Table II. Complete phenotypic information for CHRNA7 CNV patients.

Three hundred and sixty three individuals with CHRNA7 CNVs were identified. Patients are listed by deletion or duplication and breakpoints. Number of individuals, including number affected and number with no reported phenotype is indicated in the appropriate box. Phenotypes only include those reported in more than two individuals, except for BP3-BP5 duplications due to the small number in the literature. Phenotypic data includes only individuals with reported phenotypes. Phenotypes are based on what was reported in the literature, but it is possible that unreported conditions may also be present in patients.

Breakpoints	Number of Cases	Inheritance	Phenotypes	References
Deletions
	14 Total	50% (n=7) Unknown	75% (n=9) Cognitive Deficitsa	[2], [7], [8], [9], [10], [11], [13], [14], [16], [22]
	12 Affected	28.6% (n=4) De Novo	66.7% (n=8) Language Impairment
	2 No Reported Phenotype	14.3% (n=2) Maternal (Affected)	58.3% (n=7) Dysmorphic Features
		7.1% (n=1) Maternal (Unaffected)	50% (n=6) Medical Condition
BP3-BP5			41.7% (n=5) Seizures b
			41.7% (n=5) Overweight c
			41.7% (n=5) ADHD d
			41.7% (n=5) Abnormal Behavior
			33.3% (n=4) Neurological Condition
			33.3% (n=4) Hypotonia
			33.3% (n=4) Eye Pathologies
			25% (n=4) Short Stature
			25% (n=4) ASD
	208 Total	58.2% (n=121) Unknown	55% (n=105) Cognitive Deficits	[2], [8], [9], [10], [11], [12], [13], [15], [16], [18], [19], [20], [21], [22], [23], [24], [26], [27], [28], [29], [30], [31],[32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [49]
	191 Affected	14.4% (n=39) Maternal (Unaffected)	37.2% (n=71) Seizures
	17 No Reported Phenotype	8.7% (n=18) De Novo	28.3% (n=54) Language Impairment
		5.3% (n=11) Paternal (Unaffected)	24.6% (n=47) Dysmorphic Features
		5.8% (n=12) Maternal (Affected)	24.1% (n=46) Abnormal Behavior
		3.4% (n=7) Paternal (Affected)	13.6% (n=26) Schizophrenia
			13.1% (n=25) Mood Disorder e
			11.5% (n=22) ASD
			9.4% (n=18) ADHD
BP4-BP5			7.32% (n=14) Hypotonia
			7.32% (n=14) Medical Condition
			6.8% (n=13) Neurological Condition
			5.2% (n=10) Short Stature
			4.7% (n=9) Eye Pathology
			4.2% (n=8) Microcephaly
			3.1% (n=6) Sleeping Problems
			2.6% (n=5) Macrocephaly
			2.6% (n=5) Overweight
			52.8% (n=19) Cognitive Deficits	[9], [13], [20], [32], [50], [52], [53], [54], [78]
	42 Total	54.8% (n=23) Unknown	36.1% (n=13) Seizures
	36 Affected	16.7% (n= 7) Maternal (Affected)	25% (n=9) Dysmorphic Features
	6 No Reported Phenotype	11.9% (n=5) Paternal (Affected)	19.4% (n=7) Abnormal Behavior
		7.1% (n=3) Maternal (Unaffected	16.7% (n=6) ASD
		7.1% (n=3) Paternal (Unaffected)	13.9% (n=5) Langauge Impairment
		2.3% (n=1) De Novo	13.9% (n=5) ADHD
D-CHRNA7-BP5			13.9% (n=5) Failure to Thrive
			11.1% (n=4) Mood Disorder
			11.1% (n=4) Hypotonia
			11.1% (n=4) Medical Condition
			8.3% (n=3) Neurological Condition
			8.3% (n=3) Overweight
			8.3% (n=3) Eye Pathology
Duplications
	4 Total	50% (n=2) Unknown	75% (n=3) Cognitive Deficits	[16], [17]
	3 Affected	25% (n=1) Maternal (Affected)	50% (n=2) ASD
	1 No Reported Phenotype	25% (n=1) Paternal (Unaffected)	50% (n=2) Mood Disorder
BP3-BP5			50% (n=2) ADHD
			25% (n=1) Hypotonia
			25% (n=1) Overweight
	18 Total	61.1% (n=11) Unknown	43.8% (n=7) Cognitive Deficits	[16], [27], [42], [46], [47], [48], [49]
	16 Affected	27.8% (n=5) De Novo	43.8% (n=7) ASD
	2 No Reported Phenotype	5.6% Paternal (Unaffected)	31.3% (n=5) Language Impairment
		5.6% Maternal (Unaffected)	31.3% (n=5) ADHD
BP4-BP5			25% (n=4) Abnormal Behavior
			25% (n=4) Dysmorphic Features
			18.8% (n=3) Seizures
			18.8% (n=3) Mood Disorder
	67 Total	79.1% (n=53) Unknown	28.3% (n=17) Cognitive Deficits	[1], [31], [32], [43], [46], [49], [53], [57], [58], [59]
	60 Affected	7.5% (n=5) Maternal (Unaffected)	28.3% (n=17) Schizophrenia
	7 No Reported Phenotype	6% (n=4) Maternal (Affected)	18.3% (n=11) ADHD
		4.5% (n=3) Paternal (Unaffected)	18.3% (n=11) Mood Disorder
		3% (n=2) Paternal (Affected)	15% (n=9) ASD
D-CHRNA7-BP5			11.7% (n=7) Hypotonia
			8.3% (n=5) Language Impairment
			6.7% (n=4) Seizures
			5% (n=3) Neurological Condition
			5% (n=3) Dysmorphic Features

BP: breakpoint, EEG: electroencephalogram, ASD: autism spectrum disorder, ADHD: attention deficit hyperactivity disorder,

^aCognitive deficits include intellectual disability, developmental delay, and learning difficulties;

^bSeizures includes epilepsy and abnormal EEG findings;

^cOverweight includes obesity;

^dADHD includes hyperactivity and attention difficulties;

^eMood disorders include anxiety, bipolar disorder, depression, and unspecified mood disorders.