Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes

Vysotskiy, Mikhail; Zhong, Xue; Miller-Fleming, Tyne W.; Zhou, Dan; Cox, Nancy J.; Weiss, Lauren A.

doi:10.1186/s13073-021-00972-1

Table 1 Selected 16p11.2 gene associations with PheWAS traits

From: Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes

Gene	PheWAS trait	P value	Reason for inclusion
NPIPB11	Psychosis^a	1.04 × 10⁻⁵	Brain-related, PheWS
	Schizophrenia and other psychotic disorders	0.0016	Brain-related
	Dysphagia	0.0031	Del/dup
	Infantile cerebral palsy	0.0039	Dup, brain-related
BOLA2	Schizophrenia and other psychotic disorders	0.0082	Brain-related
BOLA2	Psychosis^b	0.0083	Brain-related
SLX1B	Psychosis^a	3.03 × 10⁻⁵	Brain-related, PheWS
SLX1B	Schizophrenia and other psychotic disorders	0.000606	Brain-related
CA5AP1	Developmental delays and disorders	0.005	Del/dup, brain-related
CA5AP1	Pervasive developmental disorders	0.01	Del/dup, brain-related
SPN	Failure to thrive (childhood)	0.0039	Dup
C16orf54	Essential hypertension^a	2.8 × 10⁻⁵	PheWS
C16orf54	Bariatric surgery	0.0019	Brain-related
PRRT2	Other specified nonpsychotic and/or transient mental disorders	0.0031	Brain-related
PRRT2	Alteration of consciousness	0.0079	Brain-related
MVP	Dysphagia	0.003	Del/dup
MVP	Symptoms involving head and neck	0.0073	Brain-related
CDIPT	GERD	0.0032	Del
SEZ6L2	Other specified nonpsychotic and/or transient mental disorders	0.0025	Brain-related
	Schizophrenia and other psychotic disorders	0.0029	Brain-related
	Alteration of consciousness	0.0029	Brain-related
ASPHD1	Substance addiction and disorders	0.0015	Brain-related
ASPHD1	Upper gastrointestinal congenital anomalies	0.0044	Del
KCTD13	Lack of coordination	0.0023	Del, brain-related
TMEM219	Mental retardation	0.00034	Del/dup, brain-related
TAOK2	Cardiomegaly	0.01	Dup
HIRIP3	Acute cystitis^a	2.9 × 10⁻⁶	PheWS
HIRIP3	Disorders of uterus, NEC^a	1.3 × 10⁻⁵	PheWS
INO80E	Skull and face fracture and other intercranial injury	1.9 × 10⁻¹⁵	Brain-related, PheWS
	Substance addiction and disorders	0.0032	Brain-related
	Other specified cardiac dysrhythmias	0.0034	Del
FAM57B	Upper gastrointestinal congenital anomalies	0.0011	Del
ALDOA	Neurological disorders	0.0014	Del/dup, brain-related
	Upper gastrointestinal congenital anomalies	0.0029	Del
	Antisocial/borderline personality disorder	0.0043	Brain-related
	Altered mental status	0.0043	Del, brain-related
	Other specified nonpsychotic and/or transient mental disorders	0.0052	Brain-related
	Abnormal movement	0.007	Del/dup, brain-related
	Convulsions	0.0072	Dup, brain-related
TBX6	Chromosomal anomalies and genetic disorders	0.0011	Del/dup
TBX6	Upper gastrointestinal congenital anomalies	0.0059	Del
YPEL3	Chromosomal anomalies and genetic disorders	0.0035	Del/dup
	Other specified cardiac dysrhythmias	0.0038	Del
	Delayed milestones	0.0053	Del/dup, brain-related
MAPK3	Substance addiction and disorders	0.00063	Brain-related
	Delayed milestones	0.0014	Del/dup, brain-related
	Aphasia/speech disturbance	0.0036	Del, brain-related
	Psychosis^b	0.0054	Brain-related
	Upper gastrointestinal congenital anomalies	0.0092	Del
CORO1A	Dysphagia	0.00034	Del/dup
CORO1A	Dementias	0.013	Brain-related
SULT1A3	Upper gastrointestinal congenital anomalies	0.0033	Del
	Obsessive-compulsive disorders	0.0042	Brain-related
	Altered mental status	0.006	Del, brain-related
	Swelling, mass, or lump in head and neck [Space-occupying lesion, intracranial NOS]	0.01	Brain-related
CD2BP2	Substance addiction and disorders	0.0034	Brain-related
CD2BP2	Dysphagia	0.0055	Del/dup
TBC1D10B	Schizophrenia and other psychotic disorders	0.0013	Drain-related
	Psychosis	0.0028	Brain-related
	Alcoholic liver damage	0.0045	Brain-related
	Lack of coordination	0.011	Del, brain-related
MYLPF	Morbid obesity	0.0037	Brain-related
ZNF48	Bariatric surgery^c	0.0071	Brain-related
SEPT1	Other specified nonpsychotic and/or transient mental disorders	0.00055	Brain-related
	Alteration of consciousness	0.0018	Brain-related
	Ill-defined descriptions and complications of heart disease	0.0019	Dup
	Psychosis^c	0.0035	Brain-related
	Substance addiction and disorders	0.0068	Brain-related

Possible reasons for inclusion are (1) del, dup, or del/dup: trait is over-represented in 16p11.2 deletion carriers, duplication carriers, or both (P < 2.8 × 10⁻⁵); (2) brain-related trait; (3) PheWS, phenome-wide significant
^aPhenome-wide significant gene-trait pair (P < 3.3 × 10⁻⁵)
^bNot significant after conditional analysis
^cIn an independent dataset, this brain-related gene-trait pair reached P < 0.05 and was in the top 5% of genes associated with this trait overall

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ISSN: 1756-994X

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