BioMed Research International

Research Article

Identification of a Novel Variant of ARHGAP29 in a Chinese Family with Nonsyndromic Cleft Lip and Palate

Table 1

Variants identified by WES in combination with NSCL/P-related gene-filtering in the present family.


Gene	Variant	Mutation taster	PolyPhen-2	SIFT	1000G	ExAC	gnomAD	OMIM clinical phenotype	American College of Medical Genetics classification

ARHGAP29	c.2615C > T, p.A872V	D (1.000)	D (1.000)	D (0.001)	—	—	—	—	PM1, PM2, PP1
ARHGAP29	c.1252G > A, p.V418I	D (0.938)	B (0.241)	T (0.804)	0.00120	0.00149	0.00157	—	BS4, BP4
ESRP2	c.1610A > C, p.Y537S	D (1.000)	D (1.000)	D (0.000)	0.00399	0.00094	0.00109	—	PP3, BS4
ABCA12	c.1892G > A, p.R631Q	P (1.000)	B (0.050)	T (0.195)	0.00679	0.00525	0.00669	AR, ichthyosis, congenital, autosomal recessive 4A; AR ichthyosis, congenital, autosomal recessive 4B.	BS4, BP4
BMP2	c.393A > T, p.R131S	D (1.000)	D (0.575)	D (0.001)	0.00020	0.00058	0.00061	AD, brachydactyly, type A2; AD, short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies; AR HFE hemochromatosis, modifier of.	PP3, BS4
GLI3	c.3746G > A, p.C1249Y	P (1.000)	B (0.000)	T (1.000)	—	0.00006	0.00005	Somatic, hypothalamic hamartomas; AD, Greig cephalopolysyndactyly syndrome; AD, Pallister-Hall syndrome; AD, polydactyly, postaxial, types A1 and B; AD, polydactyly, preaxial, type IV.	BS4, BP4
CHD7	c.2496C > G, p.N832K	D (1.000)	D (0.900)	D (0.002)	—	—	0.00000	AD, CHARGE syndrome; AD, hypogonadotropic hypogonadism 5 with or without anosmia	PM2, PP3, BS4
MYH9	c.4872_4876delinsTCACG, p.I1626V	D (0.840)	B (0.041)	—	—	—	—	AD, deafness, autosomal dominant 17; AD, macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss	PM2, BS4

D: disease causing; B: benign; T: tolerated; P: polymorphism; AR: autosomal recessive; AD: autosomal dominant. pathogenic: PVS1>PS1>…>PS4>PM1-6>PP1-5; benign: BA1>BS1-4>BP1-7. PVS: pathogenic very strong; PS: pathogenic strong; PM: pathogenic moderate; PP: pathogenic supporting; BA: benign stand-alone; BS: benign strong; BP: benign supporting.