Table 5.

Summary of most highly prioritized variants in each study participant^a

Participants	Genes	Total depth coverage	Impact	Nucleotide description	Protein position	Associated phenotype	Functional association	Report category
1	ATP13A4	43	NS damaging	g.1938A>T	p.Glu646Asp	ASD, CAS	Postulated roles in the developing nervous system and early neuronal development	VUS
	KIAA0319	96	NS damaging	c.931G>A	p.Ala311Thr	Developmental dyslexia, SLI	Adhesion between migrating neurons radial glial fibers	VUS
2	ATP13A4	59	NS damaging	g.1938A>T	p.Glu646Asp	ASD, CAS	Postulated roles in the developing nervous system and early neuronal development	VUS
3	No reportable findings
4	CNTNAP2	39	Splice consensus	c.3714-7insTTG	N/A	Intellectual delay, ASD, CAS	Local differentiation of axons into distinct functional subdomains	VUS
	ATP13A4	63	NS damaging	g.1938A>T	p.Glu646Asp	ASD, CAS	Postulated roles in the developing nervous system and early neuronal development	VUS
5	No reportable findings
6	CNTNAP2	52	NS damaging	c.511C>T	p.Arg171Cys	Intellectual delay, ASD, CAS	Local differentiation of axons into distinct functional subdomains	Likely pathogenic
7	CNTNAP1	10	NS damaging	c.3191G>A	p.Arg1064Gln	No human phenotype	Formation and maintenance of neuronal cell connections	VUS in GUS
8	FOXP1	15	NS damaging	c.320T>C	p.Ile107Thr	Developmental delay, expressive language deficits, ASD	Regulation of gene transcription during development	Likely pathogenic
9	KIAA0319	112	NS damaging	c.931G>A	p.Ala311Thr	Developmental dyslexia, SLI	Adhesion between migrating neurons and radial glial fibers	VUS
	SETX	191	NS damaging	g.2975A>G	p.Lys992Arg	AOA2	Suggested to be involved with DNA and RNA processing	VUS in GUS
10	CNTNAP2	39	Splice consensus	c.3714-7insTTG	N/A	Intellectual delay, ASD, CAS	Local differentiation of axons into distinct functional subdomains	VUS
	KIAA0319	80	NS Damaging	c.931G>A	p.Ala311Thr	Developmental dyslexia, SLI	Adhesion between migrating neurons and radial glial fibers	VUS

^aAOA2, Ataxia and oculomotor apraxia type 2; ASD, Autism spectrum disorder; CAS, Childhood apraxia of speech; GUS, genes of uncertain significance; NS, nonsynonymous; SLI, specific language impairment; VUS, variants of uncertain significance.