Table 1 Examples of putative non-coding regulatory variants in ASD

16q21 near CDH8 (×2)

3q24 near C3orf58 (×2)

Rare inherited CNVs affecting non-genic intervals near ASD-associated genes

[13]

5′ UTR of MBD5

disruptions of 5′-UTR cause haploinsufficiency of this ASD-associated gene

[14,15,16]

EFR3A promoter

Predicted loss of transcription factor binding (×1)

[4]

Cis regulatory elements of CTN4, LEO1, RAF1, MEST

ASD with recurrent variants in intolerant genes paternally inherited deletions of the LEO1 promoter (×3)

[10]

NEUROG1

DLGAP2

HES1

FEZF1

Network differential enrichment analysis: significant neighborhood excess of non-coding variants in Simons Simplex Collection probands and nearby non-coding variants had significant differential effects on activator activities

[6]

regulatory APBB1

TADA-A (transmission and de novo association—annotation) analysis: single-nucleotide variants in a regulatory region (×3 (2 conserved))

[2]

near ARID1B, SCN2A,

NR3C2, PRKCA, DSCAM

Disruptive mutations in putative regulatory regions (DNase I hypersensitivity)

[8]

NR3C2 promoter

DLG2 promoter

Disrupting deletion overlaps functional non-coding regulatory region in the human brain (×1)

Same 2.5-kb deletion in the DLG2 promoter (×3) functional, non-coding regulatory region in developing the human brain

[11]

miR-873-5p embedded in LINGO2 intron

Rare seed mutation

[17]

CTNND2 and PTEN

ALDH5A1, GLI2, GRIN1, KCNH3,

LAMA2, and NISCH

Splicing/misregulated in genes with neurological phenotypes, increased in ASD

[3]

SMEK1

De novo non-coding mutation lying outside of a canonical splice site predicted to disrupt splicing

[6]

NRXN1, TANC2, PNPLA7

Splicing single-nucleotide variants

[2]

AK127244 (2p16.3)

Deletions directly disrupting exonic sequence in ASD (×3)

rare inherited CNVs (×5)

[13, 18, 19]

PTCHD1-AS

Deletions impacting exons of this gene in multiple males with ASD

[18, 20, 21]

MSNP1-AS (5p14.1)

Within ASD GWAS peak, increased expression in the ASD cortex, influences moesin protein levels

[22]

LINC00689 (7q36.3) LINC00693 (3p24.1)

Differentially expressed: upregulated in the ASD cortex

[23]

lnc-NR2F1 (5q15)

Shown to regulate autism risk genes and promote maturation of mouse stem cell-derived neurons

[24]