 Childhood-onset epil. Encephalopathy (615369)
CHD7 (608892) 8q12.2 CHARGE syndrome (214800)
CNTNAP2 (604569) 7q35-q36 Autism susceptibility to, 15 (612100)
CREBBP (600140) 16p13.3 Rubinstein-Taybi syndrome (180849)
DHCR7 (602858) 11q13.4 Smith-Lemli-Opitz syndrome (270400)
EHMT1(607001) 9q34.3 Kleefstra syndrome (610253)
FMR1(309550) Xq27.3 Fragile X syndrome (300624)
FOXG1 (164874) 14q12 Rett syndrome, congenital variant (613454)
FOXP1 (605515) 3p13 Mental retardation with ASD (613670)
GRIP1 (604597) 12q14.3 ASD-related disease, Fraser syndrome (219000)
HDAC8 (300269) Xq13.1 Cornelia de Lange syndrome 5 (300882)
HOXA1 (142955) 7p15.2 Bosley-Salih-Alorainy syndrome (601536)
HPRT1 (308000) Xq26.2-q26.3 Lesch-Nyhan syndrome (300322)
MAGEL2 (605283) 15q11.2 Schaaf-Yang syndrome (615547)
MECP2 (300005) Xq28 Rett syndrome (312750)
MED12 (300188) Xq13.1 Lujan-Fryns syndrome (309520)
NHS (300457) Xp22.2-p22.1 Nance-Horan syndrome (302350)
NIPBL (608667) 5p13.2 Cornelia de Lange syndrome 1 (122470)
NRXN1 (600565) 2p16.3 Chr.2p16.3 deletion syndrome (600565)
NSD1 (606681) 5q35.3 Sotos syndrome (117550)
PCDH19 (300460) Xq22.1 Early infantile epileptic  encephalopathy 9 (300088)
POGZ (614787) 1q21.3 White-Sutton syndrome (616364)
PQBP1 (300463) Xp11.23 Renpenning syndrome (309500)

PTEN (601728)

10q23.31 Macrocephaly/autism syndrome (605309)
PTPN11 (176876) 12q24.13 Noonan syndrome (163950)
RAD21 (606462) 8q24.11 Cornelia de Lange syndrome 4 (614701)
RAI1(607642) 17p11.2 Smith-Magenis syndrome (182290)
SCN1A (182389) 2q24.3 Dravet syndrome (607208)
SCN2A (182390) 2q24.3 Early infantile epileptic encephalopathy 11 (613721)
SETD2 (612778) 3p21.31 Luscan-Lumish syndrome (616831)
SLC6A1 (137165) 3p25.3

Myoclonic-atonic epilepsy (616421)

SLC6A8 (300036) Xq28 Cerebral creatine deficiency syndrome (300352)
SMC1A (300040) Xp11.22 Cornelia de Lange syndrome 2  (300590)
SMC3 (606062) 10q25.2 Cornelia de Lange syndrome 3 (610759)
TBL1XR1 (608628) 3q26.32 Mental retardation, autosomal dominant 41 (616944)
TCF4 (602272) 18q21.2 Pitt-Hopkins syndrome (610954)
TSC1 (605284) 9q9q34.1334.13 Tuberous sclerosis-1 (191100)
TSC2 (191092) 16p13.3 Tuberous sclerosis-2 (613254)
UBE3A (601623) 15q11.2 Angelman syndrome (105830)
VPS13B (607817) 8q22.2 Cohen syndrome (216550)
ZEB2 (605802) 2q22.3 Mowat-Wilson syndrome (235730)